# Index

A B C D E F G H I J K L M N O P Q R S T U V W X Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

## A

a - Static variable in class htsjdk.samtools.util.SequenceUtil
  Byte typed variables for all normal bases.
a - Variable in class htsjdk.samtools.util.Tuple
A - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderLineCount
A - Static variable in class htsjdk.samtools.util.SequenceUtil
  Byte typed variables for all normal bases.
AbstractAsyncWriter<T> - Class in htsjdk.samtools.util
  Abstract class that is designed to be extended and specialized to provide an asynchronous wrapper around any kind of Writer class that takes an object and writes it out somehow.
AbstractAsyncWriter(int) - Constructor for class htsjdk.samtools.util.AbstractAsyncWriter
  Creates an AbstractAsyncWriter that will use the provided WriterRunnable to consume from the internal queue and write records into the synchronous writer.
AbstractBAMFileIndex - Class in htsjdk.samtools
  Provides basic, generic capabilities to be used reading BAM index files.
AbstractBAMFileIndex(IndexFileBuffer, String, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.AbstractBAMFileIndex
AbstractBAMFileIndex(SeekableStream, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.AbstractBAMFileIndex
AbstractBAMFileIndex(File, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.AbstractBAMFileIndex
AbstractBAMFileIndex(File, SAMSequenceDictionary, boolean) - Constructor for class htsjdk.samtools.AbstractBAMFileIndex
AbstractFeatureCodec<FEATURE_TYPE, SOURCE> - Class in htsjdk.tribble
  Simple basic class providing much of the basic functionality of codecs Every concrete subclass must implement `FeatureCodec.canDecode(String)` to indicate whether it can decode the file.
AbstractFeatureCodec(Class) - Constructor for class htsjdk.tribble.AbstractFeatureCodec
AbstractFeatureReader<T,SOURCE> - Class in htsjdk.tribble
  jrobinso
AbstractFeatureReader(String, FeatureCodec) - Constructor for class htsjdk.tribble.AbstractFeatureReader
AbstractFeatureReader(String, FeatureCodec, Function, Function) - Constructor for class htsjdk.tribble.AbstractFeatureReader
AbstractFeatureReader.ComponentMethods - Class in htsjdk.tribble
AbstractIndex - Class in htsjdk.tribble.index
  An abstract implementation of the index class.
AbstractIndex() - Constructor for class htsjdk.tribble.index.AbstractIndex
  create an abstract index, with defaults for the version value, and empty properties and chromosome lists
AbstractIndex(AbstractIndex) - Constructor for class htsjdk.tribble.index.AbstractIndex
AbstractIndex(File) - Constructor for class htsjdk.tribble.index.AbstractIndex
AbstractIndex(String) - Constructor for class htsjdk.tribble.index.AbstractIndex
  create an index file from the target feature file
AbstractIndex(Path) - Constructor for class htsjdk.tribble.index.AbstractIndex
AbstractIndex.BlockStats - Class in htsjdk.tribble.index
AbstractIndex.IndexType - Enum Class in htsjdk.tribble.index
AbstractIterator<E> - Class in htsjdk.samtools.util
  Base class of implementing iterators.
AbstractIterator() - Constructor for class htsjdk.samtools.util.AbstractIterator
AbstractJavascriptFilter<HEADER,TYPE> - Class in htsjdk.samtools.filter
  Javascript filter with HEADER type containing TYPE records.
AbstractJavascriptFilter(File, HEADER) - Constructor for class htsjdk.samtools.filter.AbstractJavascriptFilter
  constructor using a java.io.File script, compiles the script, puts 'header' in the bindings
AbstractJavascriptFilter(Reader, HEADER) - Constructor for class htsjdk.samtools.filter.AbstractJavascriptFilter
  Constructor, compiles script, put header in the bindings
AbstractJavascriptFilter(String, HEADER) - Constructor for class htsjdk.samtools.filter.AbstractJavascriptFilter
  constructor using a java.lang.String script, compiles the script, puts 'header' in the bindings
AbstractLocusInfo<E> - Class in htsjdk.samtools.util
  The unit of iteration for AbstractLocusIterator.
AbstractLocusInfo(SAMSequenceRecord, int) - Constructor for class htsjdk.samtools.util.AbstractLocusInfo
AbstractLocusIterator<T,K> - Class in htsjdk.samtools.util
  Iterator that traverses a SAM File, accumulating information on a per-locus basis.
AbstractLocusIterator(SamReader, IntervalList, boolean) - Constructor for class htsjdk.samtools.util.AbstractLocusIterator
  Prepare to iterate through the given SAM records, skipping non-primary alignments
AbstractProgressLogger - Class in htsjdk.samtools.util
  Abstract implementation of a Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records.
AbstractProgressLogger(String, String, int) - Constructor for class htsjdk.samtools.util.AbstractProgressLogger
  Construct an AbstractProgressLogger.
AbstractRecordAndOffset - Class in htsjdk.samtools.util
  Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds to the base and quality at the genomic position described the containing AbstractLocusInfo.
AbstractRecordAndOffset(SAMRecord, int) - Constructor for class htsjdk.samtools.util.AbstractRecordAndOffset
AbstractRecordAndOffset(SAMRecord, int, AbstractRecordAndOffset.AlignmentType) - Constructor for class htsjdk.samtools.util.AbstractRecordAndOffset
AbstractRecordAndOffset.AlignmentType - Enum Class in htsjdk.samtools.util
  Classifies whether the given event is a match, insertion, or deletion.
AbstractSAMHeaderRecord - Class in htsjdk.samtools
  Base class for the various concrete records in a SAM header, providing uniform access to the attributes.
AbstractSAMHeaderRecord() - Constructor for class htsjdk.samtools.AbstractSAMHeaderRecord
AbstractVCFCodec - Class in htsjdk.variant.vcf
AbstractVCFCodec() - Constructor for class htsjdk.variant.vcf.AbstractVCFCodec
abuts(Interval) - Method in class htsjdk.samtools.util.Interval
  Returns true if this interval overlaps the other interval, otherwise false.
accept(TYPE) - Method in class htsjdk.samtools.filter.AbstractJavascriptFilter
  Evaluates this predicate on the given argument
ACCEPT_TYPE - Static variable in class htsjdk.samtools.util.htsget.HtsgetRequest
ACCEPTABLE_VERSIONS - Static variable in class htsjdk.samtools.SAMFileHeader
acceptableAlleleBases(byte[]) - Static method in interface htsjdk.variant.variantcontext.Allele
acceptableAlleleBases(byte[], boolean) - Static method in interface htsjdk.variant.variantcontext.Allele
acceptableAlleleBases(String) - Static method in interface htsjdk.variant.variantcontext.Allele
acceptableAlleleBases(String, boolean) - Static method in interface htsjdk.variant.variantcontext.Allele
Accessor() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.Accessor
AD(int[]) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype has this AD value
ADAccessor() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.ADAccessor
ADAPTIVE_ARITHMETIC - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
add(int, Genotype) - Method in class htsjdk.variant.variantcontext.GenotypesContext
add(long) - Method in class htsjdk.samtools.util.SortingLongCollection
  Add a value to the collection.
add(long, FastqReader...) - Method in class htsjdk.samtools.util.QualityEncodingDetector
  Adds the provided reader's records to the detector.
add(long, SamReader) - Method in class htsjdk.samtools.util.QualityEncodingDetector
  Adds the provided reader's records to the detector.
add(long, CloseableIterator) - Method in class htsjdk.samtools.util.QualityEncodingDetector
add(long, CloseableIterator, boolean) - Method in class htsjdk.samtools.util.QualityEncodingDetector
  Adds the provided iterator's records (optionally using the original qualities) to the detector.
add(E) - Method in class htsjdk.samtools.util.AbstractLocusInfo
  Accumulates info for one read aligned to the locus.
add(E) - Method in class htsjdk.samtools.util.DiskBackedQueue
  Add the record to the tail of the queue, spilling to disk if necessary Must check that (canAdd() == true) before calling this method
add(BAMFileSpan) - Method in class htsjdk.samtools.BAMFileSpan
  Merge one span into another
add(Chunk) - Method in class htsjdk.samtools.BAMFileSpan
  Adds a new chunk to this list.
add(CigarElement) - Method in class htsjdk.samtools.Cigar
add(CRAMCompressionRecord) - Method in class htsjdk.samtools.cram.digest.ContentDigests
add(FastqRecord) - Method in class htsjdk.samtools.util.QualityEncodingDetector
  Adds the provided record's qualities to the detector.
add(FastaSequenceIndexEntry) - Method in class htsjdk.samtools.reference.FastaSequenceIndex
  Add a new index entry to the list.
add(SAMRecord) - Method in class htsjdk.samtools.DuplicateSet
  Adds a record to the set and returns zero if either the set is empty, or it is a duplicate of the records already in the set.
add(SAMRecord) - Method in class htsjdk.samtools.util.QualityEncodingDetector
add(SAMRecord, boolean) - Method in class htsjdk.samtools.util.QualityEncodingDetector
  Adds the provided record's qualities to the detector.
add(Interval) - Method in class htsjdk.samtools.util.IntervalList
  Adds an interval to the list of intervals.
add(SamRecordWithOrdinal) - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer
  Add the given SAMRecordIndex to the buffer.
add(Genotype) - Method in class htsjdk.variant.variantcontext.GenotypesContext
  Adds a single genotype to this context.
add(VariantContext) - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
add(VariantContext) - Method in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
  add a record to the file
add(VariantContext) - Method in interface htsjdk.variant.variantcontext.writer.VariantContextWriter
add(Path) - Static method in class htsjdk.samtools.util.nio.DeleteOnExitPathHook
  Adds a `Path` for deletion on JVM exit.
add(K, V) - Method in class htsjdk.samtools.util.ListMap
  Adds a single value to the list stored under a key.
add(T) - Method in class htsjdk.samtools.util.SortingCollection
addAlignment(SAMRecord) - Method in interface htsjdk.samtools.SAMFileWriter
addAlignment(SAMRecord) - Method in class htsjdk.samtools.SAMFileWriterImpl
  Add an alignment record to be emitted by the writer.
addall(Collection) - Method in class htsjdk.samtools.util.IntervalList
  Adds a Collection of intervals to the list of intervals.
addAll(int, Collection) - Method in class htsjdk.variant.variantcontext.GenotypesContext
addAll(Collection) - Method in class htsjdk.samtools.util.DiskBackedQueue
  Add all elements from collection c to this DiskBackedQueue Must check that (canAdd() == true) before calling this method
addAll(Collection) - Method in class htsjdk.variant.variantcontext.GenotypesContext
  Adds all of the genotypes to this context See `GenotypesContext.add(Genotype)` for important information about this functions constraints and performance costs
addAll(List, List) - Method in class htsjdk.samtools.util.OverlapDetector
  Adds all items to the overlap detector.
addAllMetrics(Iterable) - Method in class htsjdk.samtools.metrics.MetricsFile
  Add multiple metric beans at once.
addAlternativeSequenceName(String) - Method in class htsjdk.samtools.SAMSequenceRecord
  Adds an alternative sequence name if it is not the same as the sequence name or it is not present already.
addAlternativeSequenceName(String, String) - Method in class htsjdk.samtools.SAMSequenceDictionary
  Add an alternative sequence name (AN tag) to a SAMSequenceRecord, including it into the aliases to retrieve the contigs (as with `SAMSequenceDictionary.addSequenceAlias(String, String)`.
addChunk(Chunk) - Method in class htsjdk.samtools.Bin
  Adds a chunk to the bin (may be the first chunk or a later one).
addClippedBasesToEndsOfCigar(Cigar, boolean, int, int, CigarOperator) - Static method in class htsjdk.samtools.util.CigarUtil
  Adds additional soft-clipped bases at the 3' and/or 5' end of the cigar.
addCoFeature(Gff3FeatureImpl) - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
  Add a feature as a coFeature of this feature.
addComment(String) - Method in class htsjdk.samtools.SAMFileHeader
addComment(String) - Method in class htsjdk.tribble.gff.Gff3Writer
  Add comment line
addDeleted(SAMRecord, int) - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo
  Accumulate info for one read with a deletion
addDirective(Gff3Codec.Gff3Directive) - Method in class htsjdk.tribble.gff.Gff3Writer
  Add a directive
addDirective(Gff3Codec.Gff3Directive, Object) - Method in class htsjdk.tribble.gff.Gff3Writer
  Add a directive with an object
addEntries(Collection) - Method in class htsjdk.samtools.cram.CRAIIndex
  Add multiple entries to the CRAI index.
addEntry(CRAIEntry) - Method in class htsjdk.samtools.cram.CRAIIndex
  Add a single entry to the CRAI index.
addExon(int, int, int, int, int) - Method in class htsjdk.tribble.bed.FullBEDFeature
addExon(FullBEDFeature.Exon) - Method in class htsjdk.tribble.bed.FullBEDFeature
addExtension(Path, String) - Static method in class htsjdk.samtools.util.IOUtil
  Adds the extension to the given path.
addFeature(Feature, long) - Method in class htsjdk.tribble.index.DynamicIndexCreator
addFeature(Feature, long) - Method in interface htsjdk.tribble.index.IndexCreator
  Add a feature to the index
addFeature(Feature, long) - Method in class htsjdk.tribble.index.interval.IntervalIndexCreator
addFeature(Feature, long) - Method in class htsjdk.tribble.index.linear.LinearIndexCreator
  add a feature to the index
addFeature(Feature, long) - Method in class htsjdk.tribble.index.tabix.AllRefsTabixIndexCreator
addFeature(Feature, long) - Method in class htsjdk.tribble.index.tabix.TabixIndexCreator
addFeature(Gff3Feature) - Method in class htsjdk.tribble.gff.Gff3Writer
  add a feature
addField(HtsgetRequestField) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
addFields(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
addFilter(String) - Method in class htsjdk.variant.variantcontext.CommonInfo
addFilters(Collection) - Method in class htsjdk.variant.variantcontext.CommonInfo
addFrag(String, int, int, boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds a skeletal fragment (non-PE) record to the set using the provided contig start and strand information.
addFrag(String, int, int, boolean, boolean, String, String, int) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.
addFrag(String, int, int, boolean, boolean, String, String, int, boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.
addFrag(String, int, int, boolean, boolean, String, String, int, boolean, boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.
addGenotype(BCF2Encoder, VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.FTGenotypesWriter
addGenotype(BCF2Encoder, VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenotypesWriter
addGenotype(BCF2Encoder, VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GTWriter
addGenotype(BCF2Encoder, VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IGFGenotypesWriter
addGenotypeData(VariantContext, Map, List, StringBuilder) - Method in class htsjdk.variant.vcf.VCFEncoder
addGzipBlock(long, long) - Method in class htsjdk.samtools.util.GZIIndex.GZIIndexer
addHeader(Header) - Method in class htsjdk.samtools.metrics.MetricsFile
  Adds a header to the collection of metrics.
addHistogram(Histogram) - Method in class htsjdk.samtools.metrics.MetricsFile
  Adds a histogram to the list of histograms in the metrics file.
addHistogram(Histogram) - Method in class htsjdk.samtools.util.Histogram
  Mutable method that allows the addition of a Histogram into the current one.
addIndexer(OutputStream) - Method in class htsjdk.samtools.util.BlockCompressedOutputStream
  Adds a GZIIndexer to the block compressed output stream to be written to the specified output stream.
addInitialChunk(Chunk) - Method in class htsjdk.samtools.Bin
  Adds the first chunk to the bin
addInserted(SAMRecord, int) - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo
  Accumulate info for one read with an insertion.
addInterval(Locatable) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
addIntervals(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
addLhs(T, Locatable) - Method in class htsjdk.samtools.util.OverlapDetector
  Adds a Locatable to the set of Locatables against which to match candidates.
addMetaDataLine(VCFHeaderLine) - Method in class htsjdk.variant.vcf.VCFHeader
  Adds a new line to the VCFHeader.
addMetric(BEAN) - Method in class htsjdk.samtools.metrics.MetricsFile
  Adds a bean to the collection of metrics.
addNotag(String) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
addNotags(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
addOther(IntervalList) - Method in class htsjdk.samtools.util.IntervalList
  A method for concatenating the intervals from one list to this one, checks for equal dictionaries.
addPair(String, int, int, int) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds a skeletal pair of records to the set using the provided contig starts.
addPair(String, int, int, int, boolean, boolean, String, String, boolean, boolean, boolean, boolean, int) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
addPair(String, int, int, int, boolean, boolean, String, String, boolean, boolean, int) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
addPair(String, int, int, int, int, boolean, boolean, String, String, boolean, boolean, boolean, boolean, int) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
addParent(Gff3FeatureImpl) - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
addPrimary(BundleResource) - Method in class htsjdk.beta.io.bundle.BundleBuilder
  Add the primary resource to the bundle.
addProgramRecord(SAMProgramRecord) - Method in class htsjdk.samtools.SAMFileHeader
addProperties(Map) - Method in class htsjdk.tribble.index.AbstractIndex
addProperties(Map) - Method in interface htsjdk.tribble.index.MutableIndex
addProperty(String, String) - Method in class htsjdk.tribble.index.AbstractIndex
addProperty(String, String) - Method in class htsjdk.tribble.index.DynamicIndexCreator
addProperty(String, String) - Method in interface htsjdk.tribble.index.MutableIndex
addProperty(String, String) - Method in class htsjdk.tribble.index.TribbleIndexCreator
addReadGroup(SAMReadGroupRecord) - Method in class htsjdk.samtools.SAMFileHeader
addRecord(SAMRecord) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  The record should already have the DS and MC tags computed
addSecondary(BundleResource) - Method in class htsjdk.beta.io.bundle.BundleBuilder
  Add a (non-primary) resource to the bundle.
addSequence(ReferenceSequence) - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Appends a new sequence to the output.
addSequence(SAMSequenceRecord) - Method in class htsjdk.samtools.SAMFileHeader
addSequence(SAMSequenceRecord) - Method in class htsjdk.samtools.SAMSequenceDictionary
addSequenceAlias(String, String) - Method in class htsjdk.samtools.SAMSequenceDictionary
  Add an alias to a SAMSequenceRecord.
addSoftClippedBasesToEndsOfCigar(Cigar, boolean, int, int) - Static method in class htsjdk.samtools.util.CigarUtil
  Adds additional soft-clipped bases at the 3' and/or 5' end of the cigar.
addStandardFormatLines(Set, boolean, String...) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
addStandardFormatLines(Set, boolean, Collection) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
  Adds header lines for each of the format fields in IDs to header, returning the set of `IDs` without standard descriptions, unless `throwErrorForMissing` is true, in which case this situation results in a `TribbleException`
addStandardInfoLines(Set, boolean, String...) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
addStandardInfoLines(Set, boolean, Collection) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
  Adds header lines for each of the info fields in `IDs` to header, returning the set of IDs without standard descriptions, unless `throwErrorForMissing` is true, in which case this situation results in a `TribbleException`.
addSymbolObservations(T, int) - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParamsCalculator
  Record one or more observations of a given symbol in the input stream.
addTag(String) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
addTagEncoding(int, ExternalCompressor, EncodingDescriptor) - Method in class htsjdk.samtools.cram.structure.CompressionHeader
addTags(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
addUnmappedFragment(String) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds an unmapped fragment read to the builder.
addUnmappedPair(String) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds a pair with both ends unmapped to the builder.
addValidationError(SAMValidationError) - Method in class htsjdk.samtools.SAMFileHeader
ADJACENT_INDEL_IN_CIGAR - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  CIGAR string contains I followed by D, or vice versa
advance() - Method in class htsjdk.samtools.SecondaryAlignmentSkippingIterator
advance() - Method in class htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
advance() - Method in class htsjdk.samtools.util.AbstractIterator
advance() - Method in class htsjdk.tribble.readers.LineIteratorImpl
advanceCurrentIntervalAndCheckIfIntervalContainsRead(SAMRecord) - Method in class htsjdk.samtools.util.EdgeReadIterator
  This function updates currentInterval according to the position of the record that it is presented and determines if the current read is fully contained in the currentInterval.
advanceSymbolStep(long, int) - Method in class htsjdk.samtools.cram.compression.rans.RANSDecodingSymbol
  Advance the rANS state by one decoded symbol.
advanceToAlignmentInContainer(int, int) - Method in class htsjdk.samtools.CRAMIterator
  Skip cached records until given alignment start position.
after(Date) - Method in class htsjdk.samtools.util.RelativeIso8601Date
AggregateFilter - Class in htsjdk.samtools.filter
  Aggregates multiple filters and provides a method for applying them all to a given record with one method call.
AggregateFilter(List) - Constructor for class htsjdk.samtools.filter.AggregateFilter
  Constructor
ALIAS_ATTRIBUTE_KEY - Static variable in class htsjdk.tribble.gff.Gff3Constants
ALIGNED_READS - Enum constant in enum class htsjdk.beta.plugin.HtsContentType
  Aligned reads content type (see `ReadsFormats` for related formats)
AlignedFilter - Class in htsjdk.samtools.filter
  Filter to either include or exclude aligned reads $Id$
AlignedFilter(boolean) - Constructor for class htsjdk.samtools.filter.AlignedFilter
AlignmentBlock - Class in htsjdk.samtools
  Represents the contiguous alignment of a subset of read bases to a reference sequence.
AlignmentContext - Class in htsjdk.samtools.cram.structure
  An AlignmentContext represents mapping information related to a collection of reads, or a single `CRAMCompressionRecord`, `Slice`, or `Container`.
AlignmentContext(ReferenceContext, int, int) - Constructor for class htsjdk.samtools.cram.structure.AlignmentContext
  Create an AlignmentContext from a reference context, start, and span.
AlignmentSpan - Class in htsjdk.samtools.cram.structure
  A span of over a single reference.
AlignmentSpan(int, int, int, int, int) - Constructor for class htsjdk.samtools.cram.structure.AlignmentSpan
  Create a new span with a multiple reads in it.
AlignmentSpan(AlignmentContext, int, int, int) - Constructor for class htsjdk.samtools.cram.structure.AlignmentSpan
  This does not retain the alignmentContext referenceContext state (its just a shorthand for passing the rest of the alignmentContext values in).
alignmentType - Variable in class htsjdk.samtools.util.AbstractRecordAndOffset
  The `AbstractRecordAndOffset.AlignmentType` of this object, which classifies whether the given event is a match, insertion, or deletion when queried from a `SamLocusIterator`.
ALL - Static variable in class htsjdk.samtools.cram.digest.ContentDigests
ALL_BYTES_USED - Static variable in class htsjdk.samtools.cram.build.CompressionHeaderFactory
allDefaults() - Static method in class htsjdk.samtools.Defaults
  Returns a map of all default values (keys are names), lexicographically sorted by keys.
Allele - Interface in htsjdk.variant.variantcontext
  Immutable representation of an allele.
ALLELE_COUNT_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
ALLELE_FREQUENCY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
ALLELE_NUMBER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
alleleIndex1 - Variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
alleleIndex2 - Variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
alleleMap - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
alleles - Variable in class htsjdk.variant.variantcontext.VariantContext
  A set of the alleles segregating in this context
alleles(String...) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
alleles(Collection) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells this builder to use this collection of alleles for the resulting VariantContext
alleles(List) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Set this genotype's alleles
alleles(List) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
Alleles - Section in class htsjdk.variant.variantcontext.VariantContext
ALLELES - Enum constant in enum class htsjdk.variant.variantcontext.VariantContext.Validation
allocateByteBuffer(int) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Allocate a new little-endian ByteBuffer of the specified size.
allocateOutputBuffer(int) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Allocate an output buffer large enough to hold compressed rANS data, including worst-case frequency table overhead and header bytes.
ALLOW_MISSING_FIELDS_IN_HEADER - Enum constant in enum class htsjdk.variant.variantcontext.writer.Options
ALLOW_UNBOUND_DESCRIPTIONS - Static variable in class htsjdk.variant.vcf.VCFHeaderLine
ALLOWED_BCF_VERSION - Static variable in class htsjdk.variant.bcf2.BCF2Codec
ALLOWED_MAJOR_VERSION - Static variable in class htsjdk.variant.bcf2.BCF2Codec
ALLOWED_MINOR_VERSION - Static variable in class htsjdk.variant.bcf2.BCF2Codec
allowFlagValues - Variable in enum class htsjdk.variant.vcf.VCFCompoundHeaderLine.SupportedHeaderLineType
AllRefsTabixIndexCreator - Class in htsjdk.tribble.index.tabix
  This is a copy of `TabixIndexCreator`, except sequence names are populated from the header, not from the ones that are seen.
AllRefsTabixIndexCreator(SAMSequenceDictionary, TabixFormat) - Constructor for class htsjdk.tribble.index.tabix.AllRefsTabixIndexCreator
ALT - Enum constant in enum class htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
ALT_A - Static variable in interface htsjdk.variant.variantcontext.Allele
ALT_C - Static variable in interface htsjdk.variant.variantcontext.Allele
ALT_G - Static variable in interface htsjdk.variant.variantcontext.Allele
ALT_HEADER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
ALT_HEADER_OFFSET - Static variable in class htsjdk.variant.vcf.VCFConstants
ALT_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
ALT_N - Static variable in interface htsjdk.variant.variantcontext.Allele
ALT_T - Static variable in interface htsjdk.variant.variantcontext.Allele
ALTERNATIVE_SEQUENCE_NAME_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
AM - Enum constant in enum class htsjdk.samtools.SAMTag
AM - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
ANCESTRAL_ALLELE_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
AP_AlignmentPositionOffset - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
append(K, V) - Method in class htsjdk.samtools.util.CollectionUtil.MultiMap
appendAll(K, Collection) - Method in class htsjdk.samtools.util.CollectionUtil.MultiMap
appendBases(byte[]) - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Adds bases to current sequence from a `byte` array.
appendBases(byte[], int, int) - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Adds bases to current sequence from a range in a `byte` array.
appendBases(String) - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Adds bases to current sequence from a `byte` array.
appendExtension(IOPath, String, Function) - Static method in class htsjdk.beta.io.IOPathUtils
  Takes an IOPath and returns a new IOPath object that keeps the same name as the original, but with the new extension added.
appendSequence(String, String, byte[]) - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Appends a new sequence to the output with or without a description.
appendSequence(String, String, int, byte[]) - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Appends a new sequence to the output with or without a description and an alternative number of bases-per-line.
appendToPath(String, String) - Static method in class htsjdk.tribble.util.ParsingUtils
  Add the `indexExtension` to the `filepath`, preserving query string elements if present.
applyIfNotNull(T, Consumer) - Static method in class htsjdk.samtools.util.CodeUtil
  Applied the Consumer on the input if the input is not null, serves as a way to avoid writing: `if(input != null){ action.apply(input); }` and replacing it with `applyIfNotNull(input,action);`
applyTo(CRAMEncodingStrategy) - Method in enum class htsjdk.samtools.cram.structure.CRAMCompressionProfile
  Apply this profile's settings to an existing strategy, overwriting the CRAM version, GZIP compression level, reads-per-slice, and compressor map.
ARCHIVE - Enum constant in enum class htsjdk.samtools.cram.structure.CRAMCompressionProfile
  Maximum compression profile.
areHeadersEqual(MetricsFile) - Method in class htsjdk.samtools.metrics.MetricsFile
areHistogramsEqual(MetricsFile) - Method in class htsjdk.samtools.metrics.MetricsFile
areInSameOrAdjacentBlocks(long, long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
areMetricsAndHistogramsEqual(File, File) - Static method in class htsjdk.samtools.metrics.MetricsFile
  Compare the metrics and histograms in two files, ignoring headers.
areMetricsEqual(MetricsFile) - Method in class htsjdk.samtools.metrics.MetricsFile
areMetricsEqual(File, File) - Static method in class htsjdk.samtools.metrics.MetricsFile
  Compare the metrics in two files, ignoring headers and histograms.
areSequenceDictionariesEqual(SAMSequenceDictionary, SAMSequenceDictionary) - Static method in class htsjdk.samtools.util.SequenceUtil
  Returns true if both parameters are null or equal, otherwise returns false
arg() - Method in record class htsjdk.samtools.cram.structure.CompressorDescriptor
  Returns the value of the `arg` record component.
array(InputStream) - Static method in class htsjdk.samtools.cram.io.CramIntArray
  Read CRAM int array from a `InputStream`.
arrayAsList(InputStream) - Static method in class htsjdk.samtools.cram.io.CramIntArray
  Read CRAM int array from a `InputStream` as a List.
arrayMax(double[]) - Static method in class htsjdk.variant.utils.GeneralUtils
AS - Enum constant in enum class htsjdk.samtools.SAMTag
AS - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
asAddressOffsetString(long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
  Return a String with the file pointer in "address:offset" form.
asBaiSeekableStreamOrNull(SeekableStream, SAMSequenceDictionary) - Static method in enum class htsjdk.samtools.SamIndexes
asBaiStreamOrNull(InputStream, SAMSequenceDictionary) - Static method in enum class htsjdk.samtools.SamIndexes
AsciiFeatureCodec<T> - Class in htsjdk.tribble
  A convenience base class for codecs that want to read in features from ASCII lines.
AsciiFeatureCodec(Class) - Constructor for class htsjdk.tribble.AsciiFeatureCodec
AsciiLineReader - Class in htsjdk.tribble.readers
  A simple class that provides `AsciiLineReader.readLine()` functionality around a PositionalBufferedStream `BufferedReader` and its `BufferedReader.readLine()` method should be used in preference to this class (when the `LocationAware` functionality is not required) because it offers greater performance.
AsciiLineReader() - Constructor for class htsjdk.tribble.readers.AsciiLineReader
AsciiLineReader(PositionalBufferedStream) - Constructor for class htsjdk.tribble.readers.AsciiLineReader
  Deprecated.
  8/8/2017 use `AsciiLineReader.from(InputStream)`
AsciiLineReader(InputStream) - Constructor for class htsjdk.tribble.readers.AsciiLineReader
  Deprecated.
  8/8/2017 use `AsciiLineReader.from(InputStream)`
AsciiLineReaderIterator - Class in htsjdk.tribble.readers
  A class that iterates over the lines and line positions in an `AsciiLineReader`.
AsciiLineReaderIterator(AsciiLineReader) - Constructor for class htsjdk.tribble.readers.AsciiLineReaderIterator
AsciiWriter - Class in htsjdk.samtools.util
  Fast (I hope) buffered Writer that converts char to byte merely by casting, rather than charset conversion.
AsciiWriter(OutputStream) - Constructor for class htsjdk.samtools.util.AsciiWriter
asEmptyIfNull(Object) - Static method in class htsjdk.samtools.util.StringUtil
asFastqRecord(SAMRecord) - Static method in class htsjdk.samtools.fastq.FastqEncoder
  Converts a `SAMRecord` into a `FastqRecord`.
asSAMRecord(FastqRecord, SAMFileHeader) - Static method in class htsjdk.samtools.fastq.FastqEncoder
  Converts a `FastqRecord` into a simple unmapped `SAMRecord`.
asSAMRecord(FastqRecord, SAMFileHeader, BiConsumer) - Static method in class htsjdk.samtools.fastq.FastqEncoder
  Converts a `FastqRecord` into a simple unmapped `SAMRecord`.
ASSEMBLY_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
assertBundleContainsIndex(Bundle) - Static method in class htsjdk.beta.codecs.reads.ReadsCodecUtils
  InternalAPI The stated contract for decoders is that the index must be included in the bundle in order to use index queries, but some codecs use readers that *always* tries to resolve the index, which would violate that and allow some cases to work that shouldn't, so enforce the contract manually so that someday when we use a different implementation, no backward compatibility issue will be introduced.
assertBundleContainsIndex(Bundle) - Static method in class htsjdk.beta.codecs.variants.vcf.VariantsCodecUtils
  InternalAPI The stated contract for decoders is that the index must be included in the bundle in order to use index queries, but some codecs use readers that *always* tries to resolve the index, which would violate that and allow some cases to work that shouldn't, so enforce the contract manually so that someday when we use a different implementation, no backward compatibility issue will be introduced.
assertCharactersNotInString(String, char...) - Static method in class htsjdk.samtools.util.StringUtil
  Checks that a String doesn't contain one or more characters of interest.
assertDirectoryIsReadable(File) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that a directory is non-null, extent, readable and a directory otherwise a runtime exception is thrown.
assertDirectoryIsWritable(File) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that a directory is non-null, extent, writable and a directory otherwise a runtime exception is thrown.
assertDirectoryIsWritable(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that a directory is non-null, extent, writable and a directory otherwise a runtime exception is thrown.
assertFileIsReadable(File) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that a file is non-null, exists, is not a directory and is readable.
assertFileIsReadable(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that a file is non-null, exists, is not a directory and is readable.
assertFileIsWritable(File) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that a file is non-null, and is either extent and writable, or non-existent but that the parent directory exists and is writable.
assertFileIsWritable(Path) - Static method in class htsjdk.samtools.util.IOUtil
  In some filesystems (e.g.
assertFilesAreReadable(List) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that each file is non-null, exists, is not a directory and is readable.
assertFilesAreWritable(List) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that each file is non-null, and is either extent and writable, or non-existent but that the parent directory exists and is writable.
assertFilesEqual(File, File) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that the two files are the same length, and have the same content, otherwise throws a runtime exception.
assertFileSizeNonZero(File) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that a file is of non-zero length
AssertingIterator(CloseableIterator) - Constructor for class htsjdk.samtools.SamReader.AssertingIterator
assertInputIsValid(String) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that an input is is non-null, a URL or a file, exists, and if its a file then it is not a directory and is readable.
assertInputsAreValid(List) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that each string is non-null, exists or is a URL, and if it is a file then not a directory and is readable.
assertIntervalsOptimized(QueryInterval[]) - Static method in class htsjdk.samtools.QueryInterval
assertMate(SAMRecord, SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil
assertNonDefectiveFile(File) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
  Deprecated.
assertNonDefectivePath(Path) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
assertOpen() - Method in class htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator
assertOrderedNonOverlapping(Iterator, SAMSequenceDictionary) - Static method in class htsjdk.samtools.util.IntervalUtil
  Throws RuntimeException if the given intervals are not locus ordered and non-overlapping
assertPairValid(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMTestUtil
  Basic sanity check for a pair of SAMRecords.
assertPathsAreReadable(List) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that each path is non-null, exists, is not a directory and is readable.
assertReadValid(SAMRecord) - Static method in class htsjdk.samtools.SAMTestUtil
  Basic sanity check for a SAMRecord.
assertSameDictionary(SAMSequenceDictionary) - Method in class htsjdk.samtools.SAMSequenceDictionary
  Non-comprehensive `SAMSequenceDictionary.equals(Object)`-assertion: instead of calling `SAMSequenceRecord.equals(Object)` on constituent `SAMSequenceRecord`s in this dictionary against its pair in the target dictionary, in order, call `SAMSequenceRecord.isSameSequence(SAMSequenceRecord)`.
assertSequenceDictionariesEqual(SAMSequenceDictionary, SAMSequenceDictionary) - Static method in class htsjdk.samtools.util.SequenceUtil
  Throws an exception if both parameters are non-null and unequal.
assertSequenceDictionariesEqual(SAMSequenceDictionary, SAMSequenceDictionary, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
  Throws an exception if both (first) parameters are non-null and unequal (if checkPrefixOnly, checks prefix of lists only).
assertSequenceDictionariesEqual(SAMSequenceDictionary, SAMSequenceDictionary, File, File) - Static method in class htsjdk.samtools.util.SequenceUtil
  Throws an exception if both parameters are non-null and unequal, including the filenames.
assertSequenceListsEqual(List, List) - Static method in class htsjdk.samtools.util.SequenceUtil
  default signature that forces the lists to be the same size
assertSequenceListsEqual(List, List, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
  Throws an exception only if both (first) parameters are not null optionally check that one list is a (nonempty) prefix of the other.
assertSorted(SAMFileHeader.SortOrder) - Method in class htsjdk.samtools.CRAMIterator
assertSorted(SAMFileHeader.SortOrder) - Method in class htsjdk.samtools.SamReader.AssertingIterator
assertSorted(SAMFileHeader.SortOrder) - Method in interface htsjdk.samtools.SAMRecordIterator
  Establishes that records returned by this iterator are expected to be in the specified sort order.
assignReadName() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Assign a synthetic read name based on the sequential index if no name was decoded.
asString(long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
AsyncBlockCompressedInputStream - Class in htsjdk.samtools.util
  Asynchronous read-ahead implementation of `BlockCompressedInputStream`.
AsyncBlockCompressedInputStream(SeekableStream) - Constructor for class htsjdk.samtools.util.AsyncBlockCompressedInputStream
AsyncBlockCompressedInputStream(SeekableStream, InflaterFactory) - Constructor for class htsjdk.samtools.util.AsyncBlockCompressedInputStream
AsyncBlockCompressedInputStream(File) - Constructor for class htsjdk.samtools.util.AsyncBlockCompressedInputStream
AsyncBlockCompressedInputStream(File, InflaterFactory) - Constructor for class htsjdk.samtools.util.AsyncBlockCompressedInputStream
AsyncBlockCompressedInputStream(InputStream) - Constructor for class htsjdk.samtools.util.AsyncBlockCompressedInputStream
AsyncBlockCompressedInputStream(InputStream, InflaterFactory) - Constructor for class htsjdk.samtools.util.AsyncBlockCompressedInputStream
AsyncBlockCompressedInputStream(URL) - Constructor for class htsjdk.samtools.util.AsyncBlockCompressedInputStream
AsyncBlockCompressedInputStream(URL, InflaterFactory) - Constructor for class htsjdk.samtools.util.AsyncBlockCompressedInputStream
AsyncBufferedIterator<T> - Class in htsjdk.samtools.util
  Iterator that uses a dedicated background thread to perform read-ahead to improve throughput at the expense of increased latency.
AsyncBufferedIterator(Iterator, int) - Constructor for class htsjdk.samtools.util.AsyncBufferedIterator
  Creates a new iterator that traverses the given iterator on a background thread
AsyncBufferedIterator(Iterator, int, int) - Constructor for class htsjdk.samtools.util.AsyncBufferedIterator
  Creates a new iterator that traverses the given iterator on a background thread
AsyncBufferedIterator(Iterator, int, int, String) - Constructor for class htsjdk.samtools.util.AsyncBufferedIterator
  Creates a new iterator that traverses the given iterator on a background thread
AsyncFastqWriter - Class in htsjdk.samtools.fastq
  Implementation of a FastqWriter that provides asynchronous output.
AsyncFastqWriter(FastqWriter, int) - Constructor for class htsjdk.samtools.fastq.AsyncFastqWriter
AsyncVariantContextWriter - Class in htsjdk.variant.variantcontext.writer
  AsyncVariantContextWriter that can be wrapped around an underlying AsyncVariantContextWriter to provide asynchronous output.
AsyncVariantContextWriter(VariantContextWriter) - Constructor for class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
  Creates a new AsyncVariantContextWriter wrapping the provided VariantContextWriter.
AsyncVariantContextWriter(VariantContextWriter, int) - Constructor for class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
  Creates an AsyncVariantContextWriter wrapping the provided VariantContextWriter and using the specified queue size for buffer VariantContexts.
AsyncWriterPool - Class in htsjdk.io
  Implementation of an asynchronous writer pool.
AsyncWriterPool() - Constructor for class htsjdk.io.AsyncWriterPool
  Create an AsyncWriterPool using all available processors.
AsyncWriterPool(int) - Constructor for class htsjdk.io.AsyncWriterPool
  Create an AsyncWriterPool using the specified number of `threads`.
atEoln() - Method in class htsjdk.samtools.util.FastLineReader
AtomicInt(VCFCompoundHeaderLine, Map) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.AtomicInt
attribute(String, Object) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype has this attribute key / value pair.
attribute(String, Object) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Puts the key -> value mapping into this builder's attributes
ATTRIBUTE_DELIMITER - Static variable in class htsjdk.tribble.gff.Gff3Constants
attributes(Map) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells this builder to use this map of attributes for the resulting `VariantContext`.
attributes(Map) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype has these attributes.
attributesEqual(AbstractSAMHeaderRecord) - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
  For use in the equals() method of the concrete class.
attributesHashCode() - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
  For use in the hashCode() method of the concrete class.
available() - Method in class htsjdk.samtools.cram.io.CountingInputStream
available() - Method in class htsjdk.samtools.cram.io.CRAMByteReader
  Return the number of bytes remaining to be read.
available() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
available() - Method in class htsjdk.samtools.seekablestream.SeekableStream
  The return value of this method is unusable for any purpose, and we are only implementing it because certain Java classes like `GZIPInputStream` incorrectly rely on it to detect EOF
available() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
available() - Method in class htsjdk.samtools.util.CoordSpanInputSteam
  Returns how many bytes are left in the current chunk.
available() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream

## B

b - Variable in class htsjdk.samtools.util.Tuple
b - Variable in class htsjdk.tribble.util.TabixUtils.TIndex
B1 - Enum constant in enum class htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS
B5 - Enum constant in enum class htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS
BA_Base - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
BAI - Enum constant in enum class htsjdk.samtools.SamIndexes
BAI_INDEX - Static variable in class htsjdk.samtools.util.FileExtensions
BAI_INDEX_SUFFIX - Static variable in interface htsjdk.samtools.BAMIndex
  Deprecated.
  since June 2019 Use `FileExtensions.BAI_INDEX` instead.
BAIEntry - Class in htsjdk.samtools.cram
  Class used to construct a BAI index for a CRAM file.
BAIEntry(CRAIEntry) - Constructor for class htsjdk.samtools.cram.BAIEntry
  Create a BAIEntry from a CRAIEntry (used to read a .crai as a .bai).
BAIEntry(ReferenceContext, AlignmentSpan, long, long, int) - Constructor for class htsjdk.samtools.cram.BAIEntry
BAM - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetFormat
BAM - Static variable in class htsjdk.beta.plugin.reads.ReadsFormats
  BAM file format.
BAM - Static variable in class htsjdk.samtools.util.FileExtensions
BAM_CSI_TYPE - Static variable in class htsjdk.samtools.SamReader.Type
BAM_DEFAULT_VERSION - Static variable in class htsjdk.beta.codecs.reads.bam.BAMCodec
BAM_FILE_EXTENSION - Static variable in class htsjdk.samtools.BamFileIoUtils
  Deprecated.
  since June 2019 Use `FileExtensions.BAM` instead.
BAM_FILE_MISSING_TERMINATOR_BLOCK - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  BAM appears to be healthy, but is an older file so doesn't have terminator block.
BAM_HTSGET_TYPE - Static variable in class htsjdk.samtools.SamReader.Type
BAM_LIDX_SHIFT - Static variable in class htsjdk.samtools.LinearIndex
BAM_TYPE - Static variable in class htsjdk.samtools.SamReader.Type
BAMCodec - Class in htsjdk.beta.codecs.reads.bam
  InternalAPI Base class for `BundleResourceType.FMT_READS_BAM` codecs.
BAMCodec() - Constructor for class htsjdk.beta.codecs.reads.bam.BAMCodec
BAMCodecV1_0 - Class in htsjdk.beta.codecs.reads.bam.bamV1_0
  BAM v1.0 codec.
BAMCodecV1_0() - Constructor for class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMCodecV1_0
BamConverter - Class in htsjdk.samtools
  Simple command-line tool for reading and optionally converting BAM files, primarily for experimenting with BAM read-path profiling.
BamConverter() - Constructor for class htsjdk.samtools.BamConverter
BAMDecoder - Class in htsjdk.beta.codecs.reads.bam
  InternalAPI Base class for `BundleResourceType.FMT_READS_BAM` decoders.
BAMDecoder(Bundle, ReadsDecoderOptions) - Constructor for class htsjdk.beta.codecs.reads.bam.BAMDecoder
  Create a BAM decoder for the given input bundle.
BAMDecoderOptions - Class in htsjdk.beta.codecs.reads.bam
  Decoder options specific to BAM decoders.
BAMDecoderOptions() - Constructor for class htsjdk.beta.codecs.reads.bam.BAMDecoderOptions
bamDecoderOptionsToSamReaderFactory(SamReaderFactory, BAMDecoderOptions) - Static method in class htsjdk.beta.codecs.reads.ReadsCodecUtils
BAMDecoderV1_0 - Class in htsjdk.beta.codecs.reads.bam.bamV1_0
  BAM v1.0 decoder.
BAMDecoderV1_0(Bundle, ReadsDecoderOptions) - Constructor for class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
  Create a V1.0 BAM decoder for the given input bundle.
BAMEncoder - Class in htsjdk.beta.codecs.reads.bam
  InternalAPI Base class for `BundleResourceType.FMT_READS_BAM` encoders.
BAMEncoder(Bundle, ReadsEncoderOptions) - Constructor for class htsjdk.beta.codecs.reads.bam.BAMEncoder
  InternalAPI Create a BAM encoder for the given output bundle.
BAMEncoderOptions - Class in htsjdk.beta.codecs.reads.bam
  Encoder options specific to BAM encoders.
BAMEncoderOptions() - Constructor for class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
BAMEncoderV1_0 - Class in htsjdk.beta.codecs.reads.bam.bamV1_0
  BAM v1.0 encoder.
BAMEncoderV1_0(Bundle, ReadsEncoderOptions) - Constructor for class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMEncoderV1_0
  Create a V1.0 BAM encoder for the given output bundle.
BamFileIoUtils - Class in htsjdk.samtools
BamFileIoUtils() - Constructor for class htsjdk.samtools.BamFileIoUtils
BAMFileReader - Class in htsjdk.samtools
  Class for reading and querying BAM files.
BAMFileReader.BAMQueryFilteringIterator - Class in htsjdk.samtools
  Pull SAMRecords from a coordinate-sorted iterator, and filter out any that do not match the filter.
BAMFileSpan - Class in htsjdk.samtools
  An ordered list of chunks, capable of representing a set of discontiguous regions in the BAM file.
BAMFileSpan() - Constructor for class htsjdk.samtools.BAMFileSpan
  Create a new empty list of chunks.
BAMFileSpan(Chunk) - Constructor for class htsjdk.samtools.BAMFileSpan
  Convenience constructor to construct a BAM file span from a single chunk.
BAMFileSpan(List) - Constructor for class htsjdk.samtools.BAMFileSpan
  Create a new chunk list from the given list of chunks.
BAMFileWriter - Class in htsjdk.samtools
  Concrete implementation of SAMFileWriter for writing gzipped BAM files.
BAMFileWriter(File) - Constructor for class htsjdk.samtools.BAMFileWriter
BAMFileWriter(File, int) - Constructor for class htsjdk.samtools.BAMFileWriter
BAMFileWriter(OutputStream, File) - Constructor for class htsjdk.samtools.BAMFileWriter
BAMFileWriter(OutputStream, File, int) - Constructor for class htsjdk.samtools.BAMFileWriter
BAMFileWriter(OutputStream, File, int, DeflaterFactory) - Constructor for class htsjdk.samtools.BAMFileWriter
BAMFileWriter(OutputStream, String, int, DeflaterFactory) - Constructor for class htsjdk.samtools.BAMFileWriter
BAMIndex - Interface in htsjdk.samtools
  A basic interface for querying BAM indices.
BAMIndexer - Class in htsjdk.samtools
  Class for both constructing BAM index content and writing it out.
BAMIndexer(File, SAMFileHeader) - Constructor for class htsjdk.samtools.BAMIndexer
BAMIndexer(OutputStream, SAMFileHeader) - Constructor for class htsjdk.samtools.BAMIndexer
  Prepare to index a BAM.
BAMIndexer(OutputStream, SAMFileHeader, boolean) - Constructor for class htsjdk.samtools.BAMIndexer
  Prepare to index a BAM.
BAMIndexer(Path, SAMFileHeader) - Constructor for class htsjdk.samtools.BAMIndexer
BAMIndexMerger - Class in htsjdk.samtools
  Merges BAM index files for (headerless) parts of a BAM file into a single index file.
BAMIndexMerger(OutputStream, long) - Constructor for class htsjdk.samtools.BAMIndexMerger
BAMIndexMetaData - Class in htsjdk.samtools
  Metadata about the bam index contained within the bam index.
BAMIndexSuffix - Static variable in interface htsjdk.samtools.BAMIndex
  Deprecated.
  since June 2019 Use `FileExtensions.BAI_INDEX` instead.
BamIndexValidator - Class in htsjdk.samtools
  Class to validate (at two different levels of thoroughness) the index for a BAM file.
BamIndexValidator() - Constructor for class htsjdk.samtools.BamIndexValidator
BamIndexValidator.IndexValidationStringency - Enum Class in htsjdk.samtools
BAMQueryFilteringIterator(CloseableIterator, BAMIteratorFilter) - Constructor for class htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator
BAMQueryMultipleIntervalsIteratorFilter - Class in htsjdk.samtools
  Filters out records that do not match any of the given intervals and query type.
BAMQueryMultipleIntervalsIteratorFilter(QueryInterval[], boolean) - Constructor for class htsjdk.samtools.BAMQueryMultipleIntervalsIteratorFilter
BAMQueryMultipleIntervalsIteratorFilter(List, boolean) - Constructor for class htsjdk.samtools.HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter
BAMRecord - Class in htsjdk.samtools
  Wrapper class for binary BAM records.
BAMRecord(SAMFileHeader, int, int, short, short, int, int, int, int, int, int, int, byte[]) - Constructor for class htsjdk.samtools.BAMRecord
  Create a new BAM Record.
BAMRecordCodec - Class in htsjdk.samtools
  Class for translating between in-memory and disk representation of BAMRecord.
BAMRecordCodec(SAMFileHeader) - Constructor for class htsjdk.samtools.BAMRecordCodec
BAMRecordCodec(SAMFileHeader, SAMRecordFactory) - Constructor for class htsjdk.samtools.BAMRecordCodec
BAMSBIIndexer - Class in htsjdk.samtools
  Writes SBI files for BAM files, as understood by `SBIIndex`.
BAMSBIIndexer() - Constructor for class htsjdk.samtools.BAMSBIIndexer
BAMStartingAtIteratorFilter - Class in htsjdk.samtools
  A decorating iterator that filters out records that do not match the given reference and start position.
BAMStartingAtIteratorFilter(int, int) - Constructor for class htsjdk.samtools.BAMStartingAtIteratorFilter
BAMStreamWriter - Class in htsjdk.samtools
  Class for writing SAMRecords in BAM format to an output stream.
BAMStreamWriter(OutputStream, OutputStream, OutputStream, long, SAMFileHeader) - Constructor for class htsjdk.samtools.BAMStreamWriter
  Create a BAMStreamWriter for writing.
BARCODE_QUALITY_DELIMITER - Static variable in class htsjdk.samtools.util.SamConstants
  The recommend separator to use when specifying multiple barcode quality scores together in the same tag.
BARCODE_SEQUENCE_DELIMITER - Static variable in class htsjdk.samtools.util.SamConstants
  The recommended separator to use when specifying multiple barcodes together in the same tag.
BARCODE_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
base(byte, byte) - Method in class htsjdk.samtools.cram.structure.SubstitutionMatrix
  Given a reference base and a substitution code, return the corresponding substitution base.
BASE_URL_FOR_HTTP_TESTS - Static variable in class htsjdk.samtools.util.TestUtil
  Base url where all test files for http tests are found
baseAndProbDiffToSqValue(int, byte) - Static method in class htsjdk.samtools.SQTagUtil
  Deprecated.
  Compress a base and a log probabiliy difference (-10log10(p3/p2)) into a single byte so that it can be output in a SAMRecord's SQ field.
baseAndProbDiffToSqValue(SQTagUtil.SQBase, byte) - Static method in class htsjdk.samtools.SQTagUtil
  Deprecated.
  Compress a base and a log probabiliy difference (-10log10(p3/p2)) into a single byte so that it can be output in a SAMRecord's SQ field.
basename(File) - Static method in class htsjdk.samtools.util.IOUtil
  Returns the name of the file minus the extension (i.e.
BaseQualityScore - Class in htsjdk.samtools.cram.encoding.readfeatures
  A read feature representing a single quality score in a read.
BaseQualityScore(int, byte) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
Bases - Class in htsjdk.samtools.cram.encoding.readfeatures
Bases(int, byte[]) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Bases
BASES_SIZE - Static variable in class htsjdk.samtools.cram.structure.SubstitutionMatrix
basesEqual(byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil
  Efficiently compare two IUPAC base codes, simply returning true if they are equal (ignoring case), without considering the set relationships between ambiguous codes.
basesMatch(byte[]) - Method in interface htsjdk.variant.variantcontext.Allele
basesMatch(byte[]) - Method in class htsjdk.variant.variantcontext.SimpleAllele
basesMatch(Allele) - Method in interface htsjdk.variant.variantcontext.Allele
basesMatch(Allele) - Method in class htsjdk.variant.variantcontext.SimpleAllele
basesMatch(String) - Method in interface htsjdk.variant.variantcontext.Allele
basesMatch(String) - Method in class htsjdk.variant.variantcontext.SimpleAllele
BasicFastqWriter - Class in htsjdk.samtools.fastq
  In general FastqWriterFactory should be used so that AsyncFastqWriter can be enabled, but there are some cases in which that behavior is explicitly not wanted.
BasicFastqWriter(File) - Constructor for class htsjdk.samtools.fastq.BasicFastqWriter
BasicFastqWriter(File, boolean) - Constructor for class htsjdk.samtools.fastq.BasicFastqWriter
BasicFastqWriter(PrintStream) - Constructor for class htsjdk.samtools.fastq.BasicFastqWriter
BB_Bases - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
BC - Enum constant in enum class htsjdk.samtools.SAMTag
BC - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
BCF - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetFormat
BCF - Enum constant in enum class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType
BCF - Static variable in class htsjdk.beta.plugin.variants.VariantsFormats
  BCF format.
BCF - Static variable in class htsjdk.samtools.util.FileExtensions
BCF_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  since June 2019 Use `FileExtensions.BCF` instead.
BCF_STREAM - Enum constant in enum class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType
BCF2Codec - Class in htsjdk.variant.bcf2
  Decode BCF2 files
BCF2Codec() - Constructor for class htsjdk.variant.bcf2.BCF2Codec
BCF2Codec.LazyData - Class in htsjdk.variant.bcf2
BCF2Codec.SitesInfoForDecoding - Class in htsjdk.variant.bcf2
BCF2Decoder - Class in htsjdk.variant.bcf2
BCF2Decoder() - Constructor for class htsjdk.variant.bcf2.BCF2Decoder
BCF2Decoder(byte[]) - Constructor for class htsjdk.variant.bcf2.BCF2Decoder
  Create a new decoder ready to read BCF2 data from the byte[] recordBytes, for testing purposes
BCF2Encoder - Class in htsjdk.variant.variantcontext.writer
  See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2Encoder() - Constructor for class htsjdk.variant.variantcontext.writer.BCF2Encoder
BCF2FieldEncoder - Class in htsjdk.variant.variantcontext.writer
  See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2FieldEncoder.AtomicInt - Class in htsjdk.variant.variantcontext.writer
  Specialized int encoder for atomic (non-list) integers
BCF2FieldEncoder.Flag - Class in htsjdk.variant.variantcontext.writer
BCF2FieldEncoder.Float - Class in htsjdk.variant.variantcontext.writer
BCF2FieldEncoder.GenericInts - Class in htsjdk.variant.variantcontext.writer
BCF2FieldEncoder.IntArray - Class in htsjdk.variant.variantcontext.writer
BCF2FieldEncoder.StringOrCharacter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter - Class in htsjdk.variant.variantcontext.writer
  See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2FieldWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
BCF2FieldWriter.FTGenotypesWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.GenericSiteWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.GenotypesWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.GTWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.IGFGenotypesWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.IntegerTypeGenotypesWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.SiteWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriter.StaticallyTypeGenotypesWriter - Class in htsjdk.variant.variantcontext.writer
BCF2FieldWriterManager - Class in htsjdk.variant.variantcontext.writer
  See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2FieldWriterManager() - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager
BCF2GenotypeFieldDecoders - Class in htsjdk.variant.bcf2
  An efficient scheme for building and obtaining specialized genotype field decoders.
BCF2GenotypeFieldDecoders(VCFHeader) - Constructor for class htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders
BCF2GenotypeFieldDecoders.Decoder - Interface in htsjdk.variant.bcf2
  Decoder a field (implicit from creation) encoded as typeDescriptor in the decoder object in the GenotypeBuilders one for each sample in order.
BCF2LazyGenotypesDecoder - Class in htsjdk.variant.bcf2
  Lazy version of genotypes decoder for BCF2 genotypes
BCF2Type - Enum Class in htsjdk.variant.bcf2
  BCF2 types and associated information
BCF2Utils - Class in htsjdk.variant.bcf2
  Common utilities for working with BCF2 files Includes convenience methods for encoding, decoding BCF2 type descriptors (size + type)
BCFVersion - Class in htsjdk.variant.bcf2
  Simple holder for BCF version information User: depristo Date: 8/2/12 Time: 2:16 PM
BCFVersion(int, int) - Constructor for class htsjdk.variant.bcf2.BCFVersion
BD - Enum constant in enum class htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS
BED - Static variable in class htsjdk.samtools.util.FileExtensions
BED - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
BED_EXTENSION - Static variable in class htsjdk.tribble.bed.BEDCodec
  Deprecated.
  since June 2019 Use `FileExtensions.BED` instead.
BEDCodec - Class in htsjdk.tribble.bed
  Codec for parsing BED file, as described by UCSC See https://genome.ucsc.edu/FAQ/FAQformat.html#format1
BEDCodec() - Constructor for class htsjdk.tribble.bed.BEDCodec
  Calls `BEDCodec(StartOffset)` with an argument of `StartOffset.ONE`
BEDCodec(BEDCodec.StartOffset) - Constructor for class htsjdk.tribble.bed.BEDCodec
  BED format is 0-based, but Tribble is 1-based.
BEDCodec.StartOffset - Enum Class in htsjdk.tribble.bed
  Indicate whether co-ordinates or 0-based or 1-based.
BEDFeature - Interface in htsjdk.tribble.bed
before(Date) - Method in class htsjdk.samtools.util.RelativeIso8601Date
BEFORE_MOST_UPSTREAM_LOC - Static variable in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
beg - Variable in class htsjdk.tribble.util.TabixUtils.TIntv
BEGIN - Enum constant in enum class htsjdk.samtools.util.EdgingRecordAndOffset.Type
BETA - Enum constant in enum class htsjdk.samtools.cram.structure.EncodingID
  Binary coding with sufficient leading 0 bits to store each value with the same length
BetaAPI - Annotation Interface in htsjdk.annotations
  Annotation indicating that a package, class, method, or type is release level "BETA", and is not part of the stable public API.
BetaIntegerCodec - Class in htsjdk.samtools.cram.encoding.core
  Encodes integers by adding a constant offset value to a range of values in order to reduce the necessary number of bits needed to store each value.
BetaIntegerCodec(BitInputStream, BitOutputStream, int, int) - Constructor for class htsjdk.samtools.cram.encoding.core.BetaIntegerCodec
  Given integers to encode in the range MIN to MAX:
BetaIntegerEncoding - Class in htsjdk.samtools.cram.encoding.core
BetaIntegerEncoding(int, int) - Constructor for class htsjdk.samtools.cram.encoding.core.BetaIntegerEncoding
BF_BitFlags - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
BFQ - Enum constant in enum class htsjdk.samtools.fastq.FastqConstants.FastqExtensions
BGI - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Deprecated.
  Use SAMReadGroupRecord.PlatformValue.DNBSEQ instead.
BGZF - Enum constant in enum class htsjdk.samtools.util.GzipCodec.Format
BGZF_ID1 - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
BGZF_ID2 - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
BGZF_LEN - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
Bin - Class in htsjdk.samtools
  An individual bin in a BAM file.
Bin(int, int) - Constructor for class htsjdk.samtools.Bin
BIN_GENOMIC_SPAN - Static variable in class htsjdk.samtools.GenomicIndexUtil
  Reports the total amount of genomic data that any bin can index.
binary() - Method in class htsjdk.samtools.util.ftp.FTPClient
BinaryCodec - Class in htsjdk.samtools.util
  Encapsulates file representation of various primitive data types.
BinaryCodec() - Constructor for class htsjdk.samtools.util.BinaryCodec
  Ambiguous whether reading or writing until set{In,Out}putStream is called
BinaryCodec(File, boolean) - Constructor for class htsjdk.samtools.util.BinaryCodec
  Constructs BinaryCodec from a file and set its mode to writing or not
BinaryCodec(InputStream) - Constructor for class htsjdk.samtools.util.BinaryCodec
  Constructs BinaryCodec from an input stream
BinaryCodec(OutputStream) - Constructor for class htsjdk.samtools.util.BinaryCodec
  Constructs BinaryCodec from an output stream
BinaryCodec(String, boolean) - Constructor for class htsjdk.samtools.util.BinaryCodec
  Constructs BinaryCodec from a file name and set its mode to writing or not
BinaryCodec(Path, boolean) - Constructor for class htsjdk.samtools.util.BinaryCodec
  Constructs BinaryCodec from a file and set its mode to writing or not
BinaryFeatureCodec<T> - Class in htsjdk.tribble
  Implements common methods of `FeatureCodec`s that read from `PositionalBufferedStream`s.
BinaryFeatureCodec() - Constructor for class htsjdk.tribble.BinaryFeatureCodec
BinaryTagCodec - Class in htsjdk.samtools
  Converter between disk and in-memory representation of a SAMRecord tag.
BinaryTagCodec(BinaryCodec) - Constructor for class htsjdk.samtools.BinaryTagCodec
  For writing tags.
binaryToEnum(int) - Static method in enum class htsjdk.samtools.CigarOperator
bindings - Variable in class htsjdk.samtools.filter.AbstractJavascriptFilter
  javascript bindings
BinList - Class in htsjdk.samtools
  Provides a list of all bins which could exist in the BAM file.
BinList(int, BitSet) - Constructor for class htsjdk.samtools.BinList
  Create a new BinList over sequenceCount sequences, consisting of the given bins.
BinList(Bin[], int) - Constructor for class htsjdk.samtools.BinningIndexContent.BinList
BinningIndexBuilder - Class in htsjdk.samtools
  Builder for a BinningIndexContent object.
BinningIndexBuilder(int) - Constructor for class htsjdk.samtools.BinningIndexBuilder
BinningIndexBuilder(int, int) - Constructor for class htsjdk.samtools.BinningIndexBuilder
BinningIndexBuilder(int, int, boolean) - Constructor for class htsjdk.samtools.BinningIndexBuilder
BinningIndexBuilder.FeatureToBeIndexed - Interface in htsjdk.samtools
  coordinates are 1-based, inclusive
BinningIndexContent - Class in htsjdk.samtools
  In-memory representation of the binning index for a single reference.
BinningIndexContent(int, BinningIndexContent.BinList, LinearIndex) - Constructor for class htsjdk.samtools.BinningIndexContent
BinningIndexContent.BinList - Class in htsjdk.samtools
  This class is used to encapsulate the list of Bins store in the BAMIndexContent While it is currently represented as an array, we may decide to change it to an ArrayList or other structure
binomialCoefficient(int, int) - Static method in class htsjdk.variant.utils.BinomialCoefficientUtil
  Binomial Coefficient, "`n choose k`", the number of `k`-element subsets that can be selected from an `n`-element set.
BinomialCoefficientUtil - Class in htsjdk.variant.utils
  A modified version of the Apache Math implementation of binomial coefficient calculation Derived from code within the CombinatoricsUtils and FastMath classes within Commons Math3 (https://commons.apache.org/proper/commons-math/) Included here for use in Genotype Likelihoods calculation, instead of adding Commons Math3 as a dependency Commons Math3 is licensed using the Apache License 2.0 Full text of this license can be found here: https://www.apache.org/licenses/LICENSE-2.0.txt This product includes software developed at The Apache Software Foundation (http://www.apache.org/).
BinomialCoefficientUtil() - Constructor for class htsjdk.variant.utils.BinomialCoefficientUtil
binTolevel(int) - Static method in class htsjdk.samtools.GenomicIndexUtil
  Return the binning index level for the given bin.
BinWithOffset - Class in htsjdk.samtools
  An individual bin of a CSI index for BAM files.
BinWithOffset(int, int, long) - Constructor for class htsjdk.samtools.BinWithOffset
bisulfiteBasesEqual(boolean, byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil
  Returns true if the bases are equal OR if the mismatch can be accounted for by bisulfite treatment.
bisulfiteBasesEqual(byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil
bisulfiteBasesMatchWithAmbiguity(boolean, byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil
  Same as above, but use `readBaseMatchesRefBaseWithAmbiguity` instead of `basesEqual`.
BitInputStream - Interface in htsjdk.samtools.cram.io
  An interface to describe the requirements for reading bit data as opposed to bytes.
BitOutputStream - Interface in htsjdk.samtools.cram.io
  An interface to describe the requirements for writing out bits as opposed to bytes.
Block - Class in htsjdk.samtools.cram.structure.block
  Class representing CRAM block concept and some methods to operate with block content.
Block - Class in htsjdk.tribble.index
  Represents a contiguous block of bytes in a file, defined by a start position and size (in bytes)
Block(long, long) - Constructor for class htsjdk.tribble.index.Block
Block(BlockCompressionMethod, BlockContentType, int, byte[], int) - Constructor for class htsjdk.samtools.cram.structure.block.Block
  Protected constructor of a generic Block, to be called by static factory methods and subclasses.
Block(URI, Map, HtsgetClass) - Constructor for class htsjdk.samtools.util.htsget.HtsgetResponse.Block
BLOCK_COMPRESSED - Static variable in class htsjdk.samtools.util.FileExtensions
BLOCK_COMPRESSED_EXTENSIONS - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  Use since June 2019 `FileExtensions.BLOCK_COMPRESSED` instead.
BLOCK_COMPRESSED_EXTENSIONS - Static variable in class htsjdk.tribble.AbstractFeatureReader
  Deprecated.
  since June 2019 use `FileExtensions.BLOCK_COMPRESSED` instead.
BLOCK_COMPRESSED_VCF - Enum constant in enum class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType
BLOCK_FOOTER_LENGTH - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
BLOCK_HEADER_LENGTH - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
BLOCK_LENGTH_OFFSET - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
BlockCompressedFilePointerUtil - Class in htsjdk.samtools.util
  Static for manipulating virtual file pointers in BGZF files.
BlockCompressedFilePointerUtil() - Constructor for class htsjdk.samtools.util.BlockCompressedFilePointerUtil
BlockCompressedIndexedFastaSequenceFile - Class in htsjdk.samtools.reference
  A block-compressed FASTA file driven by an index for fast lookups.
BlockCompressedIndexedFastaSequenceFile(IOPath, IOPath, FastaSequenceIndex, GZIIndex) - Constructor for class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Create a BlockCompressedIndexedFastaSequenceFile from explicitly provided files.
BlockCompressedIndexedFastaSequenceFile(String, SeekableStream, FastaSequenceIndex, SAMSequenceDictionary, GZIIndex) - Constructor for class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Initialize the given indexed fasta sequence file stream.
BlockCompressedIndexedFastaSequenceFile(Path) - Constructor for class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
BlockCompressedIndexedFastaSequenceFile(Path, FastaSequenceIndex) - Constructor for class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
BlockCompressedIndexedFastaSequenceFile(Path, FastaSequenceIndex, GZIIndex) - Constructor for class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
BlockCompressedInputStream - Class in htsjdk.samtools.util
  Utility class for reading BGZF block compressed files.
BlockCompressedInputStream(SeekableStream) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
  For providing some arbitrary data source.
BlockCompressedInputStream(SeekableStream, InflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
  For providing some arbitrary data source.
BlockCompressedInputStream(File) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
  Use this ctor if you wish to call seek()
BlockCompressedInputStream(File, InflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
  Use this ctor if you wish to call seek()
BlockCompressedInputStream(InputStream) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
  Note that seek() is not supported if this ctor is used.
BlockCompressedInputStream(InputStream, boolean) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
  Note that seek() is not supported if this ctor is used.
BlockCompressedInputStream(InputStream, boolean, InflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
  Note that seek() is not supported if this ctor is used.
BlockCompressedInputStream(InputStream, InflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
  Note that seek() is not supported if this ctor is used.
BlockCompressedInputStream(URL) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
BlockCompressedInputStream(URL, InflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
BlockCompressedInputStream(Path) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream
  Equivalent constructor for Path as the one that takes a File.
BlockCompressedInputStream.DecompressedBlock - Class in htsjdk.samtools.util
BlockCompressedInputStream.FileTermination - Enum Class in htsjdk.samtools.util
BlockCompressedOutputStream - Class in htsjdk.samtools.util
  Writer for a file that is a series of gzip blocks (BGZF format).
BlockCompressedOutputStream(File) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Uses default compression level, which is 5 unless changed by setCompressionLevel Note: this constructor uses the default `DeflaterFactory`, see `BlockCompressedOutputStream.getDefaultDeflaterFactory()`.
BlockCompressedOutputStream(File, int) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Prepare to compress at the given compression level
BlockCompressedOutputStream(File, int, DeflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Prepare to compress at the given compression level
BlockCompressedOutputStream(OutputStream, File) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Uses default compression level, which is 5 unless changed by setCompressionLevel Note: this constructor uses the default `DeflaterFactory`, see `BlockCompressedOutputStream.getDefaultDeflaterFactory()`.
BlockCompressedOutputStream(OutputStream, File, int) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Note: this constructor uses the default `DeflaterFactory`, see `BlockCompressedOutputStream.getDefaultDeflaterFactory()`.
BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Creates the output stream.
BlockCompressedOutputStream(OutputStream, Path) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Uses default compression level, which is 5 unless changed by setCompressionLevel Note: this constructor uses the default `DeflaterFactory`, see `BlockCompressedOutputStream.getDefaultDeflaterFactory()`.
BlockCompressedOutputStream(OutputStream, Path, int) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Note: this constructor uses the default `DeflaterFactory`, see `BlockCompressedOutputStream.getDefaultDeflaterFactory()`.
BlockCompressedOutputStream(OutputStream, Path, int, DeflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Creates the output stream.
BlockCompressedOutputStream(String) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Uses default compression level, which is 5 unless changed by setCompressionLevel Note: this constructor uses the default `DeflaterFactory`, see `BlockCompressedOutputStream.getDefaultDeflaterFactory()`.
BlockCompressedOutputStream(String, int) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Prepare to compress at the given compression level Note: this constructor uses the default `DeflaterFactory`, see `BlockCompressedOutputStream.getDefaultDeflaterFactory()`.
BlockCompressedOutputStream(Path, int, DeflaterFactory) - Constructor for class htsjdk.samtools.util.BlockCompressedOutputStream
  Prepare to compress at the given compression level
BlockCompressedStreamConstants - Class in htsjdk.samtools.util
  Constants shared by BlockCompressed{Input,Output}Stream classes
BlockCompressedStreamConstants() - Constructor for class htsjdk.samtools.util.BlockCompressedStreamConstants
BlockCompressionMethod - Enum Class in htsjdk.samtools.cram.structure.block
  The block compression methods specified by Section 8 of the CRAM spec.
BlockContentType - Enum Class in htsjdk.samtools.cram.structure.block
  The block content types specified by Section 8.1 of the CRAM spec
blockCopyBamFile(File, OutputStream, boolean, boolean) - Static method in class htsjdk.samtools.BamFileIoUtils
blockCopyBamFile(Path, OutputStream, boolean, boolean) - Static method in class htsjdk.samtools.BamFileIoUtils
  Copy data from a BAM file to an OutputStream by directly copying the gzip blocks.
BlockGunzipper - Class in htsjdk.samtools.util
  Alternative to GZIPInputStream, for decompressing GZIP blocks that are already loaded into a byte[].
blockIsFullyDecoded() - Method in class htsjdk.variant.bcf2.BCF2Decoder
BlockStats() - Constructor for class htsjdk.tribble.index.AbstractIndex.BlockStats
BND - Enum constant in enum class htsjdk.variant.variantcontext.StructuralVariantType
  breakend structural variation.
body - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetClass
BQ - Enum constant in enum class htsjdk.samtools.SAMTag
BQ - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
BREAKEND_EXTENDING_LEFT - Static variable in interface htsjdk.variant.variantcontext.Allele
BREAKEND_EXTENDING_RIGHT - Static variable in interface htsjdk.variant.variantcontext.Allele
breakIntervalsAtBandMultiples(List, int) - Static method in class htsjdk.samtools.util.IntervalList
  Given a list of Intervals and a band multiple, this method will return a list of Intervals such that all of the intervals do not straddle integer multiples of that band.
BrowseableBAMIndex - Interface in htsjdk.samtools
  An index interface with additional functionality for querying and inspecting the structure of a BAM index.
BS_BaseSubstitutionCode - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
BUFFER_SIZE - Static variable in class htsjdk.samtools.Defaults
  Buffer size, in bytes, used whenever reading/writing files or streams.
BufferedLineReader - Class in htsjdk.samtools.util
  Implementation of LineReader that is a thin wrapper around BufferedReader.
BufferedLineReader(InputStream) - Constructor for class htsjdk.samtools.util.BufferedLineReader
BufferedLineReader(InputStream, int) - Constructor for class htsjdk.samtools.util.BufferedLineReader
build() - Method in class htsjdk.beta.io.bundle.BundleBuilder
  Create a bundle from this builder's accumulated builder state, and reset the builder state.
build() - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Create the `FastaReferenceWriter`.
build() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Validate and build the `VariantContextWriter`.
build(OpenOption...) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Validate and build the `VariantContextWriter`.
buildAlleleStrings(VariantContext) - Static method in class htsjdk.variant.vcf.VCFEncoder
  return a Map containing Allele -> String(allele position) for all Alleles in VC (as well as NO_CALL) ex: A,T,TC -> { A:0, T:1, TC:2, NO_CALL:EMPTY_ALLELE} This may be efficient when looking up values for many genotypes per VC
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.core.BetaIntegerEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanByteEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanIntegerEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.core.experimental.GolombIntegerEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.core.GammaIntegerEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.core.SubexponentialIntegerEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.CRAMEncoding
  Instantiate the codec represented by this encoding by supplying it with the appropriate streams
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.external.ByteArrayStopEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.external.ExternalByteArrayEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.external.ExternalByteEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.external.ExternalIntegerEncoding
buildCodec(SliceBlocksReadStreams, SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.external.ExternalLongEncoding
buildFromFasta(Path) - Static method in class htsjdk.samtools.reference.FastaSequenceIndexCreator
  Builds a FastaSequenceIndex on the fly from a FASTA file.
buildIndex(Path) - Static method in class htsjdk.samtools.util.GZIIndex
  Builds a `GZIIndex` on the fly from a BGZIP file.
buildReadCodec(SliceBlocksReadStreams) - Method in class htsjdk.samtools.cram.encoding.CRAMEncoding
  Convenience initializer method for read codecs
buildStripeUncompressedSizes(int) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Compute the uncompressed size for each stripe stream.
buildSymsOrder0(int[]) - Method in class htsjdk.samtools.cram.compression.rans.RANSEncode
  Set up encoding symbols for Order-0 from the given normalized frequency table.
buildSymsOrder1(int[][]) - Method in class htsjdk.samtools.cram.compression.rans.RANSEncode
  Set up encoding symbols for Order-1 from the given normalized frequency tables.
buildWriteCodec(SliceBlocksWriteStreams) - Method in class htsjdk.samtools.cram.encoding.CRAMEncoding
  Convenience initializer method for write codecs
Bundle - Class in htsjdk.beta.io.bundle
  An immutable collection of related resources, including a (single, required) primary resource, such as "reads", "variants", "features", or "reference", plus zero or more related secondary resources ("index", "dictionary", "MD5", etc.).
Bundle(String, Collection) - Constructor for class htsjdk.beta.io.bundle.Bundle
  Create a new bundle from an existing resource collection.
BUNDLE_EXTENSION - Static variable in class htsjdk.beta.io.bundle.BundleJSON
BundleBuilder - Class in htsjdk.beta.io.bundle
  A builder class for `Bundle`s.
BundleBuilder() - Constructor for class htsjdk.beta.io.bundle.BundleBuilder
  Start a new bundle builder.
bundleContainsIndex(Bundle) - Static method in class htsjdk.beta.codecs.reads.ReadsCodecUtils
  InternalAPI Return true if the input `Bundle` contains a reads index resource
bundleContainsIndex(Bundle) - Static method in class htsjdk.beta.codecs.variants.vcf.VariantsCodecUtils
  InternalAPI Return true if the input `Bundle` contains a variants index resource
BundleJSON - Class in htsjdk.beta.io.bundle
  Methods for serializing and deserializing Bundles to and from JSON strings.
BundleJSON() - Constructor for class htsjdk.beta.io.bundle.BundleJSON
BundleResource - Interface in htsjdk.beta.io.bundle
  Interface defined for bundle resource objects that may be included in a `Bundle`.
BundleResourceBase - Class in htsjdk.beta.io.bundle
  Base class for `BundleResource` implementations.
BundleResourceBase(String, String, String) - Constructor for class htsjdk.beta.io.bundle.BundleResourceBase
  Base constructor for creating a new bundle resource.
BundleResourceType - Class in htsjdk.beta.io.bundle
  Constants for specifying standard content types and formats for resources contained in a `Bundle`.
BundleResourceType() - Constructor for class htsjdk.beta.io.bundle.BundleResourceType
bundleToSamInputResource(Bundle, ReadsDecoderOptions) - Static method in class htsjdk.beta.codecs.reads.ReadsCodecUtils
  InternalAPI Convert an input `Bundle` containing reads to a `SamInputResource`.
byCanonicalName(String) - Static method in enum class htsjdk.samtools.cram.structure.DataSeries
  Return the DataSeries associated with the two-character canonical name
By hand - Section in class htsjdk.variant.variantcontext.VariantContext
byId(int) - Static method in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
  Return the BlockCompressionMethod specified by the ID
byId(int) - Static method in enum class htsjdk.samtools.cram.structure.block.BlockContentType
  Return the BlockContentType specified by the ID
BYTE - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeriesType
  A single signed byte (256 distinct values)
BYTE_ARRAY - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeriesType
  An array of bytes.
BYTE_ARRAY_LEN - Enum constant in enum class htsjdk.samtools.cram.structure.EncodingID
  A byte array serialized as [length][elements]
BYTE_ARRAY_STOP - Enum constant in enum class htsjdk.samtools.cram.structure.EncodingID
  A byte array serialized as [elements][stop]
BYTE_SPACE_SIZE - Static variable in class htsjdk.samtools.cram.build.CompressionHeaderFactory
ByteArrayLenEncoding - Class in htsjdk.samtools.cram.encoding
  NOTE: this encoding can be a hybrid encoding in that it ALLOWS for the possibility to split it's data between the core block and an external block (i.e., if lenEncoding is CORE and byteEncoding is EXTERNAL) This has implications for data access, since some of it's data is interleaved with other data in the core block.
ByteArrayLenEncoding(CRAMEncoding, CRAMEncoding) - Constructor for class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
  Note: depending on the sub-encodings, this encoding can wind up being a core/external hybrid.
ByteArraySeekableStream - Class in htsjdk.samtools.seekablestream
  Created by vadim on 23/03/2015.
ByteArraySeekableStream(byte[]) - Constructor for class htsjdk.samtools.seekablestream.ByteArraySeekableStream
ByteArrayStopEncoding - Class in htsjdk.samtools.cram.encoding.external
ByteArrayStopEncoding(byte, int) - Constructor for class htsjdk.samtools.cram.encoding.external.ByteArrayStopEncoding
ByteModel - Class in htsjdk.samtools.cram.compression.range
  Adaptive frequency model for the CRAM 3.1 arithmetic range coder.
ByteModel(int) - Constructor for class htsjdk.samtools.cram.compression.range.ByteModel
  Create a new model for the given number of distinct symbols (0 to numSymbols-1), each starting with frequency 1.
bytes - Variable in class htsjdk.variant.bcf2.BCF2Codec.LazyData
bytesToHexString(byte[]) - Static method in class htsjdk.samtools.util.StringUtil
  Convert a byte array into a String hex representation.
bytesToString(byte[]) - Static method in class htsjdk.samtools.util.StringUtil
  /////////////////////////////////////////////////////////////////
bytesToString(byte[], int, int) - Static method in class htsjdk.samtools.util.StringUtil
byteToChar(byte) - Static method in class htsjdk.samtools.util.StringUtil
  Convert ASCII byte to ASCII char.
BZ - Enum constant in enum class htsjdk.samtools.SAMTag
BZ - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
BZIP2 - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
BZIP2ExternalCompressor - Class in htsjdk.samtools.cram.compression
BZIP2ExternalCompressor() - Constructor for class htsjdk.samtools.cram.compression.BZIP2ExternalCompressor

## C

c - Static variable in class htsjdk.samtools.util.SequenceUtil
  Byte typed variables for all normal bases.
C - Static variable in class htsjdk.samtools.util.SequenceUtil
  Byte typed variables for all normal bases.
CACHE_FILE_BASED_INDEXES - Enum constant in enum class htsjdk.samtools.SamReaderFactory.Option
  The factory's `SamReader`s' `SamReader.indexing()`'s calls to `SamReader.Indexing.getIndex()` will produce `BAMIndex`es that do some caching in memory instead of reading the index from the disk for each query operation.
calculateAltAlleleFrequency(VariantContext) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Computes the alternate allele frequency at the provided `VariantContext` by dividing its "AN" by its "AC".
calculateChromosomeCounts(VariantContextBuilder, boolean) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Update the attributes of the attributes map in the VariantContextBuilder to reflect the proper chromosome-based VCF tags based on the current VC produced by builder.make()
calculateChromosomeCounts(VariantContextBuilder, boolean, Set) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Update the attributes of the attributes map in the VariantContextBuilder to reflect the proper chromosome-based VCF tags based on the current VC produced by builder.make()
calculateChromosomeCounts(VariantContext, Map, boolean) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Update the attributes of the attributes map given the VariantContext to reflect the proper chromosome-based VCF tags
calculateChromosomeCounts(VariantContext, Map, boolean, Set) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Update the attributes of the attributes map given the VariantContext to reflect the proper chromosome-based VCF tags
calculateGc(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the fraction of bases that are G/C in the sequence
calculateMD5(byte[], int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
calculateMD5String(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
calculateMD5String(byte[], int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
calculateMdAndNm(List, byte[], byte[], int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
  Compute MD string and NM count from a read's CIGAR, bases, and a reference sequence slice.
calculateMdAndNmTags(SAMRecord, byte[], boolean, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculate MD and NM similarly to Samtools, except that N->N is a match.
calculateOATagValue(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  Function to create the OA tag value from a record.
calculatePLindex(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
calculateReadGroupRecordChecksum(File, File) - Static method in class htsjdk.samtools.SAMUtils
  Calculate a hash code from identifying information in the RG (read group) records in a SAM file's header.
calculateSamNmTag(SAMRecord, byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see `readBaseMatchesRefBaseWithAmbiguity` method).
calculateSamNmTag(SAMRecord, byte[], int) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see `readBaseMatchesRefBaseWithAmbiguity` method).
calculateSamNmTag(SAMRecord, byte[], int, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see `readBaseMatchesRefBaseWithAmbiguity` method).
calculateSamNmTagFromCigar(SAMRecord) - Static method in class htsjdk.samtools.util.SequenceUtil
  Attempts to calculate the predefined NM tag from the SAM spec using the cigar string alone.
calcVCFGenotypeKeys(VCFHeader) - Method in class htsjdk.variant.variantcontext.VariantContext
canAdd() - Method in class htsjdk.samtools.util.DiskBackedQueue
canBeHandledByLegacyUrlSupport(String) - Static method in class htsjdk.samtools.seekablestream.SeekableStreamFactory
canCreate() - Method in enum class htsjdk.tribble.index.IndexFactory.IndexType
canCreateIndexedFastaReader(File) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Deprecated.
  use `ReferenceSequenceFileFactory.canCreateIndexedFastaReader(Path)` instead.
canCreateIndexedFastaReader(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Deprecated.
  use `ReferenceSequenceFileFactory.canCreateIndexedFastaReader(Path)` instead.
canCreateIndexedFastaReader(Path) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Checks if the provided FASTA file can be open as indexed.
canDecode(String) - Method in class htsjdk.tribble.bed.BEDCodec
canDecode(String) - Method in class htsjdk.tribble.example.ExampleBinaryCodec
canDecode(String) - Method in interface htsjdk.tribble.FeatureCodec
  This function returns true iff the File potentialInput can be parsed by this codec.
canDecode(String) - Method in class htsjdk.tribble.gff.Gff3Codec
canDecode(String) - Method in class htsjdk.tribble.IntervalList.IntervalListCodec
canDecode(String) - Method in class htsjdk.variant.bcf2.BCF2Codec
canDecode(String) - Method in class htsjdk.variant.vcf.VCF3Codec
canDecode(String) - Method in class htsjdk.variant.vcf.VCFCodec
canDecodeFile(String, String) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec
canDecodeSignature(SignatureStream, String) - Method in class htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0
canDecodeSignature(SignatureStream, String) - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMCodecV1_0
canDecodeSignature(SignatureStream, String) - Method in class htsjdk.beta.codecs.reads.cram.CRAMCodec
canDecodeSignature(SignatureStream, String) - Method in class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMCodecV3_0
canDecodeSignature(SignatureStream, String) - Method in class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMCodecV3_1
canDecodeSignature(SignatureStream, String) - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec
canDecodeSignature(SignatureStream, String) - Method in class htsjdk.beta.codecs.reads.sam.SAMCodec
canDecodeSignature(SignatureStream, String) - Method in class htsjdk.beta.codecs.variants.vcf.VCFCodec
canDecodeSignature(SignatureStream, String) - Method in interface htsjdk.beta.plugin.HtsCodec
  Determine if the codec can decode an input stream by inspecting a signature embedded within the stream.
canDecodeURI(IOPath) - Method in class htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0
canDecodeURI(IOPath) - Method in class htsjdk.beta.codecs.reads.bam.BAMCodec
canDecodeURI(IOPath) - Method in class htsjdk.beta.codecs.reads.cram.CRAMCodec
canDecodeURI(IOPath) - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec
canDecodeURI(IOPath) - Method in class htsjdk.beta.codecs.reads.sam.SAMCodec
canDecodeURI(IOPath) - Method in class htsjdk.beta.codecs.variants.vcf.VCFCodec
canDecodeURI(IOPath) - Method in interface htsjdk.beta.plugin.HtsCodec
  Determine if the URI for `ioPath` (obtained via `IOPath.getURI()`) conforms to the expected URI format this codec's file format.
canEmit() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer
  Returns true if we can return the next record (it has been examined).
CANNOT_SEEK_CLOSED_STREAM_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
CANNOT_SEEK_STREAM_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
CanonicalHuffmanByteEncoding - Class in htsjdk.samtools.cram.encoding.core
  CRAMEncoding class for Huffman byte values.
CanonicalHuffmanByteEncoding(byte[], int[]) - Constructor for class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanByteEncoding
CanonicalHuffmanIntegerEncoding - Class in htsjdk.samtools.cram.encoding.core
  CRAMEncoding class for Huffman integer values.
CanonicalHuffmanIntegerEncoding(int[], int[]) - Constructor for class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanIntegerEncoding
CAPILLARY - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Capillary
CAT_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.range.RangeParams
CAT_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
CB - Enum constant in enum class htsjdk.samtools.SAMTag
CB - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
CC - Enum constant in enum class htsjdk.samtools.SAMTag
CC - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
CF_CompressionBitFlags - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
CF_DETACHED - Static variable in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
CF_HAS_MATE_DOWNSTREAM - Static variable in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
CF_QS_PRESERVED_AS_ARRAY - Static variable in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
CF_UNKNOWN_BASES - Static variable in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
CG - Enum constant in enum class htsjdk.samtools.SAMTag
CG - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
CG_TAG_FOUND_IN_ATTRIBUTES - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  The CG Tag should only be used in BAM format to hold a large cigar
Chained - Enum constant in enum class htsjdk.samtools.DownsamplingIteratorFactory.Strategy
CHAINED_DESCRIPTION - Static variable in class htsjdk.samtools.DownsamplingIteratorFactory
chainSAMProgramRecord(SAMFileHeader, SAMProgramRecord) - Static method in class htsjdk.samtools.SAMUtils
  Chains `program` in front of the first "head" item in the list of SAMProgramRecords in `header`.
CHAR - Enum constant in enum class htsjdk.variant.bcf2.BCF2Type
Character - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderLineType
characterToEnum(int) - Static method in enum class htsjdk.samtools.CigarOperator
charsToBytes(char[], int, int, byte[], int) - Static method in class htsjdk.samtools.util.StringUtil
  Convert chars to bytes merely by casting
charToByte(char) - Static method in class htsjdk.samtools.util.StringUtil
  Convert ASCII char to byte.
checkBasesPerLine(int) - Static method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
checkError() - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
checkError() - Method in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
checkError() - Method in interface htsjdk.variant.variantcontext.writer.VariantContextWriter
checkImmutability() - Method in class htsjdk.variant.variantcontext.GenotypesContext
checkLine(String, FastqReader.LineType) - Method in class htsjdk.samtools.fastq.FastqReader
  Checks that the line is neither null (representing EOF) or empty (blank line in file).
checkMaxEnd() - Method in class htsjdk.samtools.util.IntervalTree.Node
checkMaxEnds() - Method in class htsjdk.samtools.util.IntervalTree
  This method is only for debugging.
checkTermination(File) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
checkTermination(SeekableByteChannel) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
  check the status of the final bzgipped block for the given bgzipped resource
checkTermination(Path) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
chr - Variable in class htsjdk.tribble.bed.SimpleBEDFeature
chr(String) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells us that the resulting VariantContext should have the specified contig chr
chr2tid(String) - Method in class htsjdk.tribble.readers.TabixReader
  return chromosome ID or -1 if it is unknown
ChrIndex - Interface in htsjdk.tribble.index
  Represents an index on a specific chromosome
ChrIndex() - Constructor for class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
  Default constructor needed for factory methods -- DO NOT REMOVE
ChrIndex() - Constructor for class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
  Default constructor needed for factory methods -- DO NOT REMOVE
ChrIndex(String) - Constructor for class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
chrIndices - Variable in class htsjdk.tribble.index.AbstractIndex
  the map of our chromosome bins
CHROM - Enum constant in enum class htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
Chunk - Class in htsjdk.samtools
  A [start,stop) file pointer pairing into the BAM file, stored as a BAM file index.
Chunk(long, long) - Constructor for class htsjdk.samtools.Chunk
cigar - Variable in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures.DecodeResult
Cigar - Class in htsjdk.samtools
  A list of CigarElements, which describes how a read aligns with the reference.
Cigar() - Constructor for class htsjdk.samtools.Cigar
Cigar(List) - Constructor for class htsjdk.samtools.Cigar
CIGAR - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
CIGAR_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
CIGAR_MAPS_OFF_REFERENCE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Bases corresponding to M operator in CIGAR are beyond the end of the reference.
CIGAR_SIZE_MULTIPLIER - Static variable in class htsjdk.samtools.BAMRecord
  Constant for converting between the number of operators in a Cigar and the length of the int[] array needed to represent it in the BAM format
cigarArrayFromElements(List) - Static method in class htsjdk.samtools.util.CigarUtil
cigarArrayFromString(String) - Static method in class htsjdk.samtools.util.CigarUtil
CigarElement - Class in htsjdk.samtools
  One component of a cigar string.
CigarElement(int, CigarOperator) - Constructor for class htsjdk.samtools.CigarElement
cigarMapsNoBasesToRef(Cigar) - Static method in class htsjdk.samtools.SAMUtils
  Determines if a cigar has any element that both consumes read bases and consumes reference bases (e.g.
CigarOperator - Enum Class in htsjdk.samtools
  The operators that can appear in a cigar string, and information about their disk representations.
cigarStringFromArray(char[]) - Static method in class htsjdk.samtools.util.CigarUtil
CigarUtil - Class in htsjdk.samtools.util
CigarUtil() - Constructor for class htsjdk.samtools.util.CigarUtil
ClassFinder - Class in htsjdk.utils
  Utility class that can scan for classes in the classpath and find all the ones annotated with a particular annotation.
ClassFinder() - Constructor for class htsjdk.utils.ClassFinder
ClassFinder(File) - Constructor for class htsjdk.utils.ClassFinder
ClassFinder(ClassLoader) - Constructor for class htsjdk.utils.ClassFinder
cleanup() - Method in class htsjdk.samtools.util.SortingCollection
  Delete any temporary files.
cleanup() - Method in class htsjdk.samtools.util.SortingLongCollection
  Delete any temporary files.
clear() - Method in class htsjdk.samtools.util.DiskBackedQueue
clear() - Method in class htsjdk.samtools.util.IntervalTree
  Remove all entries.
clear() - Method in class htsjdk.samtools.util.IntervalTreeMap
clear() - Method in class htsjdk.tribble.util.MathUtils.RunningStat
clear() - Method in class htsjdk.variant.variantcontext.GenotypesContext
clearAttributes() - Method in class htsjdk.samtools.BAMRecord
  Removes all attributes.
clearAttributes() - Method in class htsjdk.samtools.SAMRecord
  Removes all attributes.
clearAttributes() - Method in class htsjdk.variant.variantcontext.CommonInfo
clearIndexCreator() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Do not pass an `IndexCreator` to the next `VariantContextWriter` created by this builder.
clearOptions() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Remove all options from the set of `Options` for the `VariantContextWriterBuilder`.
clip3PrimeEndOfRead(SAMRecord, int, CigarOperator) - Static method in class htsjdk.samtools.util.CigarUtil
  Adds a soft- or hard-clip, based on `clipFrom` and `clippingOperator`, to the SAM record's existing cigar and, for negative strands, also adjusts the SAM record's start position.
clipEndOfRead(int, List, CigarOperator) - Static method in class htsjdk.samtools.util.CigarUtil
  Adjust the cigar based on adapter clipping.
clipOverlappingAlignedBases(SAMRecord, boolean) - Static method in class htsjdk.samtools.SAMUtils
  Returns a (possibly new) record that has been clipped if input is a mapped paired and has overlapping bases with its mate.
clipOverlappingAlignedBases(SAMRecord, int, boolean) - Static method in class htsjdk.samtools.SAMUtils
  Returns a (possibly new) SAMRecord with the given number of bases soft-clipped at the end of the read if is a mapped paired and has overlapping bases with its mate.
clone() - Method in class htsjdk.samtools.BAMFileSpan
  Deep clone the given chunk list.
clone() - Method in class htsjdk.samtools.BAMRecordCodec
clone() - Method in class htsjdk.samtools.Chunk
clone() - Method in class htsjdk.samtools.SAMFileHeader
clone() - Method in class htsjdk.samtools.SAMFileWriterFactory
clone() - Method in class htsjdk.samtools.SAMRecord
  Note that this does a shallow copy of everything, except for the attribute list, for which a copy of the list is made, but the attributes themselves are copied by reference.
clone() - Method in class htsjdk.samtools.SAMSequenceRecord
clone() - Method in class htsjdk.samtools.util.Interval
clone() - Method in class htsjdk.samtools.util.IntervalCodec
clone() - Method in class htsjdk.samtools.util.RelativeIso8601Date
clone() - Method in interface htsjdk.samtools.util.SortingCollection.Codec
  Must return a cloned copy of the codec that can be used independently of the original instance.
clone() - Method in class htsjdk.tribble.index.tabix.TabixFormat
clone() - Method in class htsjdk.variant.vcf.VCFRecordCodec
cloneValue() - Method in class htsjdk.samtools.SAMBinaryTagAndValue
close() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
close() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
close() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMEncoderV1_0
close() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
close() - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoder
close() - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
close() - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0
close() - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMEncoderV1_0
close() - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
close() - Method in class htsjdk.beta.codecs.variants.vcf.VCFEncoder
close() - Method in interface htsjdk.beta.plugin.HtsDecoder
  Close any resources associated with this decoder.
close() - Method in interface htsjdk.beta.plugin.HtsEncoder
  Close any resources associated with this decoder.
close() - Method in class htsjdk.io.AsyncWriterPool
  Asynchronously closes each writer in the pool.
close() - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Close this index and release any associated resources.
close() - Method in class htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator
close() - Method in class htsjdk.samtools.BAMFileReader
close() - Method in interface htsjdk.samtools.BAMIndex
  Close the index and release any associated resources.
close() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
close() - Method in class htsjdk.samtools.cram.io.CountingInputStream
close() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
close() - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
close() - Method in class htsjdk.samtools.CRAMFileReader
close() - Method in class htsjdk.samtools.CRAMIterator
close() - Method in class htsjdk.samtools.DownsamplingIterator
  Does nothing.
close() - Method in class htsjdk.samtools.DuplicateSetIterator
close() - Method in class htsjdk.samtools.fastq.BasicFastqWriter
close() - Method in class htsjdk.samtools.fastq.FastqReader
close() - Method in interface htsjdk.samtools.fastq.FastqWriter
close() - Method in class htsjdk.samtools.filter.FilteringSamIterator
close() - Method in class htsjdk.samtools.HtsgetBAMFileReader
close() - Method in class htsjdk.samtools.MergingSamRecordIterator
  Close down all open iterators.
close() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
close() - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Closes this writer flushing all remaining writing operation input the output resources.
close() - Method in class htsjdk.samtools.reference.FastaSequenceFile
  It's good to call this to free up memory.
close() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
close() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
close() - Method in class htsjdk.samtools.reference.ReferenceSequenceFileWalker
close() - Method in interface htsjdk.samtools.SAMFileWriter
  Must be called to flush or file will likely be defective.
close() - Method in class htsjdk.samtools.SAMFileWriterImpl
  Must be called or else file will likely be defective.
close() - Method in class htsjdk.samtools.SamReader.AssertingIterator
close() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
close() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
close() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
close() - Method in class htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel
close() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
close() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
close() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
close() - Method in class htsjdk.samtools.seekablestream.SeekableStream
close() - Method in class htsjdk.samtools.util.AbstractAsyncWriter
  Attempts to finish draining the queue and then calls synchronouslyClose() to allow implementation to do any one time clean up.
close() - Method in class htsjdk.samtools.util.AbstractLocusIterator
  Closes inner `SamIterator`.
close() - Method in class htsjdk.samtools.util.AsciiWriter
  flushes and closes underlying OutputStream.
close() - Method in class htsjdk.samtools.util.AsyncBlockCompressedInputStream
close() - Method in class htsjdk.samtools.util.AsyncBufferedIterator
close() - Method in class htsjdk.samtools.util.BinaryCodec
  Close the appropriate stream
close() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
  Closes the underlying InputStream or RandomAccessFile
close() - Method in class htsjdk.samtools.util.BlockCompressedOutputStream
  close() must be called in order to flush any remaining buffered bytes.
close() - Method in class htsjdk.samtools.util.BufferedLineReader
close() - Method in interface htsjdk.samtools.util.CloseableIterator
  Should be implemented to close/release any underlying resources.
close() - Method in class htsjdk.samtools.util.CoordSpanInputSteam
close() - Method in class htsjdk.samtools.util.DelegatingIterator
close() - Method in class htsjdk.samtools.util.FastLineReader
close() - Method in class htsjdk.samtools.util.ftp.FTPStream
close() - Method in class htsjdk.samtools.util.GZIIndex.GZIIndexer
close() - Method in class htsjdk.samtools.util.IntervalListWriter
  Closes the writer.
close() - Method in class htsjdk.samtools.util.IterableOnceIterator
  Does nothing, intended to be overridden when needed.
close() - Method in interface htsjdk.samtools.util.LineReader
close() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
close() - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
close() - Method in class htsjdk.samtools.util.MergingIterator
  Closes every CloseableIterator in this MergingIterator.
close() - Method in class htsjdk.samtools.util.PeekableIterator
  Closes the underlying iterator.
close() - Method in class htsjdk.samtools.util.PositionalOutputStream
close() - Method in class htsjdk.samtools.util.SAMRecordPrefetchingIterator
close() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer
  Close IO resources associated with each underlying BufferBlock
close() - Method in class htsjdk.samtools.util.TerminatorlessBlockCompressedOutputStream
close() - Method in interface htsjdk.tribble.FeatureReader
  Closes the reader
close() - Method in class htsjdk.tribble.gff.Gff3Writer
close() - Method in class htsjdk.tribble.readers.AsciiLineReader
close() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
close() - Method in class htsjdk.tribble.readers.LineIteratorImpl
close() - Method in interface htsjdk.tribble.readers.LineReader
close() - Method in class htsjdk.tribble.readers.LongLineBufferedReader
close() - Method in class htsjdk.tribble.readers.PositionalBufferedStream
close() - Method in class htsjdk.tribble.readers.SynchronousLineReader
close() - Method in class htsjdk.tribble.readers.TabixIteratorLineReader
close() - Method in class htsjdk.tribble.readers.TabixReader
close() - Method in class htsjdk.tribble.TabixFeatureReader
close() - Method in class htsjdk.tribble.TribbleIndexedFeatureReader
close() - Method in class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator
close() - Method in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
  attempt to close the VCF file; we need to flush the queue first
close() - Method in interface htsjdk.variant.variantcontext.writer.VariantContextWriter
  attempt to close the VCF file
close() - Method in class htsjdk.variant.vcf.VCFFileReader
close(boolean) - Method in class htsjdk.samtools.util.BlockCompressedOutputStream
close(LineIterator) - Method in class htsjdk.tribble.AsciiFeatureCodec
close(LineIterator) - Method in class htsjdk.tribble.gff.Gff3Codec
close(PositionalBufferedStream) - Method in class htsjdk.tribble.BinaryFeatureCodec
close(Object) - Static method in class htsjdk.samtools.util.CloserUtil
  Calls close() on `obj` if it implements Closeable
close(List) - Static method in class htsjdk.samtools.util.CloserUtil
  Calls close() on all elements of `objs` that implement Closeable
close(SOURCE) - Method in interface htsjdk.tribble.FeatureCodec
  Adapter method that closes the provided `SOURCE`.
CloseableIterator<T> - Interface in htsjdk.samtools.util
  This interface is used by iterators that use releasable resources during iteration.
CloseableTribbleIterator<T> - Interface in htsjdk.tribble
  The basic iterator we use in Tribble, which allows closing and basic iteration.
closeAllInstances() - Static method in class htsjdk.samtools.seekablestream.SeekableFileStream
closeAllInstances() - Static method in class htsjdk.samtools.seekablestream.SeekablePathStream
closeDataStream() - Method in class htsjdk.samtools.util.ftp.FTPClient
CloserUtil - Class in htsjdk.samtools.util
  Utility to close things that implement Closeable WARNING: This should only be used for Closeable things open for read, because it ignores exceptions, and the caller will probably want to know about exceptions when closing a file being written to, because this may indicate a failure to flush.
CloserUtil() - Constructor for class htsjdk.samtools.util.CloserUtil
CM - Enum constant in enum class htsjdk.samtools.SAMTag
CM - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
CNV - Enum constant in enum class htsjdk.variant.variantcontext.StructuralVariantType
  Copy number variable region
CO - Enum constant in enum class htsjdk.samtools.SAMTag
CO - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
code - Variable in class htsjdk.samtools.cram.structure.TagKeyCache.TagKeyInfo
  Binary tag code as computed by `SAMTag.makeBinaryTag(String)`.
code(byte, byte) - Method in class htsjdk.samtools.cram.structure.SubstitutionMatrix
  Given a reference base and a read base, find the corresponding substitution code
codec - Variable in class htsjdk.tribble.AbstractFeatureReader
Codec Components - Section in interface htsjdk.beta.plugin.HtsCodec
Codec Implementation Guidelines - Section in interface htsjdk.beta.plugin.HtsCodec
CodecLineParsingException - Exception Class in htsjdk.tribble.exception
  Class CodecLineParsingException a generic exception we use if the codec has trouble parsing the line its given
CodecLineParsingException() - Constructor for exception class htsjdk.tribble.exception.CodecLineParsingException
CodecLineParsingException(String) - Constructor for exception class htsjdk.tribble.exception.CodecLineParsingException
CodecLineParsingException(String, Throwable) - Constructor for exception class htsjdk.tribble.exception.CodecLineParsingException
CodecLineParsingException(Throwable) - Constructor for exception class htsjdk.tribble.exception.CodecLineParsingException
Codec Resolution - Section in interface htsjdk.beta.plugin.HtsCodec
CodeUtil - Class in htsjdk.samtools.util
  Miscellaneous util methods that don't fit anywhere else.
CodeUtil() - Constructor for class htsjdk.samtools.util.CodeUtil
collapseStringList(List) - Static method in class htsjdk.variant.bcf2.BCF2Utils
  Collapse multiple strings into a comma separated list ["s1", "s2", "s3"] => ",s1,s2,s3"
CollectionUtil - Class in htsjdk.samtools.util
  Small utility methods for dealing with collection classes.
CollectionUtil() - Constructor for class htsjdk.samtools.util.CollectionUtil
CollectionUtil.DefaultingMap<K,V> - Class in htsjdk.samtools.util
  A defaulting map, which returns a default value when a value that does not exist in the map is looked up.
CollectionUtil.DefaultingMap.Factory<V,K> - Interface in htsjdk.samtools.util
CollectionUtil.MultiMap<K,V> - Class in htsjdk.samtools.util
  Simple multi-map for convenience of storing collections in map values.
CollectionUtil.Partitioner<V,K> - Class in htsjdk.samtools.util
  Deprecated.
  use Collectors.groupingBy instead
colorCache - Static variable in class htsjdk.tribble.util.ParsingUtils
combine(AlignmentSpan, AlignmentSpan) - Static method in class htsjdk.samtools.cram.structure.AlignmentSpan
  Combine two AlignmentSpans
combine(IntervalList) - Method in class htsjdk.samtools.util.IntervalUtil.IntervalCombiner
combineMapqs(int, int) - Static method in class htsjdk.samtools.SAMUtils
  Hokey algorithm for combining two MAPQs into values that are comparable, being cognizant of the fact that in MAPQ world, 1 > 255 > 0.
COMMAND_LINE_TAG - Static variable in class htsjdk.samtools.SAMProgramRecord
COMMENT_PREFIX - Static variable in class htsjdk.samtools.SAMTextHeaderCodec
COMMENT_START - Static variable in class htsjdk.tribble.gff.Gff3Constants
commonInfo - Variable in class htsjdk.variant.variantcontext.VariantContext
CommonInfo - Class in htsjdk.variant.variantcontext
  Common utility routines for VariantContext and Genotype
CommonInfo(String, double, Set, Map) - Constructor for class htsjdk.variant.variantcontext.CommonInfo
ComparableTuple<A,B> - Class in htsjdk.samtools.util
  A simple extension of the Tuple class that, for comparable Types, allows comparing Tuples of non-null elements.
ComparableTuple(A, B) - Constructor for class htsjdk.samtools.util.ComparableTuple
comparator() - Method in class htsjdk.samtools.util.Histogram
  Returns the comparator used to order the keys in this histogram, or `null` if this histogram uses the natural ordering of its keys.
compare(long, long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
compare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordCoordinateComparator
compare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordDuplicateComparator
  Most stringent comparison.
compare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordQueryHashComparator
  Compares two records based on an integer hash of their read name's.
compare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordQueryNameComparator
compare(SAMRecord, SAMRecord, DuplicateScoringStrategy.ScoringStrategy) - Static method in class htsjdk.samtools.DuplicateScoringStrategy
  Compare two records based on their duplicate scores.
compare(SAMRecord, SAMRecord, DuplicateScoringStrategy.ScoringStrategy, boolean) - Static method in class htsjdk.samtools.DuplicateScoringStrategy
  Compare two records based on their duplicate scores.
compare(Interval, Interval) - Method in class htsjdk.samtools.util.IntervalCoordinateComparator
compare(VariantContext, VariantContext) - Method in class htsjdk.variant.variantcontext.VariantContextComparator
compare(T, T) - Method in class htsjdk.samtools.SAMHeaderRecordComparator
compare(T, T) - Method in class htsjdk.samtools.util.LocusComparator
compareDoubles(double, double) - Static method in class htsjdk.variant.utils.GeneralUtils
  Compares double values for equality (within 1e-6), or inequality.
compareDoubles(double, double, double) - Static method in class htsjdk.variant.utils.GeneralUtils
  Compares double values for equality (within epsilon), or inequality.
compareIntervalToRecord(QueryInterval, SAMRecord) - Static method in class htsjdk.samtools.BAMQueryMultipleIntervalsIteratorFilter
compareMapqs(int, int) - Static method in class htsjdk.samtools.SAMUtils
compareReadNames(String, String) - Static method in class htsjdk.samtools.SAMRecordQueryNameComparator
  Encapsulate algorithm for comparing read names in queryname-sorted file, since there have been conversations about changing the behavior.
compareTo(HtsVersion) - Method in class htsjdk.beta.plugin.HtsVersion
compareTo(Bin) - Method in class htsjdk.samtools.Bin
  Compare two bins to see what ordering they should appear in.
compareTo(Chunk) - Method in class htsjdk.samtools.Chunk
compareTo(BAIEntry) - Method in class htsjdk.samtools.cram.BAIEntry
  Sort by numerical order of reference sequence ID, except that unmapped-unplaced reads come last For valid reference sequence ID (placed reads): - sort by alignment start - if alignment start is equal, sort by container offset - if alignment start and container offset are equal, sort by slice offset For unmapped-unplaced reads: - ignore (invalid) alignment start value - sort by container offset - if container offset is equal, sort by slice offset
compareTo(CRAMVersion) - Method in class htsjdk.samtools.cram.common.CRAMVersion
  Compare with another version.
compareTo(CRAIEntry) - Method in class htsjdk.samtools.cram.CRAIEntry
  Sort by numerical order of reference sequence ID, except that unmapped-unplaced reads come last For valid reference sequence ID (placed reads): - sort by alignment start - if alignment start is equal, sort by container offset - if alignment start and container offset are equal, sort by slice offset For unmapped-unplaced reads: - ignore (invalid) alignment start value - sort by container offset - if container offset is equal, sort by slice offset
compareTo(ReferenceContext) - Method in class htsjdk.samtools.cram.ref.ReferenceContext
compareTo(ReadTag) - Method in class htsjdk.samtools.cram.structure.ReadTag
compareTo(QueryInterval) - Method in class htsjdk.samtools.QueryInterval
compareTo(ComparableTuple) - Method in class htsjdk.samtools.util.ComparableTuple
compareTo(Interval) - Method in class htsjdk.samtools.util.Interval
  Sort based on sequence.compareTo, then start pos, then end pos with null objects coming lexically last
compareTo(TabixReader.TPair64) - Method in class htsjdk.tribble.readers.TabixReader.TPair64
compareTo(TabixUtils.TPair64) - Method in class htsjdk.tribble.util.TabixUtils.TPair64
compareTo(Allele) - Method in class htsjdk.variant.variantcontext.SimpleAllele
compareTo(Genotype) - Method in class htsjdk.variant.variantcontext.Genotype
  comparable genotypes -> compareTo on the sample names
compareTo(Object) - Method in class htsjdk.tribble.index.interval.Interval
compareTo(Object) - Method in class htsjdk.variant.vcf.VCFContigHeaderLine
  IT IS CRITICAL THAT THIS BE OVERRIDDEN SO WE SORT THE CONTIGS IN THE CORRECT ORDER
compareTo(Object) - Method in class htsjdk.variant.vcf.VCFHeaderLine
compareTo(Date) - Method in class htsjdk.samtools.util.RelativeIso8601Date
compareToFilter(SAMRecord) - Method in class htsjdk.samtools.BAMQueryMultipleIntervalsIteratorFilter
compareToFilter(SAMRecord) - Method in class htsjdk.samtools.BAMStartingAtIteratorFilter
compatibleWith(CRAMVersion) - Method in class htsjdk.samtools.cram.common.CRAMVersion
complement(byte) - Static method in class htsjdk.samtools.util.SequenceUtil
  Returns the complement of a single byte.
ComponentMethods() - Constructor for class htsjdk.tribble.AbstractFeatureReader.ComponentMethods
CompoundFilter - Class in htsjdk.variant.variantcontext.filter
  A Predicate on VariantContexts that returns true when either all its sub-predicates are true, or none are false.
CompoundFilter(boolean) - Constructor for class htsjdk.variant.variantcontext.filter.CompoundFilter
  A constructor that will determine if this compound filter will require that *all* the included filters pass or *some* of them pass (depending on the requireAll parameter in the constructor).
compress(byte[], RANS4x8Params) - Method in class htsjdk.samtools.cram.compression.rans.RANS4x8Encode
  Compress a byte array using the rANS 4x8 codec.
compress(byte[], RANSNx16Params) - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Encode
  Compress a byte array using the rANS Nx16 codec.
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.BZIP2ExternalCompressor
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.ExternalCompressor
  Compress the data using the codec-specific context model.
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZCompExternalCompressor
  Compress quality score data using FQZComp.
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.GZIPExternalCompressor
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.LZMAExternalCompressor
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.nametokenisation.NameTokeniserExternalCompressor
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.range.RangeExternalCompressor
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.RANS4x8ExternalCompressor
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.RANSNx16ExternalCompressor
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.RAWExternalCompressor
compress(byte[], CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.compression.TrialCompressor
  Compress data.
compress(byte[], T) - Method in class htsjdk.samtools.cram.compression.rans.RANSEncode
  Compress a byte array using this rANS encoder.
compress(ByteBuffer) - Method in class htsjdk.samtools.util.GzipCodec
  Compress data and return a new ByteBuffer containing the compressed result.
compress(ByteBuffer, boolean, byte) - Method in class htsjdk.samtools.cram.compression.nametokenisation.NameTokenisationEncode
  Compress the input buffer of read names.
compress(ByteBuffer, int[]) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZCompEncode
  Compress concatenated quality scores using the FQZComp codec.
compress(ByteBuffer, int[], int[]) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZCompEncode
  Compress concatenated quality scores using the FQZComp codec with per-record BAM flags.
compress(ByteBuffer, RangeParams) - Method in class htsjdk.samtools.cram.compression.range.RangeEncode
  Compress data using the CRAM 3.1 arithmetic (range) codec with the given parameters.
compress(ByteBuffer, GzipCodec.Format) - Method in class htsjdk.samtools.util.GzipCodec
  Compress data and return a new ByteBuffer containing the compressed result.
compress(ByteBuffer, ByteBuffer) - Method in class htsjdk.samtools.util.GzipCodec
  Compress data from `input` into `output` using standard GZIP format.
compress(ByteBuffer, ByteBuffer, GzipCodec.Format) - Method in class htsjdk.samtools.util.GzipCodec
  Compress data from `input` into `output` using the specified format.
COMPRESSED_INTERVAL_LIST - Static variable in class htsjdk.samtools.util.FileExtensions
COMPRESSED_VCF - Static variable in class htsjdk.samtools.util.FileExtensions
COMPRESSED_VCF_BGZ - Static variable in class htsjdk.samtools.util.FileExtensions
COMPRESSED_VCF_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  since June 2019 Use `FileExtensions.COMPRESSED_VCF` instead.
COMPRESSED_VCF_INDEX - Static variable in class htsjdk.samtools.util.FileExtensions
COMPRESSED_VCF_INDEX_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  since June 2019 Use `FileExtensions.COMPRESSED_VCF_INDEX` instead.
compressedBasesToBytes(int, byte[], int) - Static method in class htsjdk.samtools.SAMUtils
  Convert from BAM's packed nibble representation to an ASCII byte array.
COMPRESSION_HEADER - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockContentType
COMPRESSION_LEVEL - Static variable in class htsjdk.samtools.Defaults
  Compression level to be used for writing BAM and other block-compressed outputs.
CompressionHeader - Class in htsjdk.samtools.cram.structure
CompressionHeader() - Constructor for class htsjdk.samtools.cram.structure.CompressionHeader
  Create a CompressionHeader using the default `CRAMEncodingStrategy`
CompressionHeader(CRAMVersion, InputStream) - Constructor for class htsjdk.samtools.cram.structure.CompressionHeader
  Read a COMPRESSION_HEADER Block from an InputStream and populate this CompressionHeader from its contents.
CompressionHeader(CompressionHeaderEncodingMap) - Constructor for class htsjdk.samtools.cram.structure.CompressionHeader
  Create a compression header using the given `CompressionHeaderEncodingMap`.
CompressionHeader(CompressionHeaderEncodingMap, boolean, boolean, boolean) - Constructor for class htsjdk.samtools.cram.structure.CompressionHeader
CompressionHeaderEncodingMap - Class in htsjdk.samtools.cram.structure
  Maintains a map of DataSeries to EncodingDescriptor, and a second map that contains the compressor to use for each EncodingDescriptor that represents an EXTERNAL encoding.
CompressionHeaderEncodingMap(CRAMEncodingStrategy) - Constructor for class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  Constructor used to create the encoding map for writing CRAMs.
CompressionHeaderEncodingMap(InputStream) - Constructor for class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  Constructor used to discover an encoding map from a serialized CRAM stream.
CompressionHeaderFactory - Class in htsjdk.samtools.cram.build
  Factory for creating CRAM compression headers for containers when writing to a CRAM stream.
CompressionHeaderFactory(CRAMEncodingStrategy) - Constructor for class htsjdk.samtools.cram.build.CompressionHeaderFactory
  Create a CompressionHeaderFactory using the provided CRAMEncodingStrategy.
CompressionUtils - Class in htsjdk.samtools.cram.compression
  Utility methods shared across CRAM 3.1 compression codecs (rANS, Range, Name Tokeniser, etc.), including uint7 encoding, bit-packing, and STRIPE data transformation.
CompressionUtils() - Constructor for class htsjdk.samtools.cram.compression.CompressionUtils
CompressorCache - Class in htsjdk.samtools.cram.structure
  Maintain a cache of reusable compressor instances in order to reduce the need to repeatedly instantiate them, since some, like the RANS de/compressor, allocate large numbers (~256k) of small temporary objects every time they're instantiated.
CompressorCache() - Constructor for class htsjdk.samtools.cram.structure.CompressorCache
CompressorDescriptor - Record Class in htsjdk.samtools.cram.structure
  Describes which compression method and parameters to use for a CRAM data series block.
CompressorDescriptor(BlockCompressionMethod) - Constructor for record class htsjdk.samtools.cram.structure.CompressorDescriptor
  Create a descriptor for a compression method that takes no argument (e.g., RAW, BZIP2, LZMA, NAME_TOKENISER, FQZCOMP).
CompressorDescriptor(BlockCompressionMethod, int) - Constructor for record class htsjdk.samtools.cram.structure.CompressorDescriptor
  Creates an instance of a `CompressorDescriptor` record class.
computeDuplicateScore(SAMRecord, DuplicateScoringStrategy.ScoringStrategy) - Static method in class htsjdk.samtools.DuplicateScoringStrategy
  Returns the duplicate score computed from the given fragment.
computeDuplicateScore(SAMRecord, DuplicateScoringStrategy.ScoringStrategy, boolean) - Static method in class htsjdk.samtools.DuplicateScoringStrategy
  Returns the duplicate score computed from the given fragment.
computeEndFromAlleles(List, int) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
computeEndFromAlleles(List, int, int) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Compute the end position for this VariantContext from the alleles themselves assigns this builder the stop position computed.
computeEndFromAlleles(List, int, int) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Compute the end position for this VariantContext from the alleles themselves In the trivial case this is a single BP event and end = start (open intervals) In general the end is start + ref length - 1, handling the case where ref length == 0 However, if alleles contains a symbolic allele then we use endForSymbolicAllele in all cases
computeIndexingBinIfAbsent(SAMRecord) - Method in class htsjdk.samtools.SAMRecord
  Deprecated.
  Use computeIndexingBin() if accessible or GenomicIndexUtil.regionToBin() otherwise.
computeInsertSize(SAMRecord, SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil
  Compute SAMRecord insert size
concatenate(IntervalList, IntervalList) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for merging a two IntervalLists, checks for equal dictionaries.
concatenate(Collection) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for concatenating a list of IntervalLists, checks for equal dictionaries.
connect(String) - Method in class htsjdk.samtools.util.ftp.FTPClient
  Connects to the given FTP host on the default port.
connect(String, String, UserPasswordInput) - Static method in class htsjdk.samtools.util.ftp.FTPUtils
  Connect to an FTP server
cons(T, List) - Static method in class htsjdk.variant.utils.GeneralUtils
CONSTANT_MEMORY_DESCRPTION - Static variable in class htsjdk.samtools.DownsamplingIteratorFactory
ConstantMemory - Enum constant in enum class htsjdk.samtools.DownsamplingIteratorFactory.Strategy
Constants - Class in htsjdk.samtools.cram.compression.range
Constants - Class in htsjdk.samtools.cram.compression.rans
Constants() - Constructor for class htsjdk.samtools.cram.compression.range.Constants
Constants() - Constructor for class htsjdk.samtools.cram.compression.rans.Constants
consumesReadBases() - Method in enum class htsjdk.samtools.CigarOperator
  If true, represents that this cigar operator "consumes" bases from the read bases.
consumesReferenceBases() - Method in enum class htsjdk.samtools.CigarOperator
  If true, represents that this cigar operator "consumes" bases from the reference sequence.
CONTAINED - Enum constant in enum class htsjdk.beta.plugin.interval.HtsQueryRule
  Only get records that are entirely contained with the query interval.
Container - Class in htsjdk.samtools.cram.structure
  Notes: Container will construct a container out of as many CRAMCompressionRecords as it is handed, respecting only the maximum number of slices.
Container(CRAMVersion, InputStream, long) - Constructor for class htsjdk.samtools.cram.structure.Container
  Read a Container from a CRAM stream.
Container(CompressionHeader, List, long, long) - Constructor for class htsjdk.samtools.cram.structure.Container
  Create a Container with a `ReferenceContext` derived from its `Slice`s.
Container(ContainerHeader, long) - Constructor for class htsjdk.samtools.cram.structure.Container
  Create a container for use by CramContainerHeaderIterator, which is only used to find the offsets within a CRAM stream where containers start.
ContainerFactory - Class in htsjdk.samtools.cram.build
  Aggregates SAMRecord objects into one or more `Container`s, composed of one or more `Slice`s.
ContainerFactory(SAMFileHeader, CRAMEncodingStrategy, CRAMReferenceSource) - Constructor for class htsjdk.samtools.cram.build.ContainerFactory
containerFromStream(CountingInputStream) - Method in class htsjdk.samtools.cram.build.CramContainerHeaderIterator
  Consume the entirety of the next container from the stream, but retain only the header.
containerFromStream(CountingInputStream) - Method in class htsjdk.samtools.cram.build.CramContainerIterator
  Consume the entirety of the next container from the stream.
ContainerHeader - Class in htsjdk.samtools.cram.structure
ContainerHeader(CRAMVersion, InputStream) - Constructor for class htsjdk.samtools.cram.structure.ContainerHeader
  Create a container header from an `InputStream`.
ContainerHeader(AlignmentContext, int, int, int, long, long, List, int) - Constructor for class htsjdk.samtools.cram.structure.ContainerHeader
  Create a ContainerHeader.
ContainerHeader(AlignmentContext, int, int, long, int) - Constructor for class htsjdk.samtools.cram.structure.ContainerHeader
  Create a Container from a partial set of values.
contains(IntervalList, String, long) - Static method in class htsjdk.samtools.util.IntervalUtil
  Return true if the sequence/position lie in the provided interval list.
contains(Interval, String, long) - Static method in class htsjdk.samtools.util.IntervalUtil
  Return true if the sequence/position lie in the provided interval.
contains(Locatable) - Method in interface htsjdk.samtools.util.Locatable
  Determines whether this interval contains the entire region represented by other (in other words, whether it covers it).
contains(SamRecordWithOrdinal) - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer
  Returns true if this buffer contains the record at the given index, false otherwise
contains(Object) - Method in class htsjdk.samtools.util.DiskBackedQueue
  Not supported.
contains(Object) - Method in class htsjdk.variant.variantcontext.GenotypesContext
containsAll(Collection) - Method in class htsjdk.samtools.util.DiskBackedQueue
  Not supported.
containsAll(Collection) - Method in class htsjdk.variant.variantcontext.GenotypesContext
containsBin(Bin) - Method in class htsjdk.samtools.BinningIndexContent
  Does this content have anything in this bin?
containsChromosome(String) - Method in class htsjdk.tribble.index.AbstractIndex
containsChromosome(String) - Method in interface htsjdk.tribble.index.Index
containsChromosome(String) - Method in class htsjdk.tribble.index.tabix.TabixIndex
containsChunks() - Method in class htsjdk.samtools.Bin
  Returns whether the bin currently contains chunks.
containsContained(Locatable) - Method in class htsjdk.samtools.util.IntervalTreeMap
  Test if this contains an object that is contained by 'key'
containsKey(Interval) - Method in class htsjdk.samtools.util.IntervalTreeMap
containsKey(Object) - Method in class htsjdk.samtools.util.IntervalTreeMap
containsKey(K) - Method in class htsjdk.samtools.util.Histogram
  Return whether this histogram contains the given key.
containsKey(Key) - Method in class htsjdk.samtools.util.ResourceLimitedMap
  Determine if the map contains the given key.
containsOperator(CigarOperator) - Method in class htsjdk.samtools.Cigar
  returns true if the cigar string contains the given operator
containsOverlapping(Locatable) - Method in class htsjdk.samtools.util.IntervalTreeMap
  Test overlapping interval
containsSample(String) - Method in class htsjdk.variant.variantcontext.GenotypesContext
containsSamples(Collection) - Method in class htsjdk.variant.variantcontext.GenotypesContext
ContentDigests - Class in htsjdk.samtools.cram.digest
ContentDigests.KNOWN_DIGESTS - Enum Class in htsjdk.samtools.cram.digest
Content Types - Section in interface htsjdk.beta.plugin.HtsCodec
contig - Variable in class htsjdk.tribble.MutableFeature
contig - Variable in class htsjdk.variant.variantcontext.VariantContext
  The location of this VariantContext
CONTIG_HEADER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
CONTIG_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
CONTIG_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
contigsMatch(Locatable) - Method in interface htsjdk.samtools.util.Locatable
  Determine if this is on the same contig as other this must be equivalent to this.getContig().equals(other.getContig()) but may be implemented more efficiently
convertHtsgetUriToHttp(URI) - Static method in class htsjdk.samtools.HtsgetBAMFileReader
convertHtsgetUriToHttps(URI) - Static method in class htsjdk.samtools.HtsgetBAMFileReader
Converting rods and other data structures to VariantContexts - Section in class htsjdk.variant.variantcontext.VariantContext
convertReadNamesToUpperCase(File, File) - Method in class htsjdk.samtools.example.ExampleSamUsage
  Read a SAM or BAM file, convert each read name to upper case, and write a new SAM or BAM file.
convertSolexa_1_3_QualityCharsToPhredBinary(byte[]) - Method in class htsjdk.samtools.util.SolexaQualityConverter
  Casava 1.3 stores phred-scaled qualities, but non-standard because they have 64 added to them rather than the standard 33.
convertSolexa_1_3_QualityCharsToPhredBinary(int, int, byte[]) - Method in class htsjdk.samtools.util.SolexaQualityConverter
convertSolexaQualityCharsToPhredBinary(byte[]) - Method in class htsjdk.samtools.util.SolexaQualityConverter
  Decodes an array of solexa quality ASCII chars into Phred numeric space.
convertSolexaQualityCharsToPhredChars(byte[]) - Method in class htsjdk.samtools.util.SolexaQualityConverter
  Decodes an array of solexa quality ASCII chars into Phred ASCII space.
convertToBinaryTest(FeatureReader, OutputStream) - Static method in class htsjdk.tribble.example.ExampleBinaryCodec
  Convenience method that creates an ExampleBinaryCodec file from another feature file.
convertToBinaryTest(File, File, FeatureCodec) - Static method in class htsjdk.tribble.example.ExampleBinaryCodec
  Convenience method that creates an ExampleBinaryCodec file from another feature file.
convertToLinearIndexOffset(int) - Static method in class htsjdk.samtools.LinearIndex
coordinate - Enum constant in enum class htsjdk.samtools.SAMFileHeader.SortOrder
CoordinateSortedPairInfoMap<KEY,REC> - Class in htsjdk.samtools
  Holds info about a mate pair for use when processing a coordinate sorted file.
CoordinateSortedPairInfoMap(int, CoordinateSortedPairInfoMap.Codec) - Constructor for class htsjdk.samtools.CoordinateSortedPairInfoMap
CoordinateSortedPairInfoMap.Codec<KEY,REC> - Interface in htsjdk.samtools
  Client must implement this class, which defines the way in which records are written to and read from file.
CoordMath - Class in htsjdk.samtools.util
  Static methods that encapsulate the standard SAM way of storing ranges: one-based, with both ends inclusive.
CoordMath() - Constructor for class htsjdk.samtools.util.CoordMath
CoordSpanInputSteam - Class in htsjdk.samtools.util
  An input stream that wraps a `SeekableStream` to produce only bytes specified within coordinates.
CoordSpanInputSteam(SeekableStream, long[]) - Constructor for class htsjdk.samtools.util.CoordSpanInputSteam
  Wrap `SeekableStream` to read only bytes within boundaries specified in the coords array.
copy() - Method in class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue
  Creates and returns a shallow copy of the list of tag/values.
copy() - Method in class htsjdk.samtools.SAMBinaryTagAndValue
  Creates and returns a shallow copy of the list of tag/values.
copy() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
copy(Genotype) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Copy all of the values for this builder from Genotype g
copy(GenotypesContext) - Static method in class htsjdk.variant.variantcontext.GenotypesContext
  Create a freshly allocated GenotypeContext containing the genotypes in toCopy
copy(Collection) - Static method in class htsjdk.variant.variantcontext.GenotypesContext
  Create a GenotypesContext containing the genotypes in iteration order contained in toCopy
copyDirectoryTree(File, File) - Static method in class htsjdk.samtools.util.IOUtil
  Copies a directory tree (all subdirectories and files) recursively to a destination
copyFile(File, File) - Static method in class htsjdk.samtools.util.IOUtil
  Copy input to output, overwriting output if it already exists.
copyOf(IntervalList) - Static method in class htsjdk.samtools.util.IntervalList
  creates a independent copy of the given IntervalList
copyStream(InputStream, OutputStream) - Static method in class htsjdk.samtools.util.IOUtil
  Utility method to copy the contents of input to output.
CORE - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockContentType
coreBlockInputStream - Variable in class htsjdk.samtools.cram.encoding.core.CoreCodec
coreBlockOutputStream - Variable in class htsjdk.samtools.cram.encoding.core.CoreCodec
CoreCodec<T> - Class in htsjdk.samtools.cram.encoding.core
  Superclass of Codecs which operate on Core Block bit streams Contrast with `htsjdk.samtools.cram.encoding.external.ExternalCodec<T>` for External Block byte streams
CoreCodec(BitInputStream, BitOutputStream) - Constructor for class htsjdk.samtools.cram.encoding.core.CoreCodec
  Create a new CoreCodec with associated input and output bit streams
CorruptedIndexFile(String, String, Exception) - Constructor for exception class htsjdk.tribble.TribbleException.CorruptedIndexFile
countAllele(Allele) - Method in class htsjdk.variant.variantcontext.Genotype
  Returns how many times allele appears in this genotype object?
countBases(Collection) - Static method in class htsjdk.samtools.util.Interval
  Counts the total number of bases a collection of intervals.
countDeletedBases(Cigar) - Static method in class htsjdk.samtools.util.SequenceUtil
countDeletedBases(SAMRecord) - Static method in class htsjdk.samtools.util.SequenceUtil
CountingInputStream - Class in htsjdk.samtools.cram.io
  An input stream that counts the bytes read from it.
CountingInputStream(InputStream) - Constructor for class htsjdk.samtools.cram.io.CountingInputStream
countInsertedBases(Cigar) - Static method in class htsjdk.samtools.util.SequenceUtil
countInsertedBases(SAMRecord) - Static method in class htsjdk.samtools.util.SequenceUtil
countMismatches(SAMRecord, byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the number of mismatches between the read and the reference sequence provided.
countMismatches(SAMRecord, byte[], boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the number of mismatches between the read and the reference sequence provided.
countMismatches(SAMRecord, byte[], int) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the number of mismatches between the read and the reference sequence provided.
countMismatches(SAMRecord, byte[], int, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the number of mismatches between the read and the reference sequence provided.
countMismatches(SAMRecord, byte[], int, boolean, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
CountRecords - Class in htsjdk.tribble.example
  An example of how to index a feature file, and then count all the records in the file.
CountRecords() - Constructor for class htsjdk.tribble.example.CountRecords
CP - Enum constant in enum class htsjdk.samtools.SAMTag
CP - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
CQ - Enum constant in enum class htsjdk.samtools.SAMTag
CQ - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
CR - Enum constant in enum class htsjdk.samtools.SAMTag
CR - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
CRAI - Enum constant in enum class htsjdk.samtools.SamIndexes
CRAI_INDEX_SUFFIX - Static variable in class htsjdk.samtools.cram.CRAIIndex
  Deprecated.
  since June 2019 Use `FileExtensions.CRAM_INDEX` instead.
CRAIEntry - Class in htsjdk.samtools.cram
  A class representing CRAI index entry: file and alignment offsets for each slice.
CRAIEntry(int, int, int, long, int, int) - Constructor for class htsjdk.samtools.cram.CRAIEntry
CRAIEntry(String) - Constructor for class htsjdk.samtools.cram.CRAIEntry
  Create a CRAI Entry from a serialized CRAI index line.
CRAIIndex - Class in htsjdk.samtools.cram
  CRAI index used for CRAM files.
CRAIIndex() - Constructor for class htsjdk.samtools.cram.CRAIIndex
CRAIIndexMerger - Class in htsjdk.samtools.cram
  Merges CRAM index files for (headerless) parts of a CRAM file into a single index file.
CRAIIndexMerger(OutputStream, long) - Constructor for class htsjdk.samtools.cram.CRAIIndexMerger
CRAM - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetFormat
CRAM - Static variable in class htsjdk.beta.plugin.reads.ReadsFormats
  CRAM file format.
CRAM - Static variable in class htsjdk.samtools.util.FileExtensions
CRAM_FILE_EXTENSION - Static variable in class htsjdk.samtools.cram.build.CramIO
  Deprecated.
  since June 2019 Use `FileExtensions.CRAM` instead.
CRAM_HEADER_LENGTH - Static variable in class htsjdk.samtools.cram.structure.CramHeader
CRAM_ID_LENGTH - Static variable in class htsjdk.samtools.cram.structure.CramHeader
CRAM_INDEX - Static variable in class htsjdk.samtools.util.FileExtensions
CRAM_MAGIC_LENGTH - Static variable in class htsjdk.samtools.cram.structure.CramHeader
CRAM_TYPE - Static variable in class htsjdk.samtools.SamReader.Type
CRAM_v2_1 - Static variable in class htsjdk.samtools.cram.common.CramVersions
CRAM_v3 - Static variable in class htsjdk.samtools.cram.common.CramVersions
CRAM_v3_1 - Static variable in class htsjdk.samtools.cram.common.CramVersions
CRAM_VERSION_LENGTH - Static variable in class htsjdk.samtools.cram.structure.CramHeader
CRAMBAIIndexer - Class in htsjdk.samtools
  Class for both constructing BAM index content and writing it out.
CRAMBAIIndexer(OutputStream, SAMFileHeader) - Constructor for class htsjdk.samtools.CRAMBAIIndexer
  Create a CRAM indexer that writes BAI to a stream.
CRAMByteReader - Class in htsjdk.samtools.cram.io
  Unsynchronized reader over a `byte[]` for CRAM codec decode operations.
CRAMByteReader(byte[]) - Constructor for class htsjdk.samtools.cram.io.CRAMByteReader
  Create a reader over the given byte array, starting at position 0.
CRAMByteWriter - Class in htsjdk.samtools.cram.io
  Unsynchronized growable byte writer for CRAM codec encode operations.
CRAMByteWriter() - Constructor for class htsjdk.samtools.cram.io.CRAMByteWriter
  Create a writer with a default initial capacity of 256 bytes.
CRAMByteWriter(int) - Constructor for class htsjdk.samtools.cram.io.CRAMByteWriter
  Create a writer with the specified initial capacity.
CRAMCodec - Class in htsjdk.beta.codecs.reads.cram
  InternalAPI Base class for `BundleResourceType.FMT_READS_CRAM` codecs.
CRAMCodec<T> - Interface in htsjdk.samtools.cram.encoding
  An interface that defines requirements for serializing/deserializing objects into and from a stream.
CRAMCodec() - Constructor for class htsjdk.beta.codecs.reads.cram.CRAMCodec
CRAMCodecModelContext - Class in htsjdk.samtools.cram.structure
  Context model data for use by CRAM 3.1 codec write implementations that need per-record metadata beyond the raw byte stream.
CRAMCodecModelContext() - Constructor for class htsjdk.samtools.cram.structure.CRAMCodecModelContext
CRAMCodecV2_1 - Class in htsjdk.beta.codecs.reads.cram.cramV2_1
  CRAM v2.1 codec
CRAMCodecV2_1() - Constructor for class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMCodecV2_1
CRAMCodecV3_0 - Class in htsjdk.beta.codecs.reads.cram.cramV3_0
  CRAM v3.0 codec
CRAMCodecV3_0() - Constructor for class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMCodecV3_0
CRAMCodecV3_1 - Class in htsjdk.beta.codecs.reads.cram.cramV3_1
  CRAM v3.1 codec
CRAMCodecV3_1() - Constructor for class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMCodecV3_1
CramComparison - Class in htsjdk.samtools.cram
  Command-line tool for comparing two SAM/BAM/CRAM files record-by-record.
CramComparison() - Constructor for class htsjdk.samtools.cram.CramComparison
CRAMCompressionProfile - Enum Class in htsjdk.samtools.cram.structure
  Predefined CRAM compression profiles matching those in htslib/samtools.
CRAMCompressionRecord - Class in htsjdk.samtools.cram.structure
  A CRAMRecord represents a SAMRecord that has been transformed to CRAM-style representation.
CRAMCompressionRecord(long, int, int, String, int, int, int, int, int, byte[], byte[], List, List, int, int, int, int, int) - Constructor for class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Create a CRAMRecord from a set of values retrieved from a serialized Slice's data series streams.
CRAMCompressionRecord(CRAMVersion, CRAMEncodingStrategy, SAMRecord, byte[], long, Map) - Constructor for class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Create a CRAMRecord from a SAMRecord.
CramContainerHeaderIterator - Class in htsjdk.samtools.cram.build
  Iterate over CRAM containers from an input stream, and unlike `CramContainerIterator` only the header of each container is read, rather than the whole stream.
CramContainerHeaderIterator(InputStream) - Constructor for class htsjdk.samtools.cram.build.CramContainerHeaderIterator
CramContainerIterator - Class in htsjdk.samtools.cram.build
  An iterator of CRAM containers read from an `InputStream`.
CramContainerIterator(InputStream) - Constructor for class htsjdk.samtools.cram.build.CramContainerIterator
CRAMContainerStreamWriter - Class in htsjdk.samtools
  Class for writing SAMRecords into a series of CRAM containers on an output stream, with an optional index.
CRAMContainerStreamWriter(CRAMEncodingStrategy, CRAMReferenceSource, SAMFileHeader, OutputStream, CRAMIndexer, String) - Constructor for class htsjdk.samtools.CRAMContainerStreamWriter
  Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.
CRAMContainerStreamWriter(OutputStream, CRAMReferenceSource, SAMFileHeader, String, CRAMIndexer) - Constructor for class htsjdk.samtools.CRAMContainerStreamWriter
  Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.
CRAMContainerStreamWriter(OutputStream, OutputStream, CRAMReferenceSource, SAMFileHeader, String) - Constructor for class htsjdk.samtools.CRAMContainerStreamWriter
  Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.
CramConverter - Class in htsjdk.samtools.cram
  Simple command-line tool for converting between SAM/BAM/CRAM formats, primarily for experimenting with CRAM 3.1 compression profiles.
CramConverter() - Constructor for class htsjdk.samtools.cram.CramConverter
CRAMCRAIIndexer - Class in htsjdk.samtools
  Indexer for creating/reading/writing a CRAIIndex for a CRAM file/stream.
CRAMCRAIIndexer(OutputStream, SAMFileHeader) - Constructor for class htsjdk.samtools.CRAMCRAIIndexer
  Create a CRAMCRAIIndexer that writes to the given output stream.
CRAMCRAIIndexer(OutputStream, SAMFileHeader, Collection) - Constructor for class htsjdk.samtools.CRAMCRAIIndexer
  Create a CRAMCRAIIndexer that writes to the given output stream, initialized with a Collection of `CRAIEntry` objects.
CRAMDecoder - Class in htsjdk.beta.codecs.reads.cram
  InternalAPI Base class for `BundleResourceType.FMT_READS_CRAM` decoders.
CRAMDecoder(Bundle, ReadsDecoderOptions) - Constructor for class htsjdk.beta.codecs.reads.cram.CRAMDecoder
  InternalAPI Common constructor for CRAM decoders.
CRAMDecoderOptions - Class in htsjdk.beta.codecs.reads.cram
  Decoder options specific to CRAM decoders.
CRAMDecoderOptions() - Constructor for class htsjdk.beta.codecs.reads.cram.CRAMDecoderOptions
CRAMDecoderV2_1 - Class in htsjdk.beta.codecs.reads.cram.cramV2_1
  CRAM v2.1decoder.
CRAMDecoderV2_1(Bundle, ReadsDecoderOptions) - Constructor for class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMDecoderV2_1
  Create a new V2.1 CRAM decoder.
CRAMDecoderV3_0 - Class in htsjdk.beta.codecs.reads.cram.cramV3_0
  CRAM v3.0 decoder.
CRAMDecoderV3_0(Bundle, ReadsDecoderOptions) - Constructor for class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMDecoderV3_0
  Create a new CRAM V3.0 decoder.
CRAMDecoderV3_1 - Class in htsjdk.beta.codecs.reads.cram.cramV3_1
  CRAM v3.1 decoder.
CRAMDecoderV3_1(Bundle, ReadsDecoderOptions) - Constructor for class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMDecoderV3_1
  Create a new CRAM v3.1 decoder.
CRAMEncoder - Class in htsjdk.beta.codecs.reads.cram
  InternalAPI Base class for `BundleResourceType.FMT_READS_CRAM` decoders.
CRAMEncoder(Bundle, ReadsEncoderOptions) - Constructor for class htsjdk.beta.codecs.reads.cram.CRAMEncoder
  InternalAPI Create a CRAM encoder for the given output bundle.
CRAMEncoderOptions - Class in htsjdk.beta.codecs.reads.cram
  Encoder options specific to CRAM encoders.
CRAMEncoderOptions() - Constructor for class htsjdk.beta.codecs.reads.cram.CRAMEncoderOptions
CRAMEncoderV2_1 - Class in htsjdk.beta.codecs.reads.cram.cramV2_1
  CRAM v2.1 encoder.
CRAMEncoderV2_1(Bundle, ReadsEncoderOptions) - Constructor for class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMEncoderV2_1
  Create a CRAM encoder for the given output bundle.
CRAMEncoderV3_0 - Class in htsjdk.beta.codecs.reads.cram.cramV3_0
  CRAM v3.0 encoder.
CRAMEncoderV3_0(Bundle, ReadsEncoderOptions) - Constructor for class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMEncoderV3_0
  Create a new CRAM CRAM v3.0 encoder for the given output bundle.
CRAMEncoderV3_1 - Class in htsjdk.beta.codecs.reads.cram.cramV3_1
  CRAM v3.1 encoder.
CRAMEncoderV3_1(Bundle, ReadsEncoderOptions) - Constructor for class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMEncoderV3_1
  Create a new CRAM v3.1 encoder for the given output bundle.
CRAMEncoding<T> - Class in htsjdk.samtools.cram.encoding
  A base class for the various CRAM encodings.
CRAMEncoding(EncodingID) - Constructor for class htsjdk.samtools.cram.encoding.CRAMEncoding
  Create a new encoding.
CRAMEncodingStrategy - Class in htsjdk.samtools.cram.structure
  Parameters that control the encoding strategy used when writing CRAM.
CRAMEncodingStrategy() - Constructor for class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Create an encoding strategy with the `CRAMCompressionProfile.NORMAL` profile applied.
CRAMException - Exception Class in htsjdk.samtools.cram
  Created by edwardk on 8/13/15.
CRAMException() - Constructor for exception class htsjdk.samtools.cram.CRAMException
CRAMException(String) - Constructor for exception class htsjdk.samtools.cram.CRAMException
CRAMException(String, Throwable) - Constructor for exception class htsjdk.samtools.cram.CRAMException
CRAMException(Throwable) - Constructor for exception class htsjdk.samtools.cram.CRAMException
CRAMFileReader - Class in htsjdk.samtools
  `BAMFileReader` analogue for CRAM files.
CRAMFileReader(File, CRAMReferenceSource) - Constructor for class htsjdk.samtools.CRAMFileReader
  Create a CRAMFileReader from a file using the supplied reference source.
CRAMFileReader(File, File, CRAMReferenceSource) - Constructor for class htsjdk.samtools.CRAMFileReader
  Create a CRAMFileReader from a file and optional index file using the supplied reference source.
CRAMFileReader(File, File, CRAMReferenceSource, ValidationStringency) - Constructor for class htsjdk.samtools.CRAMFileReader
  Create a CRAMFileReader from a CRAM file and optional index file using the supplied reference source and validation stringency.
CRAMFileReader(File, InputStream) - Constructor for class htsjdk.samtools.CRAMFileReader
  Create a CRAMFileReader from either a file or input stream using the reference source returned by `getDefaultCRAMReferenceSource`.
CRAMFileReader(File, InputStream, CRAMReferenceSource) - Constructor for class htsjdk.samtools.CRAMFileReader
  Create a CRAMFileReader from either a file or input stream using the supplied reference source.
CRAMFileReader(InputStream, SeekableStream, CRAMReferenceSource, ValidationStringency) - Constructor for class htsjdk.samtools.CRAMFileReader
  Create a CRAMFileReader from an input stream and optional index stream using the supplied reference source and validation stringency.
CRAMFileReader(InputStream, File, CRAMReferenceSource, ValidationStringency) - Constructor for class htsjdk.samtools.CRAMFileReader
  Create a CRAMFileReader from an input stream and optional index file using the supplied reference source and validation stringency.
CRAMFileWriter - Class in htsjdk.samtools
CRAMFileWriter(CRAMEncodingStrategy, OutputStream, OutputStream, boolean, CRAMReferenceSource, SAMFileHeader, String) - Constructor for class htsjdk.samtools.CRAMFileWriter
  Create a CRAMFileWriter and optional index on output streams.
CRAMFileWriter(OutputStream, CRAMReferenceSource, SAMFileHeader, String) - Constructor for class htsjdk.samtools.CRAMFileWriter
  Create a CRAMFileWriter on an output stream.
CRAMFileWriter(OutputStream, OutputStream, boolean, CRAMReferenceSource, SAMFileHeader, String) - Constructor for class htsjdk.samtools.CRAMFileWriter
  Create a CRAMFileWriter and optional index on output streams.
CRAMFileWriter(OutputStream, OutputStream, CRAMReferenceSource, SAMFileHeader, String) - Constructor for class htsjdk.samtools.CRAMFileWriter
  Create a CRAMFileWriter and optional index on output streams.
CramHeader - Class in htsjdk.samtools.cram.structure
  A CRAM file header, including the file format definition (including CRAM version and content id), and the SAMFileHeader.
CramHeader(CRAMVersion, String) - Constructor for class htsjdk.samtools.cram.structure.CramHeader
  Create a new `CramHeader` object with the specified version and id.
CRAMIndexer - Interface in htsjdk.samtools
  Interface for indexing CRAM.
CramInt - Class in htsjdk.samtools.cram.io
  Methods to read and write CRAM int values as given in the file format specification.
CramInt() - Constructor for class htsjdk.samtools.cram.io.CramInt
CramIntArray - Class in htsjdk.samtools.cram.io
  Methods to read and write CRAM array of integers data type.
CramIntArray() - Constructor for class htsjdk.samtools.cram.io.CramIntArray
CramIO - Class in htsjdk.samtools.cram.build
  A collection of methods to read and write special values to/from CRAM files.
CramIO() - Constructor for class htsjdk.samtools.cram.build.CramIO
CRAMIterator - Class in htsjdk.samtools
CRAMIterator(SeekableStream, CRAMReferenceSource, ValidationStringency, QueryInterval[], long[]) - Constructor for class htsjdk.samtools.CRAMIterator
CRAMIterator(InputStream, CRAMReferenceSource, ValidationStringency) - Constructor for class htsjdk.samtools.CRAMIterator
CRAMLazyReferenceSource - Class in htsjdk.samtools.cram.ref
  A lazy CRAMReferenceSource implementation, for use when no explicit reference source has been provided by the user.
CRAMLazyReferenceSource() - Constructor for class htsjdk.samtools.cram.ref.CRAMLazyReferenceSource
CramRecordReader - Class in htsjdk.samtools.cram.encoding.reader
  A reader used to consume and populate encoded `CRAMCompressionRecord`s from a set of streams representing data series/blocks in a Slice.
CramRecordReader(Slice, CompressorCache, ValidationStringency) - Constructor for class htsjdk.samtools.cram.encoding.reader.CramRecordReader
  Initialize a Cram Record Reader
CRAMRecordReadFeatures - Class in htsjdk.samtools.cram.structure
  Class for handling the read features for a `CRAMCompressionRecord`.
CRAMRecordReadFeatures() - Constructor for class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
  Create a CRAMRecordReadFeatures with no actual read features (i.e.
CRAMRecordReadFeatures(SAMRecord, byte[], byte[]) - Constructor for class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
  Create the read features for a given SAMRecord.
CRAMRecordReadFeatures(List) - Constructor for class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
  Create a CRAMRecordReadFeatures from a list of read features consumed from a stream.
CRAMRecordReadFeatures.DecodeResult - Class in htsjdk.samtools.cram.structure
  Result of the fused single-pass decode: read bases, CIGAR, and optionally MD string + NM count.
CramRecordWriter - Class in htsjdk.samtools.cram.encoding.writer
  A writer that emits CRAMCompressionRecord into the various streams that represent a Slice's data series blocks.
CramRecordWriter(Slice) - Constructor for class htsjdk.samtools.cram.encoding.writer.CramRecordWriter
  Initializes a Cram Record Writer
CRAMReferenceRegion - Class in htsjdk.samtools.cram.build
  Holds a region/fragment of a reference contig.
CRAMReferenceRegion(CRAMReferenceSource, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.cram.build.CRAMReferenceRegion
CRAMReferenceSource - Interface in htsjdk.samtools.cram.ref
  Interface used to supply a reference source when reading CRAM files.
CramSpanContainerIterator - Class in htsjdk.samtools.cram.build
  An iterator of CRAM containers read from locations in a `SeekableStream`.
CramStats - Class in htsjdk.samtools.cram
  Dumps per-DataSeries compression statistics from a CRAM file.
CramStats() - Constructor for class htsjdk.samtools.cram.CramStats
CRAMVersion - Class in htsjdk.samtools.cram.common
  A class to represent a version information, 3 number: major, minor and build number.
CRAMVersion(int, int) - Constructor for class htsjdk.samtools.cram.common.CRAMVersion
CRAMVersion(String) - Constructor for class htsjdk.samtools.cram.common.CRAMVersion
CramVersions - Class in htsjdk.samtools.cram.common
CramVersions() - Constructor for class htsjdk.samtools.cram.common.CramVersions
CRC32 - Static variable in class htsjdk.samtools.cram.digest.ContentDigests
CRC32InputStream - Class in htsjdk.samtools.cram.io
  An input stream that calculates CRC32 of all the bytes passed through it.
CRC32InputStream(InputStream) - Constructor for class htsjdk.samtools.cram.io.CRC32InputStream
CRC32OutputStream - Class in htsjdk.samtools.cram.io
  An output stream that calculates CRC32 checksum of all the bytes written through the stream.
CRC32OutputStream(OutputStream) - Constructor for class htsjdk.samtools.cram.io.CRC32OutputStream
create() - Static method in class htsjdk.variant.variantcontext.GenotypesContext
  Basic creation routine
create(byte) - Static method in interface htsjdk.variant.variantcontext.Allele
create(byte[]) - Static method in interface htsjdk.variant.variantcontext.Allele
  Creates a non-Ref allele.
create(byte[], boolean) - Static method in interface htsjdk.variant.variantcontext.Allele
  Create a new Allele that includes bases and if tagged as the reference allele if isRef == true.
create(byte, boolean) - Static method in interface htsjdk.variant.variantcontext.Allele
create(int) - Static method in class htsjdk.variant.variantcontext.GenotypesContext
  Basic creation routine
create(SAMBinaryTagAndValue) - Static method in class htsjdk.samtools.cram.digest.ContentDigests
create(Allele, boolean) - Static method in interface htsjdk.variant.variantcontext.Allele
  Creates a new allele based on the provided one.
create(Genotype...) - Static method in class htsjdk.variant.variantcontext.GenotypesContext
  Create a fully resolved GenotypeContext containing genotypes
create(String) - Static method in interface htsjdk.variant.variantcontext.Allele
  Creates a non-Ref allele.
create(String, boolean) - Static method in interface htsjdk.variant.variantcontext.Allele
  Returns an allele with the given bases and reference status.
create(String, List) - Static method in class htsjdk.variant.variantcontext.GenotypeBuilder
create(String, List, double[]) - Static method in class htsjdk.variant.variantcontext.GenotypeBuilder
create(String, List, Map) - Static method in class htsjdk.variant.variantcontext.GenotypeBuilder
create(Path, boolean) - Static method in class htsjdk.samtools.reference.FastaSequenceIndexCreator
  Creates a FASTA .fai index for the provided FASTA.
create(ArrayList) - Static method in class htsjdk.variant.variantcontext.GenotypesContext
  Create a fully resolved GenotypeContext containing genotypes
create(ArrayList, Map, List) - Static method in class htsjdk.variant.variantcontext.GenotypesContext
  Create a fully resolved GenotypeContext containing genotypes, sample lookup table, and sorted sample names
create(EnumSet) - Static method in class htsjdk.samtools.cram.digest.ContentDigests
create(List) - Static method in class htsjdk.samtools.util.OverlapDetector
  Creates a new OverlapDetector with no trim and the given set of intervals.
CREATE_INDEX - Static variable in class htsjdk.samtools.Defaults
  Should BAM index files be created when writing out coordinate sorted BAM files? Default = false.
CREATE_MD5 - Static variable in class htsjdk.samtools.Defaults
  Should MD5 files be created when writing out SAM and BAM files? Default = false.
createAndWriteIndex(File, File, boolean) - Static method in class htsjdk.samtools.BAMIndexer
  Generates a BAM index file, either textual or binary, from an input BAI file.
createAndWriteNewIndex(File, File, FeatureCodec) - Static method in class htsjdk.tribble.example.CountRecords
  creates a new index, given the feature file and the codec
createBAMRecord(SAMFileHeader, int, int, short, short, int, int, int, int, int, int, int, byte[]) - Method in class htsjdk.samtools.DefaultSAMRecordFactory
  Create a new BAM Record.
createBAMRecord(SAMFileHeader, int, int, short, short, int, int, int, int, int, int, int, byte[]) - Method in interface htsjdk.samtools.SAMRecordFactory
  Create a new BAM Record.
createBeginRecord(SAMRecord, int, int, int) - Static method in class htsjdk.samtools.util.EdgingRecordAndOffset
createCompressedBlockForStream(CRAMCodecModelContext, Integer, ByteArrayOutputStream) - Method in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  Given a content ID, return a `Block` for that ID by obtaining the contents of the stream, compressing it using the compressor for that contentID, and converting the result to a `Block`.
createCompressedBlockForWriter(CRAMCodecModelContext, Integer, CRAMByteWriter) - Method in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  Same as `CompressionHeaderEncodingMap.createCompressedBlockForStream(CRAMCodecModelContext, Integer, ByteArrayOutputStream)` but accepts a `CRAMByteWriter`.
createCompressionHeader(List, boolean) - Method in class htsjdk.samtools.cram.build.CompressionHeaderFactory
  Creates a compression header for the provided list of `CRAMCompressionRecord` objects.
createCRAMEncoding(DataSeriesType, EncodingDescriptor) - Static method in class htsjdk.samtools.cram.encoding.EncodingFactory
  Use the data series value type and EncodingDescriptor to instantiate a corresponding CRAMEncoding of the correct (generic) type.
createCRAMEncoding(DataSeriesType, EncodingID, byte[]) - Static method in class htsjdk.samtools.cram.encoding.EncodingFactory
  Create an encoding of the correct type for the data series type and encoding id and params.
createDynamicIndex(File, FeatureCodec) - Static method in class htsjdk.tribble.index.IndexFactory
  Create a dynamic index with the default balancing approach
createDynamicIndex(File, FeatureCodec, IndexFactory.IndexBalanceApproach) - Static method in class htsjdk.tribble.index.IndexFactory
  create a dynamic index, given an input file, codec, and balance approach
createDynamicIndex(Path, FeatureCodec) - Static method in class htsjdk.tribble.index.IndexFactory
  Create a dynamic index with the default balancing approach
createDynamicIndex(Path, FeatureCodec, IndexFactory.IndexBalanceApproach) - Static method in class htsjdk.tribble.index.IndexFactory
  create a dynamic index, given an input path, codec, and balance approach
createEndRecord(EdgingRecordAndOffset) - Static method in class htsjdk.samtools.util.EdgingRecordAndOffset
createExternalBlock(BlockCompressionMethod, int, byte[], int) - Static method in class htsjdk.samtools.cram.structure.block.Block
  Create a new external data block with the given compression method, uncompressed content, and content ID.
createGenotypeMap(String, List, String, int) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  create a genotype map
createGZIPFileHeaderBlock(byte[]) - Static method in class htsjdk.samtools.cram.structure.block.Block
  Create a new file header block with the given uncompressed content.
createIndex(SamReader, File) - Static method in class htsjdk.samtools.BAMIndexer
  Generates a BAM index file from an input BAM file
createIndex(SamReader, File, Log) - Static method in class htsjdk.samtools.BAMIndexer
  Generates a BAM index file from an input BAM file
createIndex(SamReader, Path) - Static method in class htsjdk.samtools.BAMIndexer
  Generates a BAM index file from an input BAM file
createIndex(SamReader, Path, Log) - Static method in class htsjdk.samtools.BAMIndexer
  Generates a BAM index file from an input BAM file
createIndex(SeekableStream, File, Log, ValidationStringency) - Static method in class htsjdk.samtools.CRAMBAIIndexer
  Generates a BAI index file from an input CRAM stream
createIndex(SeekableStream, OutputStream, long) - Static method in class htsjdk.samtools.BAMSBIIndexer
  Perform indexing on the given BAM file, at the granularity level specified.
createIndex(File, FeatureCodec, IndexFactory.IndexType) - Static method in class htsjdk.tribble.index.IndexFactory
  Create a index of the specified type with default binning parameters
createIndex(File, FeatureCodec, IndexFactory.IndexType, SAMSequenceDictionary) - Static method in class htsjdk.tribble.index.IndexFactory
  Create an index of the specified type with default binning parameters
createIndex(InputStream) - Method in enum class htsjdk.tribble.index.IndexFactory.IndexType
createIndex(Path, boolean) - Static method in class htsjdk.samtools.util.GZIIndex
  Creates a `GZIIndex` from a BGZIP file and store it in memory and disk.
createIndex(Path, long) - Static method in class htsjdk.samtools.BAMSBIIndexer
  Perform indexing on the given BAM file, at the granularity level specified.
createIndex(Path, FeatureCodec, IndexFactory.IndexType) - Static method in class htsjdk.tribble.index.IndexFactory
  Create a index of the specified type with default binning parameters
createIndex(Path, FeatureCodec, IndexFactory.IndexType, SAMSequenceDictionary) - Static method in class htsjdk.tribble.index.IndexFactory
  Create an index of the specified type with default binning parameters
createIndexIterator(QueryInterval[], boolean, long[]) - Method in class htsjdk.samtools.BAMFileReader
  Prepare to iterate through SAMRecords that match the given intervals.
createIndexIterator(QueryInterval[], boolean, long[]) - Method in class htsjdk.samtools.CRAMFileReader
  Prepare to iterate through SAMRecords that match the intersection of the given intervals and chunk boundaries.
createIntervalIndex(File, FeatureCodec) - Static method in class htsjdk.tribble.index.IndexFactory
  create an interval-tree index with the default features per bin count
createIntervalIndex(File, FeatureCodec, int) - Static method in class htsjdk.tribble.index.IndexFactory
  a helper method for creating an interval-tree index
createIntervalIndex(Path, FeatureCodec) - Static method in class htsjdk.tribble.index.IndexFactory
  create an interval-tree index with the default features per bin count
createIntervalIndex(Path, FeatureCodec, int) - Static method in class htsjdk.tribble.index.IndexFactory
  a helper method for creating an interval-tree index
createLinearIndex(File, FeatureCodec) - Static method in class htsjdk.tribble.index.IndexFactory
  a helper method for creating a linear binned index with default bin size
createLinearIndex(File, FeatureCodec, int) - Static method in class htsjdk.tribble.index.IndexFactory
  a helper method for creating a linear binned index
createLinearIndex(Path, FeatureCodec) - Static method in class htsjdk.tribble.index.IndexFactory
  a helper method for creating a linear binned index with default bin size
createLinearIndex(Path, FeatureCodec, int) - Static method in class htsjdk.tribble.index.IndexFactory
  a helper method for creating a linear binned index
createMissing(String, int) - Static method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Create a new Genotype object for a sample that's missing from the VC (i.e., in the output header).
createNewSliceEntry(int, List) - Method in class htsjdk.samtools.cram.build.SliceFactory
  Add a new slice entry, and return the number of sliceEntries.
createPrivateRegistry() - Static method in class htsjdk.beta.plugin.registry.HtsCodecRegistry
  Create a mutable registry for private use.
createProgramRecord() - Method in class htsjdk.samtools.SAMFileHeader
createRawCompressionHeaderBlock(byte[]) - Static method in class htsjdk.samtools.cram.structure.block.Block
  Create a new compression header block with the given uncompressed content.
createRawCoreDataBlock(byte[]) - Static method in class htsjdk.samtools.cram.structure.block.Block
  Create a new core data block with the given uncompressed content.
createRawSliceHeaderBlock(byte[]) - Static method in class htsjdk.samtools.cram.structure.block.Block
  Create a new slice header block with the given uncompressed content.
createSAMRecord(SAMFileHeader) - Method in class htsjdk.samtools.DefaultSAMRecordFactory
  Create a new SAMRecord to be filled in
createSAMRecord(SAMFileHeader) - Method in interface htsjdk.samtools.SAMRecordFactory
  Create a new SAMRecord to be filled in
createSAMTag() - Method in class htsjdk.samtools.cram.structure.ReadTag
  Create a `SAMRecord.SAMTagAndValue` from this ReadTag's key and value.
createSlices(CompressionHeader, long) - Method in class htsjdk.samtools.cram.build.SliceFactory
  Returns a set of Slices using the records accumulated by the factory, and resets the factory state.
createTabixIndex(File, FeatureCodec, SAMSequenceDictionary) - Static method in class htsjdk.tribble.index.IndexFactory
createTabixIndex(File, FeatureCodec, TabixFormat, SAMSequenceDictionary) - Static method in class htsjdk.tribble.index.IndexFactory
createTabixIndex(Path, FeatureCodec, SAMSequenceDictionary) - Static method in class htsjdk.tribble.index.IndexFactory
createTabixIndex(Path, FeatureCodec, TabixFormat, SAMSequenceDictionary) - Static method in class htsjdk.tribble.index.IndexFactory
createTempDir(String) - Static method in class htsjdk.samtools.util.IOUtil
createTempDir(String, String) - Static method in class htsjdk.samtools.util.IOUtil
  Deprecated.
  Use `IOUtil.createTempDir(String)` instead. It turns out the mechanism was not "good enough" and caused security issues, the new implementation combines the prefix/morePrefix into a single prefix. The security flaw is fixed but due to the now extraneous morePrefix argument it is recommended to use the 1 argument form.
createTemporaryIndexedVcfFile(String, String) - Static method in class htsjdk.variant.vcf.VCFUtils
  This method creates a temporary VCF file and its appropriately named index file, and will delete them on exit.
createTemporaryIndexedVcfFromInput(File, String) - Static method in class htsjdk.variant.vcf.VCFUtils
  This method makes a copy of the input VCF and creates an index file for it in the same location.
createTempPath(String, String) - Static method in class htsjdk.beta.io.IOPathUtils
  Create a temporary file using a given name prefix and name suffix and return a `Path`.
createTempPath(String, String) - Static method in class htsjdk.beta.plugin.IOUtils
  Create a temporary file using a given name prefix and name suffix and return a `Path`.
Creating variant contexts - Section in class htsjdk.variant.variantcontext.VariantContext
CS - Enum constant in enum class htsjdk.samtools.SAMTag
CS - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
CSI - Enum constant in enum class htsjdk.samtools.SamIndexes
CSI - Static variable in class htsjdk.samtools.util.FileExtensions
CSI_INDEX_SUFFIX - Static variable in interface htsjdk.samtools.BAMIndex
  Deprecated.
  since June 2019 Use `FileExtensions.CSI` instead.
CSIIndex - Class in htsjdk.samtools
  Implementation of the CSI index for BAM files.
CSIIndex(SeekableStream, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.CSIIndex
  Constructors
CSIIndex(File, boolean, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.CSIIndex
CSIIndex(Path, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.CSIIndex
CT - Enum constant in enum class htsjdk.samtools.SAMTag
CT - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
CT_ALIGNED_READS - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
  Common primary content types
CT_FEATURES - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
CT_HAPLOID_REFERENCE - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
CT_MD5 - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
  MISCELLANEOUS Resource types
CT_READS_INDEX - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
  Secondary content types names for content type `BundleResourceType.CT_ALIGNED_READS` resources
CT_REFERENCE_DICTIONARY - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
  Secondary content types for `BundleResourceType.CT_HAPLOID_REFERENCE` resources
CT_REFERENCE_INDEX - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
CT_REFERENCE_INDEX_GZI - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
CT_VARIANT_CONTEXTS - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
CT_VARIANTS_INDEX - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
  Secondary content types for primary content type `BundleResourceType.CT_VARIANT_CONTEXTS` resources
CURRENT_VERSION - Static variable in class htsjdk.samtools.SAMFileHeader
CUSTOM_READER_FACTORY - Static variable in class htsjdk.samtools.Defaults
  Custom reader factory able to handle URL based resources like ga4gh.
CustomGzipOutputStream - Class in htsjdk.samtools.util
  Hacky little class used to allow us to set the compression level on a GZIP output stream which, for some bizarre reason, is not exposed in the standard API.
CustomGzipOutputStream(OutputStream, int) - Constructor for class htsjdk.samtools.util.CustomGzipOutputStream
CustomGzipOutputStream(OutputStream, int, int) - Constructor for class htsjdk.samtools.util.CustomGzipOutputStream
CustomReaderFactory - Class in htsjdk.samtools
  Factory for creating custom readers for accessing API based resources, e.g.
CustomReaderFactory.ICustomReaderFactory - Interface in htsjdk.samtools
  Interface to be implemented by custom factory classes that register themselves with this factory and are loaded dynamically.
CY - Enum constant in enum class htsjdk.samtools.SAMTag
CY - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.

## D

D - Enum constant in enum class htsjdk.samtools.CigarOperator
  Deletion vs.
data - Variable in class htsjdk.samtools.cram.compression.range.ByteModel
  Interleaved frequency/symbol pairs: `data[i*2]` = frequency, `data[i*2+1]` = symbol.
dataClass - Variable in class htsjdk.samtools.util.htsget.HtsgetRequest
dataFileLength() - Method in class htsjdk.samtools.SBIIndex
  Returns the length of the data file in bytes.
DataSeries - Enum Class in htsjdk.samtools.cram.structure
  Represents a specific CRAM record data series and its associated type and unique Content ID.
DATASERIES_NOT_READ_BY_HTSJDK - Static variable in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
DataSeriesReader<T> - Class in htsjdk.samtools.cram.encoding.reader
  A CRAM Data Series reader for a particular (Encoding, DataSeriesType) and associated parameters
DataSeriesReader(DataSeriesType, EncodingDescriptor, SliceBlocksReadStreams) - Constructor for class htsjdk.samtools.cram.encoding.reader.DataSeriesReader
  Initialize a Data Series reader
DataSeriesType - Enum Class in htsjdk.samtools.cram.structure
  Data series types known to CRAM.
DataSeriesWriter<T> - Class in htsjdk.samtools.cram.encoding.writer
  A CRAM Data Series writer for a particular Encoding, DataSeriesType and associated parameters
DataSeriesWriter(DataSeriesType, EncodingDescriptor, SliceBlocksWriteStreams) - Constructor for class htsjdk.samtools.cram.encoding.writer.DataSeriesWriter
  Initialize a Data Series writer
DATE_RUN_PRODUCED_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
DateParser - Class in htsjdk.samtools.util
  NOTE: This code has been taken from w3.org, and modified slightly to handle timezones of the form [-+]DDDD, and also to fix a bug in the application of time zone to the parsed date.
DateParser() - Constructor for class htsjdk.samtools.util.DateParser
DateParser.InvalidDateException - Exception Class in htsjdk.samtools.util
DBSNP_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
DEAFULT_MAX_RECORDS_IN_RAM - Static variable in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
debug(Object...) - Method in class htsjdk.samtools.util.Log
  Logs one or more message parts at level debug.
debug(Throwable, Object...) - Method in class htsjdk.samtools.util.Log
  Logs a Throwable and optional message parts at level debug.
debug(Supplier) - Method in class htsjdk.samtools.util.Log
  Logs a message at level debug.
DEBUG - Enum constant in enum class htsjdk.samtools.util.Log.LogLevel
DEBUG_MODE_ENABLED - Static variable in class htsjdk.variant.utils.GeneralUtils
  Setting this to true causes the VCF/BCF/VariantContext classes to emit debugging information to standard error
debugGetTree(String) - Method in class htsjdk.samtools.util.IntervalTreeMap
DECIMAL - Enum constant in enum class htsjdk.samtools.SamFlagField
DECIMAL_DIGITS_TO_PRINT - Static variable in class htsjdk.samtools.util.FormatUtil
decode() - Method in class htsjdk.samtools.BAMRecordCodec
  Read the next record from the input stream and convert into a java object.
decode() - Method in interface htsjdk.samtools.CoordinateSortedPairInfoMap.Codec
  Read the next key and record from the input stream and convert into a java object.
decode() - Method in class htsjdk.samtools.util.IntervalCodec
  Reads an interval from the input stream.
decode() - Method in interface htsjdk.samtools.util.SortingCollection.Codec
  Read the next record from the input stream and convert into a java object.
decode() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
  Force us to decode the genotypes, if not already done
decode() - Method in class htsjdk.variant.vcf.VCFRecordCodec
decode(char) - Static method in enum class htsjdk.tribble.annotation.Strand
  Returns the `Strand` that a `char` value represents.
decode(LineReader, String) - Method in class htsjdk.samtools.SAMSequenceDictionaryCodec
  Reads text SAM header and converts to a SAMSequenceDictionary object.
decode(LineReader, String) - Method in class htsjdk.samtools.SAMTextHeaderCodec
  Reads text SAM header and converts to a SAMFileHeader object.
decode(LineIterator) - Method in class htsjdk.tribble.AsciiFeatureCodec
  Convenience method.
decode(LineIterator) - Method in class htsjdk.tribble.gff.Gff3Codec
decode(PositionalBufferedStream) - Method in class htsjdk.tribble.example.ExampleBinaryCodec
decode(PositionalBufferedStream) - Method in class htsjdk.variant.bcf2.BCF2Codec
decode(String) - Static method in class htsjdk.samtools.TextCigarCodec
  Convert from String CIGAR representation to Cigar class representation.
decode(String) - Method in class htsjdk.samtools.TextTagCodec
  Convert typed tag in SAM text format (name:type:value) into tag name and Object value representation.
decode(String) - Static method in enum class htsjdk.tribble.annotation.Strand
  Returns the `Strand` that a `String` encodes for.
decode(String) - Method in class htsjdk.tribble.AsciiFeatureCodec
decode(String) - Method in class htsjdk.tribble.bed.BEDCodec
decode(String) - Method in enum class htsjdk.tribble.gff.Gff3Codec.Gff3Directive
decode(String) - Method in class htsjdk.tribble.IntervalList.IntervalListCodec
decode(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  decode the line into a feature (VariantContext)
decode(String[]) - Method in class htsjdk.tribble.bed.BEDCodec
decode(List, String, BCF2Decoder, byte, int, GenotypeBuilder[]) - Method in interface htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders.Decoder
decode(SOURCE) - Method in interface htsjdk.tribble.FeatureCodec
  Decode a single `Feature` from the `SOURCE`, reading no further in the underlying source than beyond that feature.
decodeFQZNewRecord(ByteBuffer, RangeCoder, FQZModels, FQZParams, FQZState) - Static method in class htsjdk.samtools.cram.compression.fqzcomp.FQZCompDecode
  Decode the header for a new record: selector, length, reverse flag, and duplicate flag.
decodeInt(byte, int) - Method in class htsjdk.variant.bcf2.BCF2Decoder
  Decode an int from the stream.
decodeInt(BCF2Type) - Method in class htsjdk.variant.bcf2.BCF2Decoder
decodeIntArray(byte, int) - Method in class htsjdk.variant.bcf2.BCF2Decoder
decodeIntArray(int, BCF2Type, int[]) - Method in class htsjdk.variant.bcf2.BCF2Decoder
  Low-level reader for int[] Requires a typeDescriptor so the function knows how many elements to read, and how they are encoded.
decodeLoc(LineIterator) - Method in class htsjdk.tribble.gff.Gff3Codec
decodeLoc(PositionalBufferedStream) - Method in class htsjdk.tribble.example.ExampleBinaryCodec
decodeLoc(PositionalBufferedStream) - Method in class htsjdk.variant.bcf2.BCF2Codec
decodeLoc(String) - Method in class htsjdk.tribble.bed.BEDCodec
decodeLoc(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  the fast decode function
decodeLoc(SOURCE) - Method in class htsjdk.tribble.AbstractFeatureCodec
decodeLoc(SOURCE) - Method in interface htsjdk.tribble.FeatureCodec
  Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.
decodeNumberOfElements(byte) - Method in class htsjdk.variant.bcf2.BCF2Decoder
decodePack(ByteBuffer, byte[], int, int) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Unpack bit-packed data back to one byte per symbol, reversing the transformation performed by `CompressionUtils.encodePack(ByteBuffer, ByteBuffer, int[], int[], int)`.
decodePercentEncodedChars(String) - Static method in class htsjdk.variant.vcf.VCFPercentEncodedTextTransformer
  Transform input strings containing embedded percent=encoded characters.
decodeSingleValue(BCF2Type) - Method in class htsjdk.variant.bcf2.BCF2Decoder
decodeSize(byte) - Static method in class htsjdk.variant.bcf2.BCF2Utils
decodeText(String) - Method in class htsjdk.variant.vcf.VCFPassThruTextTransformer
  No-op decoder for a single string
decodeText(String) - Method in class htsjdk.variant.vcf.VCFPercentEncodedTextTransformer
  Transform a single string, replacing % encoded values with their corresponding text.
decodeText(String) - Method in interface htsjdk.variant.vcf.VCFTextTransformer
  Transform a single string.
decodeText(List) - Method in class htsjdk.variant.vcf.VCFPassThruTextTransformer
  No-op decoder for lists of strings
decodeText(List) - Method in class htsjdk.variant.vcf.VCFPercentEncodedTextTransformer
  Transform a list of strings, replacing % encoded values with their corresponding text in each string.
decodeText(List) - Method in interface htsjdk.variant.vcf.VCFTextTransformer
  Transform a list of strings.
decodeType(byte) - Static method in class htsjdk.variant.bcf2.BCF2Utils
decodeTypedValue() - Method in class htsjdk.variant.bcf2.BCF2Decoder
decodeTypedValue(byte) - Method in class htsjdk.variant.bcf2.BCF2Decoder
decodeTypedValue(byte, int) - Method in class htsjdk.variant.bcf2.BCF2Decoder
decodeTypeID(byte) - Static method in class htsjdk.variant.bcf2.BCF2Utils
decompress(ByteBuffer) - Method in class htsjdk.samtools.util.GzipCodec
  Decompress GZIP or BGZF data and return a new ByteBuffer containing the result.
decompress(ByteBuffer, ByteBuffer) - Method in class htsjdk.samtools.util.GzipCodec
  Decompress GZIP or BGZF data from `input` into `output`.
DecompressedBlock(long, byte[], int) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream.DecompressedBlock
DecompressedBlock(long, int, Exception) - Constructor for class htsjdk.samtools.util.BlockCompressedInputStream.DecompressedBlock
DEEP - Enum constant in enum class htsjdk.tribble.gff.Gff3Codec.DecodeDepth
deepCopy() - Method in class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue
  Creates and returns a deep copy of the list of tag/values.
deepCopy() - Method in class htsjdk.samtools.SAMBinaryTagAndValue
  Creates and returns a deep copy of the list of tag/values.
deepCopy() - Method in class htsjdk.samtools.SAMRecord
  Returns a deep copy of the SAM record, with the following exceptions: - The header field, which shares the header reference with the original record - The file source field, which will always always be set to null in the copy
DEFAULT_BASES_PER_LINE - Static variable in class htsjdk.samtools.reference.FastaReferenceWriter
  Default number of bases per line.
DEFAULT_BASES_PER_READ - Static variable in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Default ratio of bases-per-slice to reads-per-slice.
DEFAULT_BIN_WIDTH - Static variable in class htsjdk.tribble.index.linear.LinearIndexCreator
DEFAULT_BUFFER_SIZE - Static variable in class htsjdk.samtools.seekablestream.SeekableBufferedStream
DEFAULT_CHROMOSOME_LENGTH - Static variable in class htsjdk.samtools.SAMRecordSetBuilder
DEFAULT_COMPRESSION_LEVEL - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
DEFAULT_CRAM_VERSION - Static variable in class htsjdk.samtools.cram.common.CramVersions
  The default CRAM version when creating a new CRAM output file or stream.
DEFAULT_DICTIONARY_EQUAL_TAG - Static variable in class htsjdk.samtools.SAMSequenceDictionary
DEFAULT_DUPLICATE_SCORING_STRATEGY - Static variable in class htsjdk.samtools.SAMRecordSetBuilder
DEFAULT_EXTENSION - Static variable in class htsjdk.samtools.util.GZIIndex
  Deprecated.
  since June 2019 Use `FileExtensions.GZI` instead.
DEFAULT_FEATURE_COUNT - Static variable in class htsjdk.tribble.index.interval.IntervalIndexCreator
DEFAULT_GRANULARITY - Static variable in class htsjdk.samtools.SBIIndexWriter
DEFAULT_HEADER_KEY - Static variable in class htsjdk.samtools.filter.AbstractJavascriptFilter
DEFAULT_LIFTOVER_MINMATCH - Static variable in class htsjdk.samtools.liftover.LiftOver
DEFAULT_MAX_RECORDS_TO_ITERATE - Static variable in class htsjdk.samtools.util.QualityEncodingDetector
  The maximum number of records over which the detector will iterate before making a determination, by default.
DEFAULT_MINIMUM_SINGLE_REFERENCE_SLICE_THRESHOLD - Static variable in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
DEFAULT_OPTIONS - Static variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
DEFAULT_POSITION_ALLOCATION - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.NameTokenisationDecode
DEFAULT_QUEUE_SIZE - Static variable in class htsjdk.samtools.util.AbstractAsyncWriter
DEFAULT_READS_PER_SLICE - Static variable in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
DEFAULT_SAM_EXTENSION - Static variable in class htsjdk.samtools.Defaults
  The extension to assume a sam file has when the actual file doesn't have an extension, useful for when outputing to /dev/stdout, for example.
DEFAULT_STRINGENCY - Static variable in enum class htsjdk.samtools.ValidationStringency
DEFAULT_UNCOMPRESSED_BLOCK_SIZE - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
DEFAULT_VCF_EXTENSION - Static variable in class htsjdk.samtools.Defaults
  The extension to assume a vcf has when the actual file doesn't have an extension, useful for when outputing to /dev/stdout, for example.
defaultBinSize() - Method in class htsjdk.tribble.index.linear.LinearIndexCreator
  the current default bin size
DefaultBitInputStream - Class in htsjdk.samtools.cram.io
  Must not read from delegate unless no bits left in the buffer!!!
DefaultBitInputStream(InputStream) - Constructor for class htsjdk.samtools.cram.io.DefaultBitInputStream
DefaultBitOutputStream - Class in htsjdk.samtools.cram.io
DefaultBitOutputStream(OutputStream) - Constructor for class htsjdk.samtools.cram.io.DefaultBitOutputStream
DefaultingMap(CollectionUtil.DefaultingMap.Factory, boolean) - Constructor for class htsjdk.samtools.util.CollectionUtil.DefaultingMap
  Creates a defaulting map that generates defaults from the provided factory.
DefaultingMap(V) - Constructor for class htsjdk.samtools.util.CollectionUtil.DefaultingMap
  Creates a defaulting map which defaults to the provided value and with injecting-on-default disabled.
Defaults - Class in htsjdk.samtools
  Embodies defaults for global values that affect how the SAM JDK operates.
Defaults() - Constructor for class htsjdk.samtools.Defaults
DEFAULTS - Static variable in enum class htsjdk.samtools.SamReaderFactory.Option
DefaultSAMRecordFactory - Class in htsjdk.samtools
  Default factory for creating SAM and BAM records used by the `SamReader` classes.
DefaultSAMRecordFactory() - Constructor for class htsjdk.samtools.DefaultSAMRecordFactory
DEFECTIVE - Enum constant in enum class htsjdk.samtools.util.BlockCompressedInputStream.FileTermination
DeflaterFactory - Class in htsjdk.samtools.util.zip
  Factory for `Deflater` objects used by `BlockCompressedOutputStream`.
DeflaterFactory() - Constructor for class htsjdk.samtools.util.zip.DeflaterFactory
DEL - Enum constant in enum class htsjdk.variant.variantcontext.StructuralVariantType
  Deletion relative to the reference
DelegatingIterator<T> - Class in htsjdk.samtools.util
  Simple iterator class that delegates all method calls to an underlying iterator.
DelegatingIterator(Iterator) - Constructor for class htsjdk.samtools.util.DelegatingIterator
deleteDirectoryTree(File) - Static method in class htsjdk.samtools.util.IOUtil
  Delete the given file or directory.
deleteFiles(File...) - Static method in class htsjdk.samtools.util.IOUtil
  Delete a list of files, and write a warning message if one could not be deleted.
deleteFiles(Iterable) - Static method in class htsjdk.samtools.util.IOUtil
deleteOnExit(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Register a `Path` for deletion on JVM exit.
DeleteOnExitPathHook - Class in htsjdk.samtools.util.nio
  Class to hold a set of `Path` to be delete on the JVM exit through a shutdown hook.
deletePath(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Attempt to delete a single path and log an error if it is not deleted.
deletePaths(Iterable) - Static method in class htsjdk.samtools.util.IOUtil
  Iterate through Paths and delete each one.
deletePaths(Path...) - Static method in class htsjdk.samtools.util.IOUtil
Deletion - Class in htsjdk.samtools.cram.encoding.readfeatures
  A read feature representing a deletion of one or more bases similar to `CigarOperator.D`.
Deletion - Enum constant in enum class htsjdk.samtools.util.AbstractRecordAndOffset.AlignmentType
Deletion(int, int) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Deletion
DELETION - Static variable in enum class htsjdk.samtools.CigarOperator
DELETION_ALLELE_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
DEPTH_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
deriveTypeFromKeyAndType(String, Object) - Static method in class htsjdk.samtools.cram.structure.ReadTag
  Create a ReadTag from a 4-character "XX:T" key-and-type string and a value.
deriveTypeFromValue(String, Object) - Static method in class htsjdk.samtools.cram.structure.ReadTag
  Create a ReadTag by inferring the CRAM type code from the Java type of the value.
description - Variable in enum class htsjdk.samtools.DownsamplingIteratorFactory.Strategy
DESCRIPTION_ATTRIBUTE - Static variable in class htsjdk.variant.vcf.VCFSimpleHeaderLine
DESCRIPTION_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
DESCRIPTION_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
deserializeCRAMRecords(CompressorCache, ValidationStringency) - Method in class htsjdk.samtools.cram.structure.Slice
  Reads and decodes the underlying blocks and returns a list of CRAMCompressionRecord.
detect(long, FastqReader...) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
  Reads through the records in the provided fastq reader and uses their quality scores to determine the quality format used in the fastq.
detect(long, SamReader) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
detect(long, CloseableIterator) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
detect(long, CloseableIterator, boolean) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
  Reads through the records in the provided SAM reader and uses their quality scores to determine the quality format used in the SAM.
detect(FastqReader...) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
detect(SamReader) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
detect(SamReader, FastqQualityFormat) - Static method in class htsjdk.samtools.util.QualityEncodingDetector
  Reads through the records in the provided SAM reader and uses their quality scores to sanity check the expected quality passed in.
determineIntegerType(int) - Static method in class htsjdk.variant.bcf2.BCF2Utils
determineIntegerType(int[]) - Static method in class htsjdk.variant.bcf2.BCF2Utils
determineIntegerType(List) - Static method in class htsjdk.variant.bcf2.BCF2Utils
determineOutputTypeFromFile(File) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Attempts to determine the type of file/data to write based on the File path being written to.
determineOutputTypeFromFile(Path) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Attempts to determine the type of file/data to write based on the File path being written to.
determineType() - Method in class htsjdk.variant.variantcontext.Genotype
  Internal code to determine the type of the genotype from the alleles vector
diagnosticLiftover(Interval) - Method in class htsjdk.samtools.liftover.LiftOver
DICT - Static variable in class htsjdk.samtools.util.FileExtensions
DICT_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  since June 2019 Use `FileExtensions.DICT` instead.
difference(IntervalList, IntervalList) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for finding the difference between two IntervalLists.
difference(Collection, Collection) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for finding the difference between two IntervalLists.
DIRECTIVE_START - Static variable in class htsjdk.tribble.gff.Gff3Constants
disable(SamReaderFactory.Option...) - Method in class htsjdk.samtools.SamReaderFactory
  Disables the provided `SamReaderFactory.Option`s, then returns itself.
DISABLE_SNAPPY_COMPRESSOR - Static variable in class htsjdk.samtools.Defaults
  Disable use of the Snappy compressor.
DISABLE_SNAPPY_PROPERTY_NAME - Static variable in class htsjdk.samtools.Defaults
  The name of the system property that disables snappy.
disableOnTheFlyModifications() - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  Forces all VCFCodecs to not perform any on the fly modifications to the VCF header of VCF records.
disconnect() - Method in class htsjdk.samtools.util.ftp.FTPClient
  Disconnects from the host to which we are currently connected.
DiskBackedQueue<E> - Class in htsjdk.samtools.util
  A single-ended FIFO queue.
DiskBasedBAMFileIndex - Class in htsjdk.samtools
  A class for reading BAM file indices, hitting the disk once per query.
DiskBasedBAMFileIndex(SeekableStream, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.DiskBasedBAMFileIndex
DiskBasedBAMFileIndex(File, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.DiskBasedBAMFileIndex
DiskBasedBAMFileIndex(File, SAMSequenceDictionary, boolean) - Constructor for class htsjdk.samtools.DiskBasedBAMFileIndex
divideByHistogram(Histogram) - Method in class htsjdk.samtools.util.Histogram
  Immutable method that divides the current Histogram by an input Histogram and generates a new one Throws an exception if the bins don't match up exactly
DL_DeletionLength - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
DNBSEQ - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  MGI/BGI
DO_NOT_WRITE_GENOTYPES - Enum constant in enum class htsjdk.variant.variantcontext.writer.Options
DO_REVERSE_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.fqzcomp.FQZGlobalFlags
done(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
doneAdding() - Method in class htsjdk.samtools.util.SortingCollection
  This method can be called after caller is done adding to collection, in order to possibly free up memory.
doneAddingStartIteration() - Method in class htsjdk.samtools.util.SortingLongCollection
  This method must be called after done adding, and before calling hasNext() or next().
DONT_MEMORY_MAP_INDEX - Enum constant in enum class htsjdk.samtools.SamReaderFactory.Option
  The factory's `SamReader`s' will not use memory mapping for accessing index files (which is used by default).
doOnTheFlyModifications - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
  If true, then we'll magically fix up VCF headers on the fly when we read them in
doReverse() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZGlobalFlags
DownsamplingIterator - Class in htsjdk.samtools
  Abstract base class for all DownsamplingIterators that provides a uniform interface for recording and reporting statistics bout how many records have been kept and discarded.
DownsamplingIterator(double) - Constructor for class htsjdk.samtools.DownsamplingIterator
  Constructs a downsampling iterator that aims to retain the targetProportion of reads.
DownsamplingIteratorFactory - Class in htsjdk.samtools
  A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while meeting various criteria.
DownsamplingIteratorFactory() - Constructor for class htsjdk.samtools.DownsamplingIteratorFactory
DownsamplingIteratorFactory.Strategy - Enum Class in htsjdk.samtools
  Describes the available downsampling strategies.
DP(int) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype has this DP value
DPAccessor() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.DPAccessor
DUP - Enum constant in enum class htsjdk.variant.variantcontext.StructuralVariantType
  Region of elevated copy number relative to the reference
DUP_PREVIOUS_STREAM_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
duplicate - Enum constant in enum class htsjdk.samtools.SAMFileHeader.SortOrder
DUPLICATE_PROGRAM_GROUP_ID - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Same program group id appears more than once
DUPLICATE_READ - Enum constant in enum class htsjdk.samtools.SAMFlag
DUPLICATE_READ_GROUP_ID - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Same read group id appears more than once
DUPLICATE_SAM_TAG - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  A duplicate Sam tag was found in a record.
DuplicateReadFilter - Class in htsjdk.samtools.filter
  Filter out SAMRecords with DuplicateRead flag set $Id$
DuplicateReadFilter() - Constructor for class htsjdk.samtools.filter.DuplicateReadFilter
DuplicateScoringStrategy - Class in htsjdk.samtools
  This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate during duplicate marking (see MarkDuplicates).
DuplicateScoringStrategy() - Constructor for class htsjdk.samtools.DuplicateScoringStrategy
DuplicateScoringStrategy.ScoringStrategy - Enum Class in htsjdk.samtools
DuplicateSet - Class in htsjdk.samtools
  Stores a set of records that are duplicates of each other.
DuplicateSet() - Constructor for class htsjdk.samtools.DuplicateSet
  Sets the duplicate flag by default
DuplicateSet(boolean) - Constructor for class htsjdk.samtools.DuplicateSet
DuplicateSet(boolean, SAMRecordDuplicateComparator) - Constructor for class htsjdk.samtools.DuplicateSet
DuplicateSet(SAMRecordDuplicateComparator) - Constructor for class htsjdk.samtools.DuplicateSet
duplicateSetCompare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordDuplicateComparator
  Less stringent than compare, such that two records are equal enough such that their ordering within their duplicate set would be arbitrary.
DuplicateSetIterator - Class in htsjdk.samtools
  An iterator of sets of duplicates.
DuplicateSetIterator(CloseableIterator, SAMFileHeader) - Constructor for class htsjdk.samtools.DuplicateSetIterator
DuplicateSetIterator(CloseableIterator, SAMFileHeader, boolean) - Constructor for class htsjdk.samtools.DuplicateSetIterator
DuplicateSetIterator(CloseableIterator, SAMFileHeader, boolean, SAMRecordDuplicateComparator) - Constructor for class htsjdk.samtools.DuplicateSetIterator
DuplicateSetIterator(CloseableIterator, SAMFileHeader, boolean, SAMRecordDuplicateComparator, Log) - Constructor for class htsjdk.samtools.DuplicateSetIterator
  Allows the user of this iterator to skip the sorting of the input if the input is already sorted.
DupOrDiffToken(byte, String) - Constructor for class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken.DupOrDiffToken
DynamicIndexCreator - Class in htsjdk.tribble.index
  A DynamicIndexCreator creates the proper index based on an `IndexFactory.IndexBalanceApproach` and the characteristics of the file.
DynamicIndexCreator(File, IndexFactory.IndexBalanceApproach) - Constructor for class htsjdk.tribble.index.DynamicIndexCreator
DynamicIndexCreator(Path, IndexFactory.IndexBalanceApproach) - Constructor for class htsjdk.tribble.index.DynamicIndexCreator

## E

E2 - Enum constant in enum class htsjdk.samtools.SAMTag
E2 - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
E2_BASE_EQUALS_PRIMARY_BASE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Secondary base calls should not be the same as primary, unless one or the other is N
eagerDecode() - Method in class htsjdk.samtools.BAMRecord
  Force all the lazily-initialized attributes to be decoded.
eagerDecode() - Method in class htsjdk.samtools.SAMRecord
  Force all lazily-initialized data members to be initialized.
EAGERLY_DECODE - Enum constant in enum class htsjdk.samtools.SamReaderFactory.Option
  Eagerly decode `SamReader`'s `SAMRecord`s, which can reduce memory footprint if many fields are being read per record, or if fields are going to be updated.
EBI_REFERENCE_SERVICE_URL_MASK - Static variable in class htsjdk.samtools.Defaults
  A mask (pattern) to use when building EBI reference service URL for a given MD5 checksum.
EdgeReadIterator - Class in htsjdk.samtools.util
  Iterator that traverses a SAM File, accumulating information on a per-locus basis.
EdgeReadIterator(SamReader) - Constructor for class htsjdk.samtools.util.EdgeReadIterator
  Prepare to iterate through the given SAM records, skipping non-primary alignments.
EdgeReadIterator(SamReader, IntervalList) - Constructor for class htsjdk.samtools.util.EdgeReadIterator
  Prepare to iterate through the given SAM records, skipping non-primary alignments.
EdgeReadIterator(SamReader, IntervalList, boolean) - Constructor for class htsjdk.samtools.util.EdgeReadIterator
  Prepare to iterate through the given SAM records, skipping non-primary alignments
EdgingRecordAndOffset - Class in htsjdk.samtools.util
  Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds to the base and quality for the start of alignment block at the genomic position described by the AbstractLocusInfo.
EdgingRecordAndOffset.Type - Enum Class in htsjdk.samtools.util
  Describes the type of `TypedRecordAndOffset`, whether it represents the start or the end of an alignment block.
element() - Method in class htsjdk.samtools.util.DiskBackedQueue
ELEMENT - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Element Biosciences
EMBEDDED_REFERENCE_ABSENT_CONTENT_ID - Static variable in class htsjdk.samtools.cram.structure.Slice
emitSafeRecords() - Method in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
EMPTY_ALLELE - Static variable in class htsjdk.variant.vcf.VCFConstants
EMPTY_ALTERNATE_ALLELE_FIELD - Static variable in class htsjdk.variant.vcf.VCFConstants
EMPTY_GENOTYPE - Static variable in class htsjdk.variant.vcf.VCFConstants
EMPTY_GZIP_BLOCK - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
EMPTY_HEADER - Static variable in class htsjdk.tribble.FeatureCodecHeader
  A public instance representing no header
EMPTY_ID_FIELD - Static variable in class htsjdk.variant.vcf.VCFConstants
EMPTY_INFO_FIELD - Static variable in class htsjdk.variant.vcf.VCFConstants
EMPTY_READ - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
EMPTY_STRING - Static variable in class htsjdk.samtools.util.StringUtil
  Returns `Object.toString()` of the provided value if it isn't null; "" otherwise.
emptyID() - Method in class htsjdk.variant.variantcontext.VariantContext
enable(SamReaderFactory.Option...) - Method in class htsjdk.samtools.SamReaderFactory
  Enables the provided `SamReaderFactory.Option`s, then returns itself.
enableAdaptiveIndexing - Static variable in class htsjdk.tribble.index.linear.LinearIndex
enableCrcChecking(boolean) - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Set whether to check CRC for subsequent iterator or query requests.
enableFileSource(SamReader, boolean) - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Set whether to write the source of every read into the source SAMRecords.
enableIndexCaching(boolean) - Method in class htsjdk.samtools.BAMFileReader
  If true, uses the caching version of the index reader.
enableIndexMemoryMapping(boolean) - Method in class htsjdk.samtools.BAMFileReader
  If false, disable the use of memory mapping for accessing index files (default behavior is to use memory mapping).
EnaRefService - Class in htsjdk.samtools.cram.ref
EnaRefService() - Constructor for class htsjdk.samtools.cram.ref.EnaRefService
encloses(int, int, int, int) - Static method in class htsjdk.samtools.util.CoordMath
  Returns true if the "inner" coords and totally enclosed by the "outer" coords.
encode() - Method in enum class htsjdk.tribble.annotation.Strand
  Returns a string representation of this `Strand`
encode(Cigar) - Static method in class htsjdk.samtools.TextCigarCodec
  Convert from Cigar class representation to String.
encode(FastqRecord) - Static method in class htsjdk.samtools.fastq.FastqEncoder
  Encodes a FastqRecord in the String FASTQ format.
encode(SAMRecord) - Method in class htsjdk.samtools.BAMRecordCodec
  Write object to OutputStream.
encode(SAMRecord) - Static method in class htsjdk.samtools.fastq.FastqEncoder
  Encodes a SAMRecord in the String FASTQ format.
encode(SAMSequenceDictionary) - Method in class htsjdk.samtools.SAMSequenceDictionaryCodec
  Convert `SAMSequenceDictionary` from in-memory representation to text representation.
encode(Interval) - Method in class htsjdk.samtools.util.IntervalCodec
  Writes the interval to the output stream.
encode(VariantContext) - Method in class htsjdk.variant.vcf.VCFEncoder
  encodes a `VariantContext` as a VCF line Depending on the use case it may be more efficient to `VCFEncoder.write(Appendable, VariantContext)` directly instead of creating an intermediate string.
encode(VariantContext) - Method in class htsjdk.variant.vcf.VCFRecordCodec
encode(Writer, SAMFileHeader) - Method in class htsjdk.samtools.SAMTextHeaderCodec
  Convert SAMFileHeader from in-memory representation to text representation.
encode(Writer, SAMFileHeader, boolean) - Method in class htsjdk.samtools.SAMTextHeaderCodec
  Convert SAMFileHeader from in-memory representation to text representation.
encode(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
  Totally generic encoder that examines o, determines the best way to encode it, and encodes it This method is incredibly slow, but it's only used for UnitTests so it doesn't matter
encode(String, Object) - Method in class htsjdk.samtools.TextTagCodec
  Convert in-memory representation of tag to SAM text representation.
encode(KEY, REC) - Method in interface htsjdk.samtools.CoordinateSortedPairInfoMap.Codec
  Write object to output stream.
encode(T) - Method in interface htsjdk.samtools.util.SortingCollection.Codec
  Write object to output stream
encodeAsChar() - Method in enum class htsjdk.tribble.annotation.Strand
  Returns a single char encoding of this `Strand`.
encodeGtField(VariantContext, Genotype) - Static method in class htsjdk.variant.vcf.VCFEncoder
  Easy way to generate the GT field for a Genotype.
encodeHeaderLine(boolean) - Method in class htsjdk.samtools.SAMSequenceDictionaryCodec
  Write Header line.
encodePack(ByteBuffer, ByteBuffer, int[], int[], int) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Pack input symbols into a smaller number of bits per value based on the number of distinct symbols.
encodeRawBytes(int, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeRawChar(byte) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeRawFloat(double) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeRawInt(int, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeRawMissingValue(BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeRawMissingValues(int, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeRawString(String, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeRawValue(T, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeRawValues(Collection, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeSequenceRecord(SAMSequenceRecord) - Method in class htsjdk.samtools.SAMSequenceDictionaryCodec
  Write `SAMSequenceRecord`.
EncodeToken - Class in htsjdk.samtools.cram.compression.nametokenisation.tokens
  A token that represents one fragment of a read name that has been tokenized.
EncodeToken(byte, String, int) - Constructor for class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken
EncodeToken(byte, String, String) - Constructor for class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken
  Token types TOKEN_DELTA, TOKEN_DELTA0, TOKEN_DIGITS, TOKEN_DIGITS0 all have a relative value that differs from the actual value of the original fragment, and for those token types, we need to preserve both during the encoding process.
EncodeToken.DupOrDiffToken - Class in htsjdk.samtools.cram.compression.nametokenisation.tokens
EncodeToken.EndToken - Class in htsjdk.samtools.cram.compression.nametokenisation.tokens
encodeType(int, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeTyped(Object, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeTyped(List, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeTypeDescriptor(int, BCF2Type) - Static method in class htsjdk.variant.bcf2.BCF2Utils
encodeTypedFloat(double) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeTypedInt(int) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeTypedInt(int, BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeTypedMissing(BCF2Type) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeTypedString(byte[]) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeTypedString(String) - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
encodeUntypedTag(String, Object) - Method in class htsjdk.samtools.TextTagCodec
  Encode a standard header tag, which should not have a type field.
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.AtomicInt
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
  Key abstract method that should encode a value of the given type into the encoder.
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Flag
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Float
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.GenericInts
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.IntArray
encodeValue(BCF2Encoder, Object, BCF2Type, int) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
EncodingDescriptor - Class in htsjdk.samtools.cram.structure
  A class for representing an encoding, including encoding-specific parameters, suitable for serialization to/from a stream.
EncodingDescriptor(EncodingID, byte[]) - Constructor for class htsjdk.samtools.cram.structure.EncodingDescriptor
  Representation of an encoding, including untyped encoding-specific parameters in the form of an array of bytes.
EncodingFactory - Class in htsjdk.samtools.cram.encoding
  A helper class to choose and instantiate an appropriate `CRAMEncoding` given a `DataSeriesType` and an `EncodingDescriptor`.
EncodingFactory() - Constructor for class htsjdk.samtools.cram.encoding.EncodingFactory
EncodingID - Enum Class in htsjdk.samtools.cram.structure
  Encoding ID as specified by Section 3 of the CRAM spec.
end - Variable in class htsjdk.samtools.QueryInterval
  1-based, inclusive.
end - Variable in class htsjdk.tribble.bed.SimpleBEDFeature
end - Variable in class htsjdk.tribble.MutableFeature
end - Variable in class htsjdk.tribble.util.TabixUtils.TIntv
END - Enum constant in enum class htsjdk.samtools.util.EdgingRecordAndOffset.Type
END_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
END_OF_LINE_CHARACTER - Static variable in class htsjdk.tribble.gff.Gff3Constants
endOfBlock() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
endPositionColumn - Variable in class htsjdk.tribble.index.tabix.TabixFormat
  One-based index of the column in the file being indexed containing the end position.
endsAtStartOf(QueryInterval) - Method in class htsjdk.samtools.QueryInterval
EndToken() - Constructor for class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken.EndToken
engine - Static variable in class htsjdk.variant.variantcontext.VariantContextUtils
  Use a `Lazy` `JexlEngine` instance to avoid class-loading issues.
ensureSampleNameMap() - Method in class htsjdk.variant.variantcontext.GenotypesContext
ensureSampleNameMap() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
  Overrides the ensure* functionality.
ensureSampleOrdering() - Method in class htsjdk.variant.variantcontext.GenotypesContext
ensureSampleOrdering() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
entrySet() - Method in class htsjdk.samtools.util.IntervalTreeMap
enumToBinary(CigarOperator) - Static method in enum class htsjdk.samtools.CigarOperator
enumToCharacter(CigarOperator) - Static method in enum class htsjdk.samtools.CigarOperator
  Returns the character that should be used within a SAM file.
eof() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
eof() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
eof() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
eof() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
eof() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
eof() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
eof() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
eof() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
eof() - Method in class htsjdk.samtools.seekablestream.SeekableStream
eof() - Method in class htsjdk.samtools.util.FastLineReader
EOF_ALIGNMENT_SPAN - Static variable in class htsjdk.samtools.cram.build.CramIO
EOF_ALIGNMENT_START - Static variable in class htsjdk.samtools.cram.build.CramIO
EOF_BLOCK_SIZE_V2 - Static variable in class htsjdk.samtools.cram.build.CramIO
EOF_BLOCK_SIZE_V3 - Static variable in class htsjdk.samtools.cram.build.CramIO
EOF_CONTAINER_CONTEXT - Static variable in class htsjdk.samtools.cram.structure.AlignmentContext
EOF_VALUE - Static variable in interface htsjdk.samtools.util.LineReader
EQ - Enum constant in enum class htsjdk.samtools.CigarOperator
  Matches the reference.
equals(Allele, boolean) - Method in interface htsjdk.variant.variantcontext.Allele
equals(Allele, boolean) - Method in class htsjdk.variant.variantcontext.SimpleAllele
  Returns true if this and other are equal.
equals(Object) - Method in class htsjdk.beta.io.bundle.Bundle
equals(Object) - Method in class htsjdk.beta.io.bundle.BundleResourceBase
equals(Object) - Method in class htsjdk.beta.io.bundle.InputStreamResource
equals(Object) - Method in class htsjdk.beta.io.bundle.IOPathResource
equals(Object) - Method in class htsjdk.beta.io.bundle.OutputStreamResource
equals(Object) - Method in class htsjdk.beta.io.bundle.SeekableStreamResource
equals(Object) - Method in class htsjdk.beta.plugin.HtsVersion
equals(Object) - Method in class htsjdk.io.HtsPath
equals(Object) - Method in class htsjdk.samtools.Bin
  See whether two bins are equal.
equals(Object) - Method in class htsjdk.samtools.BinningIndexContent.BinList
equals(Object) - Method in class htsjdk.samtools.BinningIndexContent
equals(Object) - Method in class htsjdk.samtools.Chunk
equals(Object) - Method in class htsjdk.samtools.Cigar
equals(Object) - Method in class htsjdk.samtools.CigarElement
equals(Object) - Method in class htsjdk.samtools.cram.common.CRAMVersion
  Check if another version is exactly the same as this one.
equals(Object) - Method in class htsjdk.samtools.cram.common.MutableInt
equals(Object) - Method in class htsjdk.samtools.cram.compression.ExternalCompressor
equals(Object) - Method in class htsjdk.samtools.cram.compression.GZIPExternalCompressor
equals(Object) - Method in class htsjdk.samtools.cram.compression.RANS4x8ExternalCompressor
equals(Object) - Method in class htsjdk.samtools.cram.compression.RANSNx16ExternalCompressor
equals(Object) - Method in class htsjdk.samtools.cram.CRAIEntry
equals(Object) - Method in class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanIntegerEncoding
equals(Object) - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParams
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
equals(Object) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
equals(Object) - Method in class htsjdk.samtools.cram.ref.ReferenceContext
equals(Object) - Method in class htsjdk.samtools.cram.structure.AlignmentContext
equals(Object) - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
equals(Object) - Method in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
equals(Object) - Method in record class htsjdk.samtools.cram.structure.CompressorDescriptor
  Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
equals(Object) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
equals(Object) - Method in class htsjdk.samtools.cram.structure.CramHeader
equals(Object) - Method in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
equals(Object) - Method in class htsjdk.samtools.cram.structure.EncodingDescriptor
equals(Object) - Method in class htsjdk.samtools.cram.structure.ReadTag
equals(Object) - Method in class htsjdk.samtools.fastq.FastqRecord
equals(Object) - Method in class htsjdk.samtools.LinearIndex
equals(Object) - Method in class htsjdk.samtools.metrics.MetricBase
  An equals method that checks equality by asserting that the classes are of the exact same type and that all public fields are equivalent.
equals(Object) - Method in class htsjdk.samtools.metrics.MetricsFile
  Checks that the headers, metrics and histogram are all equal.
equals(Object) - Method in class htsjdk.samtools.metrics.StringHeader
  Checks equality on the value of the header.
equals(Object) - Method in class htsjdk.samtools.metrics.VersionHeader
  Equals method that checks that both the item and version string are equal.
equals(Object) - Method in class htsjdk.samtools.QueryInterval
equals(Object) - Method in class htsjdk.samtools.reference.FastaSequenceIndex
  Compare two FastaSequenceIndex objects for equality.
equals(Object) - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
  Compare this index entry to another index entry.
equals(Object) - Method in class htsjdk.samtools.SAMBinaryTagAndValue
equals(Object) - Method in class htsjdk.samtools.SAMFileHeader
equals(Object) - Method in class htsjdk.samtools.SAMProgramRecord
equals(Object) - Method in class htsjdk.samtools.SAMReadGroupRecord
equals(Object) - Method in class htsjdk.samtools.SAMRecord
equals(Object) - Method in class htsjdk.samtools.SAMSequenceDictionary
  Returns `true` if the two dictionaries are the same.
equals(Object) - Method in class htsjdk.samtools.SAMSequenceRecord
equals(Object) - Method in class htsjdk.samtools.SBIIndex
equals(Object) - Method in class htsjdk.samtools.SBIIndex.Header
equals(Object) - Method in class htsjdk.samtools.util.GZIIndex
equals(Object) - Method in class htsjdk.samtools.util.GZIIndex.IndexEntry
equals(Object) - Method in class htsjdk.samtools.util.Histogram.Bin
  Checks the equality of the bin by ID and value.
equals(Object) - Method in class htsjdk.samtools.util.Histogram
  Checks that the labels and values in the two histograms are identical.
equals(Object) - Method in class htsjdk.samtools.util.Interval
  Equals method that agrees with `Interval.compareTo(Interval)`.
equals(Object) - Method in class htsjdk.samtools.util.IntervalList
equals(Object) - Method in class htsjdk.samtools.util.IntervalTreeMap
equals(Object) - Method in class htsjdk.samtools.util.RelativeIso8601Date
equals(Object) - Method in class htsjdk.samtools.util.Tuple
equals(Object) - Method in class htsjdk.tribble.gff.Gff3BaseData
equals(Object) - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
equals(Object) - Method in class htsjdk.tribble.gff.SequenceRegion
equals(Object) - Method in class htsjdk.tribble.index.Block
equals(Object) - Method in class htsjdk.tribble.index.interval.Interval
equals(Object) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
equals(Object) - Method in class htsjdk.tribble.index.tabix.TabixFormat
equals(Object) - Method in class htsjdk.tribble.index.tabix.TabixIndex
equals(Object) - Method in class htsjdk.variant.bcf2.BCFVersion
equals(Object) - Method in interface htsjdk.variant.variantcontext.Allele
equals(Object) - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
equals(Object) - Method in class htsjdk.variant.variantcontext.SimpleAllele
equals(Object) - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
  returns true if we're equal to another compound header line
equals(Object) - Method in class htsjdk.variant.vcf.VCFContigHeaderLine
equals(Object) - Method in class htsjdk.variant.vcf.VCFHeaderLine
equals(Object) - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
equalsExcludingDescription(VCFCompoundHeaderLine) - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
equalsIgnoreOrder(Bundle, Bundle) - Static method in class htsjdk.beta.io.bundle.Bundle
equalsIgnoreProperties(Object) - Method in class htsjdk.tribble.index.AbstractIndex
equalsIgnoreProperties(Object) - Method in interface htsjdk.tribble.index.Index
  Returns true if this and obj are 'effectively' equivalent indices.
equalsIgnoreProperties(Object) - Method in class htsjdk.tribble.index.tabix.TabixIndex
equalsWithStrandAndName(Object) - Method in class htsjdk.samtools.util.Interval
  Equals method that also checks strand and name
equivalent(SAMProgramRecord) - Method in class htsjdk.samtools.SAMProgramRecord
equivalent(SAMReadGroupRecord) - Method in class htsjdk.samtools.SAMReadGroupRecord
error(Object...) - Method in class htsjdk.samtools.util.Log
  Logs one or more message parts at level error.
error(String) - Method in class htsjdk.samtools.fastq.FastqReader
  Generates an error message with line number information.
error(String) - Method in class htsjdk.variant.bcf2.BCF2Codec
error(Throwable, Object...) - Method in class htsjdk.samtools.util.Log
  Logs a Throwable and optional message parts at level error.
error(Supplier) - Method in class htsjdk.samtools.util.Log
  Logs a message part at level error.
ERROR - Enum constant in enum class htsjdk.samtools.SAMValidationError.Severity
ERROR - Enum constant in enum class htsjdk.samtools.util.Log.LogLevel
escapeString(String) - Method in class htsjdk.tribble.gff.Gff3Writer
  escape a String.
estimateSdViaMad() - Method in class htsjdk.samtools.util.Histogram
  Returns a value that is intended to estimate the mean of the distribution, if the distribution is essentially normal, by using the median absolute deviation to remove the effect of erroneous massive outliers.
ExampleBinaryCodec - Class in htsjdk.tribble.example
  An example binary codec that encodes / decodes contig / start / stop values via DataInputStreams
ExampleBinaryCodec() - Constructor for class htsjdk.tribble.example.ExampleBinaryCodec
Example Content Type: Reads - Section in interface htsjdk.beta.plugin.HtsCodec
ExampleSamUsage - Class in htsjdk.samtools.example
ExampleSamUsage() - Constructor for class htsjdk.samtools.example.ExampleSamUsage
EXCLUDE_INTERVALS_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
execute(String) - Static method in class htsjdk.samtools.util.ProcessExecutor
  Executes the command via Runtime.getRuntime().exec() then writes stderr to log.error and stdout to log.info and blocks until the command is complete.
execute(String[]) - Static method in class htsjdk.samtools.util.ProcessExecutor
  Executes the command via Runtime.getRuntime().exec() then writes stderr to log.error and stdout to log.info and blocks until the command is complete.
execute(String[], String) - Static method in class htsjdk.samtools.util.ProcessExecutor
  Executes the command via Runtime.getRuntime().exec(), writes `outputStreamString` to the process output stream if it is not null, then writes stderr to log.error and stdout to log.info and blocks until the command is complete.
executeAndReturnInterleavedOutput(String) - Static method in class htsjdk.samtools.util.ProcessExecutor
  Execute the command and capture stdout and stderr.
executeAndReturnInterleavedOutput(String[]) - Static method in class htsjdk.samtools.util.ProcessExecutor
  Execute the command and capture stdout and stderr.
executeAndReturnResult(String) - Static method in class htsjdk.samtools.util.ProcessExecutor
executeCommand(String) - Method in class htsjdk.samtools.util.ftp.FTPClient
  Executes the given FTP command on our current connection, returning the three digit response code from the server.
EXHAUSTIVE - Enum constant in enum class htsjdk.samtools.BamIndexValidator.IndexValidationStringency
exhaustivelyTestIndex(SamReader) - Static method in class htsjdk.samtools.BamIndexValidator
exists() - Method in class htsjdk.tribble.util.FTPHelper
exists() - Method in class htsjdk.tribble.util.HTTPHelper
exists() - Method in class htsjdk.tribble.util.RemoteURLHelper
exists() - Method in interface htsjdk.tribble.util.URLHelper
exitStatus - Variable in class htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput
ExitStatusAndOutput(int, String, String) - Constructor for class htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput
Exon(int, int) - Constructor for class htsjdk.tribble.bed.FullBEDFeature.Exon
  Constructs ...
Exon2(int, int, int, int) - Constructor for class htsjdk.tribble.bed.FullBEDFeature.Exon2
exp - Variable in class htsjdk.variant.variantcontext.VariantContextUtils.JexlVCMatchExp
EXPECTED_ALLELE_COUNT_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
explodeStringList(String) - Static method in class htsjdk.variant.bcf2.BCF2Utils
  Inverse operation of collapseStringList.
EXT_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.range.RangeParams
extend(Allele, byte[]) - Static method in interface htsjdk.variant.variantcontext.Allele
extensionMap - Static variable in class htsjdk.beta.codecs.reads.cram.CRAMCodec
EXTERNAL - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockContentType
EXTERNAL - Enum constant in enum class htsjdk.samtools.cram.structure.EncodingID
  Shove the data into a byte array for compressing later with a generic compressor like GZIP.
externalBlockContentId - Variable in class htsjdk.samtools.cram.encoding.external.ExternalEncoding
ExternalByteArrayCodec - Class in htsjdk.samtools.cram.encoding.external
  Encode/decode byte arrays using an External Data Block.
ExternalByteArrayCodec(CRAMByteReader, CRAMByteWriter) - Constructor for class htsjdk.samtools.cram.encoding.external.ExternalByteArrayCodec
ExternalByteArrayEncoding - Class in htsjdk.samtools.cram.encoding.external
ExternalByteArrayEncoding(int) - Constructor for class htsjdk.samtools.cram.encoding.external.ExternalByteArrayEncoding
ExternalByteEncoding - Class in htsjdk.samtools.cram.encoding.external
ExternalByteEncoding(int) - Constructor for class htsjdk.samtools.cram.encoding.external.ExternalByteEncoding
ExternalCompressor - Class in htsjdk.samtools.cram.compression
  Abstract base class for CRAM external block compressors.
ExternalCompressor(BlockCompressionMethod) - Constructor for class htsjdk.samtools.cram.compression.ExternalCompressor
ExternalEncoding<T> - Class in htsjdk.samtools.cram.encoding.external
ExternalEncoding(int) - Constructor for class htsjdk.samtools.cram.encoding.external.ExternalEncoding
ExternalIntegerEncoding - Class in htsjdk.samtools.cram.encoding.external
ExternalIntegerEncoding(int) - Constructor for class htsjdk.samtools.cram.encoding.external.ExternalIntegerEncoding
ExternalLongEncoding - Class in htsjdk.samtools.cram.encoding.external
ExternalLongEncoding(int) - Constructor for class htsjdk.samtools.cram.encoding.external.ExternalLongEncoding
extractDictionary(File) - Static method in class htsjdk.variant.utils.SAMSequenceDictionaryExtractor
  Deprecated.
  in favor of `SAMSequenceDictionaryExtractor.extractDictionary(Path)`
extractDictionary(Path) - Static method in class htsjdk.variant.utils.SAMSequenceDictionaryExtractor
extraStrictValidation(Allele, Allele, Set) - Method in class htsjdk.variant.variantcontext.VariantContext
  Run all extra-strict validation tests on a Variant Context object

## F

FailsVendorReadQualityFilter - Class in htsjdk.samtools.filter
  Filter for filtering out reads that do not pass the quality filter $Id$
FailsVendorReadQualityFilter() - Constructor for class htsjdk.samtools.filter.FailsVendorReadQualityFilter
FAST - Enum constant in enum class htsjdk.samtools.cram.structure.CRAMCompressionProfile
  Speed-optimized profile.
FASTA - Static variable in class htsjdk.beta.plugin.hapref.HaploidReferenceFormats
  Fasta format
FASTA - Static variable in class htsjdk.samtools.util.FileExtensions
  extensions for read files and related formats.
FASTA_DIRECTIVE - Enum constant in enum class htsjdk.tribble.gff.Gff3Codec.Gff3Directive
FASTA_EXTENSIONS - Static variable in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Deprecated.
  since June 2019 Use `FileExtensions.FASTA` instead.
FASTA_INDEX - Static variable in class htsjdk.samtools.util.FileExtensions
FASTA_INDEX_EXTENSION - Static variable in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Deprecated.
  since June 2019 Use `FileExtensions.FASTA_INDEX` instead.
FASTACodecV1_0 - Class in htsjdk.beta.codecs.hapref.fasta
  The v1.0 FASTA codec.
FASTACodecV1_0() - Constructor for class htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0
FASTADecoderV1_0 - Class in htsjdk.beta.codecs.hapref.fasta
  The v1.0 FASTA decoder.
FASTADecoderV1_0(Bundle) - Constructor for class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
FastaReferenceWriter - Class in htsjdk.samtools.reference
  Writes a FASTA formatted reference file.
FastaReferenceWriterBuilder - Class in htsjdk.samtools.reference
  Buider for a `FastaReferenceWriter`
FastaReferenceWriterBuilder() - Constructor for class htsjdk.samtools.reference.FastaReferenceWriterBuilder
FastaSequenceFile - Class in htsjdk.samtools.reference
  Implementation of ReferenceSequenceFile for reading from FASTA files.
FastaSequenceFile(IOPath, IOPath, boolean) - Constructor for class htsjdk.samtools.reference.FastaSequenceFile
  Constructs a FastaSequenceFile that reads from the specified fasta and dictionary file.
FastaSequenceFile(File, boolean) - Constructor for class htsjdk.samtools.reference.FastaSequenceFile
  Constructs a FastaSequenceFile that reads from the specified file.
FastaSequenceFile(String, SeekableStream, SAMSequenceDictionary, boolean) - Constructor for class htsjdk.samtools.reference.FastaSequenceFile
  Constructs a FastaSequenceFile that reads from the specified stream (which must not be compressed, i.e.
FastaSequenceFile(Path, boolean) - Constructor for class htsjdk.samtools.reference.FastaSequenceFile
  Constructs a FastaSequenceFile that reads from the specified file.
FastaSequenceIndex - Class in htsjdk.samtools.reference
  Reads/writes a fasta index file (.fai), as generated by `samtools faidx`.
FastaSequenceIndex() - Constructor for class htsjdk.samtools.reference.FastaSequenceIndex
  Empty, protected constructor for unit testing.
FastaSequenceIndex(File) - Constructor for class htsjdk.samtools.reference.FastaSequenceIndex
  Build a sequence index from the specified file.
FastaSequenceIndex(InputStream) - Constructor for class htsjdk.samtools.reference.FastaSequenceIndex
  Build a sequence index from the specified input stream.
FastaSequenceIndex(Path) - Constructor for class htsjdk.samtools.reference.FastaSequenceIndex
  Build a sequence index from the specified file.
FastaSequenceIndexCreator - Class in htsjdk.samtools.reference
  Static methods to create an `FastaSequenceIndex`.
FastaSequenceIndexEntry - Class in htsjdk.samtools.reference
  Hold an individual entry in a fasta sequence index file.
FastaSequenceIndexEntry(String, long, long, int, int, int) - Constructor for class htsjdk.samtools.reference.FastaSequenceIndexEntry
  Create a new entry with the given parameters.
FastGenotype - Class in htsjdk.variant.variantcontext
  This class encompasses all the basic information about a genotype.
FastGenotype(String, List, boolean, int, int, int[], int[], String, Map) - Constructor for class htsjdk.variant.variantcontext.FastGenotype
  The only way to make one of these, for use by GenotypeBuilder only
FastLineReader - Class in htsjdk.samtools.util
  Line-oriented InputStream reader that uses one buffer for disk buffering and line-termination-finding, in order to improve performance.
FastLineReader(InputStream) - Constructor for class htsjdk.samtools.util.FastLineReader
FASTQ - Enum constant in enum class htsjdk.samtools.fastq.FastqConstants.FastqExtensions
FASTQ - Enum constant in enum class htsjdk.samtools.util.QualityEncodingDetector.FileContext
FASTQ_GZ - Enum constant in enum class htsjdk.samtools.fastq.FastqConstants.FastqExtensions
FastqConstants - Class in htsjdk.samtools.fastq
FastqConstants() - Constructor for class htsjdk.samtools.fastq.FastqConstants
FastqConstants.FastqExtensions - Enum Class in htsjdk.samtools.fastq
FastqEncoder - Class in htsjdk.samtools.fastq
  Codec for encoding records into FASTQ format.
FastqQualityFormat - Enum Class in htsjdk.samtools.util
  Enumeration for FastQ quality score formats formats.
FastqReader - Class in htsjdk.samtools.fastq
  Reads a FASTQ file with four lines per record.
FastqReader(BufferedReader) - Constructor for class htsjdk.samtools.fastq.FastqReader
FastqReader(File) - Constructor for class htsjdk.samtools.fastq.FastqReader
FastqReader(File, boolean) - Constructor for class htsjdk.samtools.fastq.FastqReader
  Constructor
FastqReader(File, BufferedReader) - Constructor for class htsjdk.samtools.fastq.FastqReader
FastqReader(File, BufferedReader, boolean) - Constructor for class htsjdk.samtools.fastq.FastqReader
  Constructor
FastqReader.LineType - Enum Class in htsjdk.samtools.fastq
  Enum of the types of lines we see in Fastq.
FastqRecord - Class in htsjdk.samtools.fastq
  Simple representation of a FASTQ record, without any conversion
FastqRecord(FastqRecord) - Constructor for class htsjdk.samtools.fastq.FastqRecord
  Copy constructor
FastqRecord(String, byte[], String, byte[]) - Constructor for class htsjdk.samtools.fastq.FastqRecord
  Constructor for byte[] arrays
FastqRecord(String, String, String, String) - Constructor for class htsjdk.samtools.fastq.FastqRecord
  Default constructor
fastqToPhred(byte[]) - Static method in class htsjdk.samtools.SAMUtils
  Converts printable qualities in Sanger fastq format to binary phred scores.
fastqToPhred(char) - Static method in class htsjdk.samtools.SAMUtils
  Convert a single printable ASCII FASTQ format phred score to binary phred score.
fastqToPhred(String) - Static method in class htsjdk.samtools.SAMUtils
  Convert a string with phred scores in printable ASCII FASTQ format to an array of binary phred scores.
FastqWriter - Interface in htsjdk.samtools.fastq
  Simple interface for a class that can write out fastq records.
FastqWriterFactory - Class in htsjdk.samtools.fastq
  Factory class for creating FastqWriter objects.
FastqWriterFactory() - Constructor for class htsjdk.samtools.fastq.FastqWriterFactory
FC_FeatureCode - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
Feature - Interface in htsjdk.tribble
  Marker interface for Locatables with Tribble support.
FeatureCodec<FEATURE_TYPE, SOURCE> - Interface in htsjdk.tribble
  The base interface for classes that read in features.
FeatureCodecHeader - Class in htsjdk.tribble
  A class to represent a header of a feature containing file.
FeatureCodecHeader(Object, long) - Constructor for class htsjdk.tribble.FeatureCodecHeader
  Create a FeatureCodecHeader indicating the contents of the header (can be null) and the byte position in the file where the header ends (not inclusive).
FeatureFileDoesntExist(String, String) - Constructor for exception class htsjdk.tribble.TribbleException.FeatureFileDoesntExist
FeatureReader<T> - Interface in htsjdk.tribble
  the basic interface that feature sources need to match
FEATURES - Enum constant in enum class htsjdk.beta.plugin.HtsContentType
  Features content type (see `htsjdk.beta.plugin.features` for related formats)
fetchReferenceBases(int) - Method in class htsjdk.samtools.cram.build.CRAMReferenceRegion
  Return the reference bases for an entire contig given a reference contig index.
fetchReferenceBasesByRegion(int, int, int) - Method in class htsjdk.samtools.cram.build.CRAMReferenceRegion
  Get the reference bases for a region of a reference contig.
fetchReferenceBasesByRegion(AlignmentContext) - Method in class htsjdk.samtools.cram.build.CRAMReferenceRegion
  Fetch the bases to span an `AlignmentContext`.
FI - Enum constant in enum class htsjdk.samtools.SAMTag
FI - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
FIELD_DELIMITER - Static variable in class htsjdk.tribble.gff.Gff3Constants
FIELD_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
FIELD_SEPARATOR_CHAR - Static variable in class htsjdk.variant.vcf.VCFConstants
fields - Variable in class htsjdk.samtools.util.htsget.HtsgetRequest
FILE_EXTENSION - Static variable in class htsjdk.samtools.SBIIndex
  Deprecated.
  since June 2019 Use `FileExtensions.SBI` instead.
FILE_HEADER - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockContentType
FILE_SCHEME - Static variable in class htsjdk.samtools.seekablestream.SeekableStreamFactory
FILE_TYPES - Static variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
FileAppendStreamLRUCache - Class in htsjdk.samtools.util
  LRU cache of OutputStreams to handle situation in which it is necessary to have more FileOutputStreams than resource limits will allow.
FileAppendStreamLRUCache(int) - Constructor for class htsjdk.samtools.util.FileAppendStreamLRUCache
fileExtension() - Method in class htsjdk.samtools.SamReader.Type
  The recommended file extension for SAMs of this type, without a period.
FileExtensions - Class in htsjdk.samtools.util
  Contains file extension constants for read, alignment, variant and annotation files
FileExtensions() - Constructor for class htsjdk.samtools.util.FileExtensions
File format example - Section in class htsjdk.variant.vcf.VCFCodec
fileHeaderTypeIdentifier - Variable in enum class htsjdk.tribble.index.AbstractIndex.IndexType
fileNameSuffix - Variable in enum class htsjdk.samtools.SamIndexes
fileOrderCompare(SAMRecord, SAMRecord) - Method in interface htsjdk.samtools.SAMRecordComparator
  Less stringent compare method than the regular compare.
fileOrderCompare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordCoordinateComparator
  Less stringent compare method than the regular compare.
fileOrderCompare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordDuplicateComparator
  Less stringent than duplicateSetCompare, such that two records are equal enough such that their ordering in a sorted SAM file would be arbitrary.
fileOrderCompare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordQueryHashComparator
  Compares two records based on an integer hash of their read names.
fileOrderCompare(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.SAMRecordQueryNameComparator
  Less stringent compare method than the regular compare.
filesToPaths(Collection) - Static method in class htsjdk.samtools.util.IOUtil
  Takes a list of Files and converts them to a list of Paths Runs .toPath() on the contents of the input.
fileSuffix(File) - Static method in class htsjdk.samtools.util.IOUtil
  Returns the name of the file extension (i.e.
FileTruncatedException - Exception Class in htsjdk.samtools
  Thrown when it is possible to detect that a SAM or BAM file is truncated.
FileTruncatedException() - Constructor for exception class htsjdk.samtools.FileTruncatedException
FileTruncatedException(String) - Constructor for exception class htsjdk.samtools.FileTruncatedException
FileTruncatedException(String, Throwable) - Constructor for exception class htsjdk.samtools.FileTruncatedException
FileTruncatedException(Throwable) - Constructor for exception class htsjdk.samtools.FileTruncatedException
filter(String) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Most efficient version of setting filters -- just set the filters string to filters
filter(String) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Adds the given filter to the list of filters
FILTER - Enum constant in enum class htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
FILTER_CODE_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
FILTER_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
filterByVersion(List, HtsVersion) - Method in class htsjdk.beta.plugin.registry.HtsCodecResolver
  Filter the candidate codecs, returning only those that match the requested version.
filterHash - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
FilteringIterator - Class in htsjdk.samtools.filter
  Deprecated.
  use `FilteringSamIterator` instead
FilteringIterator - Class in htsjdk.variant.variantcontext.filter
  Deprecated.
  since 2/29/16 use `FilteringVariantContextIterator` instead
FilteringIterator(Iterator, SamRecordFilter) - Constructor for class htsjdk.samtools.filter.FilteringIterator
  Deprecated.
FilteringIterator(Iterator, SamRecordFilter, boolean) - Constructor for class htsjdk.samtools.filter.FilteringIterator
  Deprecated.
FilteringIterator(Iterator, VariantContextFilter) - Constructor for class htsjdk.variant.variantcontext.filter.FilteringIterator
  Deprecated.
FilteringSamIterator - Class in htsjdk.samtools.filter
  Filtering Iterator which takes a filter and an iterator and iterates through only those records which are not rejected by the filter.
FilteringSamIterator(Iterator, SamRecordFilter) - Constructor for class htsjdk.samtools.filter.FilteringSamIterator
  Constructor
FilteringSamIterator(Iterator, SamRecordFilter, boolean) - Constructor for class htsjdk.samtools.filter.FilteringSamIterator
  Constructor
FilteringVariantContextIterator - Class in htsjdk.variant.variantcontext.filter
  A filtering iterator for VariantContexts that takes a base iterator and a VariantContextFilter.
FilteringVariantContextIterator(Iterator, VariantContextFilter) - Constructor for class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator
  Constructor of an iterator based on the provided iterator and predicate.
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.AggregateFilter
  Determines whether a SAMRecord matches this filter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.AlignedFilter
  Determines whether a SAMRecord matches this filter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.DuplicateReadFilter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.FailsVendorReadQualityFilter
  Determines whether a SAMRecord matches this filter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.InsertSizeFilter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.IntervalFilter
  Determines whether a SAMRecord matches this filter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.IntervalKeepPairFilter
  Determines whether a SAMRecord matches this filter.
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.InvertFilter
  Determines whether a SAMRecord matches this filter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.JavascriptSamRecordFilter
  read is filtered out if the javascript program returns false
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.MappingQualityFilter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.OverclippedReadFilter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.ReadNameFilter
  Determines whether a SAMRecord matches this filter
filterOut(SAMRecord) - Method in interface htsjdk.samtools.filter.SamRecordFilter
  Determines whether a SAMRecord matches this filter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.SecondaryAlignmentFilter
  Returns true if the read is marked as secondary.
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.SecondaryOrSupplementaryFilter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.SolexaNoiseFilter
  Determines whether a SAMRecord matches this filter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.TagFilter
  Determines whether a SAMRecord matches this filter
filterOut(SAMRecord) - Method in class htsjdk.samtools.filter.WholeReadClippedFilter
  Determines whether a SAMRecord matches this filter
filterOut(SAMRecord) - Method in class htsjdk.samtools.HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.AggregateFilter
  Determines whether a pair of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.AlignedFilter
  Determines whether a pair of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.DuplicateReadFilter
  Determines whether a pair of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.FailsVendorReadQualityFilter
  Determines whether a pair of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.InsertSizeFilter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.IntervalFilter
  Determines whether a pair of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.IntervalKeepPairFilter
  Determines whether a pair of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.InvertFilter
  Determines whether a pair of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.JavascriptSamRecordFilter
  return true of both records are filteredOut (AND)
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.MappingQualityFilter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.OverclippedReadFilter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.ReadNameFilter
  Determines whether a pair of SAMRecords matches this filter
filterOut(SAMRecord, SAMRecord) - Method in interface htsjdk.samtools.filter.SamRecordFilter
  Determines whether a pair of SAMRecords matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.SecondaryAlignmentFilter
  Returns true if either read is marked as secondary.
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.SecondaryOrSupplementaryFilter
  Determines whether a pair of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.SolexaNoiseFilter
  Determines whether a pair of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.TagFilter
  Determines whether a paired of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.filter.WholeReadClippedFilter
  Determines whether a paired of SAMRecord matches this filter
filterOut(SAMRecord, SAMRecord) - Method in class htsjdk.samtools.HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter
filters(String...) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  varargs version of #filters
filters(String...) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  `VariantContextBuilder.filters`
filters(List) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Tells this builder to make a Genotype object that has had filters applied, which may be empty (passes) or have some value indicating the reasons why it's been filtered.
filters(Set) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  This builder's filters are set to this value filters can be `null` -> meaning there are no filters
FILTERS - Enum constant in enum class htsjdk.variant.variantcontext.VariantContext.Validation
filtersWereApplied() - Method in class htsjdk.variant.variantcontext.CommonInfo
filtersWereApplied() - Method in class htsjdk.variant.variantcontext.VariantContext
finalize() - Method in class htsjdk.samtools.util.DiskBackedQueue
  Clean up disk resources in case clear() has not been explicitly called (as would be preferable) Closes the input and output streams associated with this DiskBackedQueue and deletes the temporary file
finalizeAll() - Method in class htsjdk.samtools.util.ResourceLimitedMap
  Remove all the values from the map, and call functory.finalizeValue() on each of them.
finalizeIndex() - Method in class htsjdk.tribble.index.AbstractIndex
finalizeIndex(long) - Method in class htsjdk.tribble.index.DynamicIndexCreator
finalizeIndex(long) - Method in interface htsjdk.tribble.index.IndexCreator
  Create the index, given the stream of features passed in to this point
finalizeIndex(long) - Method in class htsjdk.tribble.index.interval.IntervalIndexCreator
  finalize the index; create a tree index given the feature list passed in so far
finalizeIndex(long) - Method in class htsjdk.tribble.index.linear.LinearIndexCreator
  finalize the index; producing an index object
finalizeIndex(long) - Method in class htsjdk.tribble.index.tabix.AllRefsTabixIndexCreator
finalizeIndex(long) - Method in class htsjdk.tribble.index.tabix.StreamBasedTabixIndexCreator
finalizeIndex(long) - Method in class htsjdk.tribble.index.tabix.TabixIndexCreator
finalizeValue(Key, Value) - Method in interface htsjdk.samtools.util.ResourceLimitedMapFunctor
  Clean up an existing value in conjunction with removing from ResourceLimitedMap.
find(int, int) - Method in class htsjdk.samtools.util.IntervalTree
  Find an interval.
find(short) - Method in class htsjdk.samtools.SAMBinaryTagAndValue
  Returns the SAMBinaryTagAndValue that contains the required tag, or null if not contained.
find(String, Class) - Method in class htsjdk.utils.ClassFinder
  Scans the classpath for classes within the specified package and sub-packages that extend the parentType.
find(List, int, int, int) - Static method in class htsjdk.samtools.cram.CRAIIndex
  Currently unused, but retained for the native rai query implementation
findAndLoadSequenceDictionary(Path) - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Attempts to find and load the sequence dictionary if present.
findAndLoadSequenceDictionary(Path) - Method in class htsjdk.samtools.reference.FastaSequenceFile
  Attempts to find and load the sequence dictionary if present.
findAndLoadSequenceDictionary(Path) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Attempts to find and load the sequence dictionary if present.
findByIndex(int) - Method in class htsjdk.samtools.util.IntervalTree
  Find the nth interval in the tree.
findByName(String) - Static method in enum class htsjdk.samtools.SAMFlag
findFastaIndex(Path) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
findFastaIndex(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
findIndex(File) - Static method in class htsjdk.samtools.SamFiles
  Finds the index file associated with the provided SAM file.
findIndex(Path) - Static method in class htsjdk.samtools.SamFiles
  Finds the index file associated with the provided SAM file.
findLastAlignedEntry(List) - Static method in class htsjdk.samtools.cram.CRAIIndex
  Currently unused, but retained for the native rai query implementation
findOverlapping(Interval) - Method in class htsjdk.tribble.index.interval.IntervalTree
findQualityTrimPoint(byte[], int) - Static method in class htsjdk.samtools.util.TrimmingUtil
  Implements phred-style quality trimming.
findRequiredFastaIndexFile(Path) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
findRequiredFastaIndexFile(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
findSequenceDictionary(File) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Deprecated.
  use findSequenceDictionary(Path) instead.
findSequenceDictionary(File) - Static method in class htsjdk.samtools.reference.FastaSequenceFile
  Deprecated.
  use findSequenceDictionary(Path) instead.
findSequenceDictionary(File) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Deprecated.
  use findSequenceDictionary(Path) instead.
findSequenceDictionary(Path) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Attempts to locate the sequence dictionary file adjacent to the reference fasta file.
findSequenceDictionary(Path) - Static method in class htsjdk.samtools.reference.FastaSequenceFile
  Attempts to locate the sequence dictionary file adjacent to the reference fasta file.
findSequenceDictionary(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Attempts to locate the sequence dictionary file adjacent to the reference fasta file.
findVirtualOffsetOfFirstRecordInBam(SeekableStream) - Static method in class htsjdk.samtools.SAMUtils
  Returns the virtual file offset of the first record in a BAM file - i.e.
findVirtualOffsetOfFirstRecordInBam(File) - Static method in class htsjdk.samtools.SAMUtils
  Returns the virtual file offset of the first record in a BAM file - i.e.
findVirtualOffsetOfFirstRecordInBam(Path) - Static method in class htsjdk.samtools.SAMUtils
finish() - Method in class htsjdk.samtools.BAMFileWriter
finish() - Method in class htsjdk.samtools.BAMIndexer
  After all the alignment records have been processed, finish is called.
finish() - Method in class htsjdk.samtools.CRAMBAIIndexer
  After all the slices have been processed, finish is called.
finish() - Method in class htsjdk.samtools.CRAMCRAIIndexer
  Finish creating the index by writing the accumulated entries out to the stream.
finish() - Method in class htsjdk.samtools.CRAMFileWriter
finish() - Method in interface htsjdk.samtools.CRAMIndexer
  Finish creating the index by writing the accumulated entries out.
finish() - Method in class htsjdk.samtools.SAMFileWriterImpl
  Do any required flushing here.
finish() - Method in class htsjdk.samtools.SAMTextWriter
  Do any required flushing here.
finish(boolean) - Method in class htsjdk.samtools.BAMStreamWriter
  Finish writing and close all the streams.
finish(boolean) - Method in class htsjdk.samtools.CRAMContainerStreamWriter
  Finish writing to the stream.
finish(long) - Method in class htsjdk.samtools.BAMIndexMerger
finish(long) - Method in class htsjdk.samtools.cram.CRAIIndexMerger
finish(long) - Method in class htsjdk.samtools.IndexMerger
  Finish merging the indexes, and close the output stream.
finish(long) - Method in class htsjdk.samtools.SBIIndexMerger
  Complete the index, and close the output stream.
finish(long) - Method in class htsjdk.tribble.index.tabix.TabixIndexMerger
finish(long, long) - Method in class htsjdk.samtools.SBIIndexWriter
  Complete the index, and close the output stream.
finish(long, long, byte[], byte[]) - Method in class htsjdk.samtools.SBIIndexWriter
  Complete the index, and close the output stream.
FIRST_OF_PAIR - Enum constant in enum class htsjdk.samtools.SAMFlag
FIRST_OF_PAIR - Static variable in class htsjdk.samtools.fastq.FastqConstants
FIVE_GBS - Static variable in class htsjdk.samtools.util.IOUtil
Flag - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderLineType
Flag(VCFCompoundHeaderLine, Map) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Flag
FLAG - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
flags - Variable in class htsjdk.tribble.index.AbstractIndex
flags - Variable in class htsjdk.tribble.index.tabix.TabixFormat
  Describes interpretation of file being indexed.
flatten() - Method in interface htsjdk.tribble.gff.Gff3Feature
  Flatten this feature and all descendents into a set of features.
flatten() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
  flatten this feature and all descendents into a set of features
Float - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderLineType
Float(VCFCompoundHeaderLine, Map) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Float
FLOAT - Enum constant in enum class htsjdk.variant.bcf2.BCF2Type
FLOW_ORDER_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
flush() - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
flush() - Method in class htsjdk.samtools.fastq.BasicFastqWriter
flush() - Method in class htsjdk.samtools.util.AsciiWriter
  flushes underlying OutputStream
flush() - Method in class htsjdk.samtools.util.BlockCompressedOutputStream
  WARNING: flush() affects the output format, because it causes the current contents of uncompressedBuffer to be compressed and written, even if it isn't full.
flush() - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
FLUSH_DIRECTIVE - Enum constant in enum class htsjdk.tribble.gff.Gff3Codec.Gff3Directive
flushStreamsToBlocks(CRAMCodecModelContext) - Method in class htsjdk.samtools.cram.structure.SliceBlocksWriteStreams
  Compress and write each stream to a corresponding Block.
FMT_READS_BAM - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
FMT_READS_CRAM - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
FMT_READS_HTSGET_BAM - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
FMT_READS_INDEX_BAI - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
  Formats for secondary content type `BundleResourceType.CT_READS_INDEX` resources
FMT_READS_INDEX_CRAI - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
FMT_READS_INDEX_CSI - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
FMT_READS_SAM - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
  Formats for primary content type `BundleResourceType.CT_ALIGNED_READS`
FMT_VARIANTS_BCF - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
FMT_VARIANTS_VCF - Static variable in class htsjdk.beta.io.bundle.BundleResourceType
  Format names for content type `BundleResourceType.CT_VARIANT_CONTEXTS`
FN_NumberOfReadFeatures - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
FOR_SEEK_TIME - Enum constant in enum class htsjdk.tribble.index.IndexFactory.IndexBalanceApproach
FOR_SIZE - Enum constant in enum class htsjdk.tribble.index.IndexFactory.IndexBalanceApproach
FORCE_BCF - Enum constant in enum class htsjdk.variant.variantcontext.writer.Options
format - Variable in class htsjdk.samtools.util.htsget.HtsgetRequest
format(boolean) - Method in class htsjdk.samtools.util.FormatUtil
  Formats a boolean value to a String.
format(char) - Method in class htsjdk.samtools.util.FormatUtil
  Formats a char as a string.
format(double) - Method in class htsjdk.samtools.util.FormatUtil
  Formats a double to a floating point string.
format(float) - Method in class htsjdk.samtools.util.FormatUtil
  Formats a float to a floating point string.
format(int) - Method in enum class htsjdk.samtools.SamFlagField
  Returns the string associated with this flag field.
format(int) - Method in class htsjdk.samtools.util.FormatUtil
  Formats an int to an integer string.
format(long) - Method in class htsjdk.samtools.util.FormatUtil
  Formats a long to an integer string.
format(short) - Method in class htsjdk.samtools.util.FormatUtil
  Formats a short to an integer string.
format(Iso8601Date) - Method in class htsjdk.samtools.util.FormatUtil
  Formats date and time
format(Enum) - Method in class htsjdk.samtools.util.FormatUtil
  Formats an enum to the String representation of an enum.
format(Object) - Method in class htsjdk.samtools.util.FormatUtil
  Attempts to determine the type of value and format it appropriately.
format(Date) - Method in class htsjdk.samtools.util.FormatUtil
  Formats a date to a date string without time.
FORMAT - Enum constant in enum class htsjdk.variant.vcf.VCFCompoundHeaderLine.SupportedHeaderLineType
FORMAT_FIELD_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
FORMAT_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
Format: - Section in enum class htsjdk.variant.variantcontext.VariantContext.Type
Formats That Use a Custom URI or Protocol Scheme - Section in interface htsjdk.beta.plugin.HtsCodec
FormatUtil - Class in htsjdk.samtools.util
  Simple class used to format object values into a standard format for printing.
FormatUtil() - Constructor for class htsjdk.samtools.util.FormatUtil
  Constructs a new FormatUtil and initializes various internal formatters.
formatVCFDouble(double) - Static method in class htsjdk.variant.vcf.VCFEncoder
  Takes a double value and pretty prints it to a String for display
FORWARD - Static variable in enum class htsjdk.tribble.annotation.Strand
  Common alias for the `Strand.POSITIVE` strand.
FP_FeaturePosition - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
FQ - Enum constant in enum class htsjdk.samtools.fastq.FastqConstants.FastqExtensions
FQ_GZ - Enum constant in enum class htsjdk.samtools.fastq.FastqConstants.FastqExtensions
FQZCOMP - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
FQZCompDecode - Class in htsjdk.samtools.cram.compression.fqzcomp
  Decoder for the CRAM 3.1 FQZComp codec, used for compressing quality scores.
FQZCompDecode() - Constructor for class htsjdk.samtools.cram.compression.fqzcomp.FQZCompDecode
FQZCompEncode - Class in htsjdk.samtools.cram.compression.fqzcomp
  Encoder for the CRAM 3.1 FQZComp quality score compression codec.
FQZCompEncode() - Constructor for class htsjdk.samtools.cram.compression.fqzcomp.FQZCompEncode
FQZCompExternalCompressor - Class in htsjdk.samtools.cram.compression.fqzcomp
  External compressor wrapper for the FQZComp quality score codec.
FQZCompExternalCompressor(FQZCompEncode, FQZCompDecode) - Constructor for class htsjdk.samtools.cram.compression.fqzcomp.FQZCompExternalCompressor
FQZGlobalFlags - Class in htsjdk.samtools.cram.compression.fqzcomp
  Global flags byte for the FQZComp codec, read from the first byte after the version number in the FQZComp parameter header.
FQZGlobalFlags(ByteBuffer) - Constructor for class htsjdk.samtools.cram.compression.fqzcomp.FQZGlobalFlags
FQZModels - Class in htsjdk.samtools.cram.compression.fqzcomp
  Adaptive arithmetic coding models used by FQZComp for encoding and decoding quality scores.
FQZModels(FQZParams) - Constructor for class htsjdk.samtools.cram.compression.fqzcomp.FQZModels
FQZParam - Class in htsjdk.samtools.cram.compression.fqzcomp
  A single parameter block for the FQZComp quality score codec.
FQZParam(ByteBuffer, int) - Constructor for class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
FQZParams - Class in htsjdk.samtools.cram.compression.fqzcomp
  Global parameters for the FQZComp quality score codec.
FQZParams(ByteBuffer) - Constructor for class htsjdk.samtools.cram.compression.fqzcomp.FQZParams
FQZState - Class in htsjdk.samtools.cram.compression.fqzcomp
  Mutable state tracked during FQZComp encoding and decoding.
FQZState() - Constructor for class htsjdk.samtools.cram.compression.fqzcomp.FQZState
fqzUpdateContext(FQZParam, FQZState, int) - Static method in class htsjdk.samtools.cram.compression.fqzcomp.FQZCompDecode
  Update the 16-bit context value after encoding/decoding a quality score.
FQZUtils - Class in htsjdk.samtools.cram.compression.fqzcomp
  Utility methods for FQZComp table serialization.
FQZUtils() - Constructor for class htsjdk.samtools.cram.compression.fqzcomp.FQZUtils
FR - Enum constant in enum class htsjdk.samtools.SamPairUtil.PairOrientation
from(InputStream) - Static method in class htsjdk.tribble.readers.AsciiLineReader
  Create an AsciiLineReader of the appropriate type for a given InputStream.
fromCigarOperators(List) - Static method in class htsjdk.samtools.Cigar
  build a new Cigar object from a list of cigar operators.
fromCigarString(String) - Static method in class htsjdk.samtools.Cigar
  Decode a Cigar from a SAM formatted CIGAR String, uses `TextCigarCodec.decode(String)` Only performs minimal validation.
fromFile(File) - Static method in class htsjdk.samtools.util.IntervalList
  Parses an interval list from a file.
fromFiles(Collection) - Static method in class htsjdk.samtools.util.IntervalList
  Calls `IntervalList.fromFile(java.io.File)` on the provided files, and returns their `IntervalList.concatenate(Collection)`
fromFileSpan(SeekableStream, long[]) - Static method in class htsjdk.samtools.cram.build.CramSpanContainerIterator
fromGLField(String) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  Deprecated.
fromHexDigit(char) - Static method in class htsjdk.samtools.util.StringUtil
fromHtsgetURI(HtsgetInputResource, boolean, ValidationStringency, SAMRecordFactory, boolean, InflaterFactory) - Static method in class htsjdk.samtools.HtsgetBAMFileReader
  Instantiate an HtsgetBAMFileReader from an HtsgetInputResource, attempting to convert it to an https resource then a http resource if the server does not support https
fromInt(int) - Static method in enum class htsjdk.samtools.cram.compression.range.RangeParams.ORDER
fromInt(int) - Static method in enum class htsjdk.samtools.cram.compression.rans.RANSParams.ORDER
fromLog10Likelihoods(double[]) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
fromName(SAMFileHeader, String) - Static method in class htsjdk.samtools.util.IntervalList
  Creates an IntervalList from the given sequence name
fromPath(Path) - Static method in class htsjdk.samtools.util.IntervalList
  Parses an interval list from a path.
fromPLField(String) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
fromPLs(int[]) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
fromQueryIntervalArray(QueryInterval[], SAMSequenceDictionary) - Static method in class htsjdk.beta.plugin.interval.HtsIntervalUtils
fromReader(BufferedReader) - Static method in class htsjdk.samtools.util.IntervalList
  Parses an interval list from a reader in a stream based fashion.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.core.BetaIntegerEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanByteEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanIntegerEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.core.experimental.GolombIntegerEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.core.GammaIntegerEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.core.SubexponentialIntegerEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.external.ByteArrayStopEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.external.ExternalByteArrayEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.external.ExternalByteEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.external.ExternalIntegerEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromSerializedEncodingParams(byte[]) - Static method in class htsjdk.samtools.cram.encoding.external.ExternalLongEncoding
  Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
fromString(String) - Static method in class htsjdk.samtools.util.BufferedLineReader
  Returns a `BufferedLineReader` that gets its input from a String.
fromVcf(VCFFileReader) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Deprecated.
  since July 2018 since use `VCFFileReader.toIntervalList(VCFFileReader)` instead
fromVcf(VCFFileReader, boolean) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Deprecated.
  since July 2018 since use `VCFFileReader.toIntervalList(VCFFileReader, boolean)` instead
fromVcf(File) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Deprecated.
  since July 2018 use `VCFFileReader.toIntervalList(Path)` instead
fromVcf(File, boolean) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Deprecated.
  since July 2018 use `VCFFileReader.toIntervalList(Path, boolean)` instead
FS - Enum constant in enum class htsjdk.samtools.SAMTag
FS - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
FT - Enum constant in enum class htsjdk.samtools.SAMTag
FT - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
FTGenotypesWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.FTGenotypesWriter
FTPClient - Class in htsjdk.samtools.util.ftp
FTPClient() - Constructor for class htsjdk.samtools.util.ftp.FTPClient
FTPHelper - Class in htsjdk.tribble.util
FTPHelper(URL) - Constructor for class htsjdk.tribble.util.FTPHelper
FTPReply - Class in htsjdk.samtools.util.ftp
FTPReply(BufferedReader) - Constructor for class htsjdk.samtools.util.ftp.FTPReply
FTPStream - Class in htsjdk.samtools.util.ftp
  A "non-seekable" ftp stream.
FTPStream(FTPClient) - Constructor for class htsjdk.samtools.util.ftp.FTPStream
FTPUtils - Class in htsjdk.samtools.util.ftp
FTPUtils() - Constructor for class htsjdk.samtools.util.ftp.FTPUtils
FullBEDFeature - Class in htsjdk.tribble.bed
  Object for full BED file.
FullBEDFeature(String, int, int) - Constructor for class htsjdk.tribble.bed.FullBEDFeature
FullBEDFeature.Exon - Class in htsjdk.tribble.bed
  A sub region of a feature.
FullBEDFeature.Exon2 - Class in htsjdk.tribble.bed
fullyDecode(VCFHeader, boolean) - Method in class htsjdk.variant.variantcontext.VariantContext
  Return a VC equivalent to this one but where all fields are fully decoded See VariantContext document about fully decoded
fullyDecoded(boolean) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Sets this builder's fully decoded state to true.
Fully decoding. - Section in class htsjdk.variant.variantcontext.VariantContext
FwdIterator(IntervalTree.Node) - Constructor for class htsjdk.samtools.util.IntervalTree.FwdIterator
FZ - Enum constant in enum class htsjdk.samtools.SAMTag
FZ - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.

## G

g - Static variable in class htsjdk.samtools.util.SequenceUtil
  Byte typed variables for all normal bases.
G - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderLineCount
G - Static variable in class htsjdk.samtools.util.SequenceUtil
  Byte typed variables for all normal bases.
GAMMA - Enum constant in enum class htsjdk.samtools.cram.structure.EncodingID
  http://en.wikipedia.org/wiki/Elias_gamma_coding
GammaIntegerEncoding - Class in htsjdk.samtools.cram.encoding.core
gatherWithBlockCopying(List, File, boolean, boolean) - Static method in class htsjdk.samtools.BamFileIoUtils
  Assumes that all inputs and outputs are block compressed VCF files and copies them without decompressing and parsing most of the gzip blocks.
GaveUpException - Exception Class in htsjdk.samtools.cram.ref
GC - Enum constant in enum class htsjdk.samtools.SAMTag
  Deprecated.
  for backwards compatibility only
GC - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
GeneralUtils - Class in htsjdk.variant.utils
  Constants and utility methods used throughout the VCF/BCF/VariantContext classes
GeneralUtils() - Constructor for class htsjdk.variant.utils.GeneralUtils
generateAllKmers(int) - Static method in class htsjdk.samtools.util.SequenceUtil
  Generates all possible unambiguous kmers (upper-case) of length and returns them as byte[]s.
generateBestGuess(QualityEncodingDetector.FileContext, FastqQualityFormat) - Method in class htsjdk.samtools.util.QualityEncodingDetector
  Make the best guess at the quality format.
generateCandidateQualities(boolean) - Method in class htsjdk.samtools.util.QualityEncodingDetector
  Processes collected quality data and applies rules to determine which quality formats are possible.
generateException(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
generateException(String, int) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec
generateIndexContent() - Method in class htsjdk.samtools.BinningIndexBuilder
  Creates the BAMIndexContent for this reference.
generateLazyNowInstance() - Static method in class htsjdk.samtools.util.RelativeIso8601Date
  Returns a "lazy now" instance.
GENERIC_FLAGS - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
GenericInts(VCFCompoundHeaderLine, Map) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.GenericInts
GenericSiteWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenericSiteWriter
GenomicIndexUtil - Class in htsjdk.samtools
  Constants and methods used by BAM and Tribble indices
GenomicIndexUtil() - Constructor for class htsjdk.samtools.GenomicIndexUtil
Genotype - Class in htsjdk.variant.variantcontext
  This class encompasses all the basic information about a genotype.
Genotype(String, String) - Constructor for class htsjdk.variant.variantcontext.Genotype
GENOTYPE_ALLELE_DEPTHS - Static variable in class htsjdk.variant.vcf.VCFConstants
GENOTYPE_FIELD_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
GENOTYPE_FIELD_SEPARATOR_CHAR - Static variable in class htsjdk.variant.vcf.VCFConstants
GENOTYPE_FILTER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
GENOTYPE_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
GENOTYPE_LIKELIHOODS_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
  Deprecated.
GENOTYPE_PL_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
GENOTYPE_POSTERIORS_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
GENOTYPE_QUALITY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
GenotypeBuilder - Class in htsjdk.variant.variantcontext
  A builder class for genotypes Provides convenience setter methods for all of the Genotype field values.
GenotypeBuilder() - Constructor for class htsjdk.variant.variantcontext.GenotypeBuilder
  Create a empty builder.
GenotypeBuilder(Genotype) - Constructor for class htsjdk.variant.variantcontext.GenotypeBuilder
  Create a new builder starting with the values in Genotype g
GenotypeBuilder(String) - Constructor for class htsjdk.variant.variantcontext.GenotypeBuilder
  Create a builder using sampleName.
GenotypeBuilder(String, List) - Constructor for class htsjdk.variant.variantcontext.GenotypeBuilder
  Make a builder using sampleName and alleles for starting values
genotypeCounts - Variable in class htsjdk.variant.variantcontext.VariantContext
  Counts for each of the possible Genotype types in this context
GenotypeJEXLContext - Class in htsjdk.variant.variantcontext
GenotypeJEXLContext(VariantContext, Genotype) - Constructor for class htsjdk.variant.variantcontext.GenotypeJEXLContext
GenotypeLikelihoods - Class in htsjdk.variant.variantcontext
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair - Class in htsjdk.variant.variantcontext
GenotypeLikelihoodsAllelePair(int, int) - Constructor for class htsjdk.variant.variantcontext.GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
genotypeNames(Collection) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
genotypeParts - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
GenotypeQualityFilter - Class in htsjdk.variant.variantcontext.filter
  A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).
GenotypeQualityFilter(int) - Constructor for class htsjdk.variant.variantcontext.filter.GenotypeQualityFilter
  Constructor as above that doesn't take a sample, instead it will look at the first genotype of the variant context.
GenotypeQualityFilter(int, String) - Constructor for class htsjdk.variant.variantcontext.filter.GenotypeQualityFilter
  Constructor for a filter that will keep VC for which the genotype quality (GQ) of sample passes a threshold.
genotypes - Variable in class htsjdk.variant.variantcontext.VariantContext
  A mapping from sampleName -> genotype objects for all genotypes associated with this context
genotypes(Genotype...) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells this builder that the resulting `VariantContext` should use a `GenotypeContext` containing genotypes
genotypes(GenotypesContext) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells this builder that the resulting `VariantContext` should use this genotype's `GenotypeContext`.
genotypes(Collection) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells this builder that the resulting `VariantContext` should use a `GenotypeContext` containing genotypes Note that genotypes can be `null`, meaning there are no genotypes
GENOTYPES - Enum constant in enum class htsjdk.variant.variantcontext.VariantContext.Validation
GenotypesContext - Class in htsjdk.variant.variantcontext
  Represents an ordered collection of Genotype objects
GenotypesContext() - Constructor for class htsjdk.variant.variantcontext.GenotypesContext
  Create an empty GenotypeContext
GenotypesContext(int) - Constructor for class htsjdk.variant.variantcontext.GenotypesContext
  Create an empty GenotypeContext, with initial capacity for n elements
GenotypesContext(ArrayList) - Constructor for class htsjdk.variant.variantcontext.GenotypesContext
  Create an GenotypeContext containing genotypes
GenotypesContext(ArrayList, Map, List) - Constructor for class htsjdk.variant.variantcontext.GenotypesContext
  Create a fully resolved GenotypeContext containing genotypes, sample lookup table, and sorted sample names
genotypesNoValidation(GenotypesContext) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
GenotypesWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenotypesWriter
GenotypeType - Enum Class in htsjdk.variant.variantcontext
  Summary types for Genotype objects
get() - Method in class htsjdk.samtools.util.Lazy
  Returns the instance associated with this `Lazy`, initializing it if necessary.
get() - Method in interface htsjdk.samtools.util.Lazy.LazyInitializer
  Deprecated.
get(int) - Method in class htsjdk.samtools.cram.structure.TagKeyCache
  Looks up the cached metadata for the given 3-byte tag ID.
get(int) - Method in class htsjdk.samtools.LinearIndex
get(int) - Method in class htsjdk.samtools.reference.ReferenceSequenceFileWalker
  Get reference sequence without validating name or length.
get(int) - Method in class htsjdk.variant.variantcontext.GenotypesContext
get(int, int) - Method in class htsjdk.samtools.util.IntervalListReferenceSequenceMask
  It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
get(int, int) - Method in interface htsjdk.samtools.util.ReferenceSequenceMask
  It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
get(int, int) - Method in class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
get(int, String, int) - Method in class htsjdk.samtools.reference.ReferenceSequenceFileWalker
  Ensure that the requested sequence is loaded.
get(Interval) - Method in class htsjdk.samtools.util.IntervalTreeMap
get(Object) - Method in class htsjdk.samtools.util.CollectionUtil.DefaultingMap
get(Object) - Method in class htsjdk.samtools.util.IntervalTreeMap
get(String) - Method in class htsjdk.beta.io.bundle.Bundle
  Get the BundleResource for the provided targetContentType string.
get(String) - Method in class htsjdk.variant.variantcontext.GenotypeJEXLContext
get(String) - Method in class htsjdk.variant.variantcontext.GenotypesContext
  Gets sample associated with this sampleName, or null if none is found
get(K) - Method in class htsjdk.samtools.util.Histogram
  Retrieves the bin associated with the given key.
get(Key) - Method in class htsjdk.samtools.util.ResourceLimitedMap
  Return an existing value, or create a new one if necessary.
getAbsolutePath() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Returns the full path to the reference file.
getAbsolutePath() - Method in class htsjdk.samtools.reference.FastaSequenceFile
  Returns the full path to the reference file.
getAbsolutePath() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Returns the full path to the reference file.
getAcceptedCount() - Method in class htsjdk.samtools.DownsamplingIterator
  Returns the number of records returned since creation of the last call to resetStatistics.
getAcceptedFraction() - Method in class htsjdk.samtools.DownsamplingIterator
  Gets the fraction of records accepted since creation or the last call to resetStatistics().
getAccessor(String) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors
  Return an accessor for field, or null if none exists
getActualValue() - Method in class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken.DupOrDiffToken
getActualValue() - Method in class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken.EndToken
getActualValue() - Method in class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken
getAD() - Method in class htsjdk.variant.variantcontext.FastGenotype
getAD() - Method in class htsjdk.variant.variantcontext.Genotype
getAliases() - Method in class htsjdk.tribble.gff.Gff3BaseData
getAliases() - Method in interface htsjdk.tribble.gff.Gff3Feature
getAlignedRecordCount() - Method in class htsjdk.samtools.BAMIndexMetaData
getAlignmentBlocks() - Method in class htsjdk.samtools.SAMRecord
  Returns blocks of the read sequence that have been aligned directly to the reference sequence.
getAlignmentBlocks(Cigar, int, String) - Static method in class htsjdk.samtools.SAMUtils
  Given a Cigar, Returns blocks of the sequence that have been aligned directly to the reference sequence.
getAlignmentContext() - Method in class htsjdk.samtools.cram.structure.Container
getAlignmentContext() - Method in class htsjdk.samtools.cram.structure.ContainerHeader
getAlignmentContext() - Method in class htsjdk.samtools.cram.structure.Slice
getAlignmentEnd() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getAlignmentEnd() - Method in class htsjdk.samtools.SAMRecord
getAlignmentEnd(int, int) - Method in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
  Compute the alignment end position from the read features, alignment start, and read length.
getAlignmentSpan() - Method in class htsjdk.samtools.cram.BAIEntry
getAlignmentSpan() - Method in class htsjdk.samtools.cram.CRAIEntry
getAlignmentSpan() - Method in class htsjdk.samtools.cram.structure.AlignmentContext
getAlignmentSpan() - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
getAlignmentStart() - Method in class htsjdk.samtools.cram.BAIEntry
getAlignmentStart() - Method in class htsjdk.samtools.cram.CRAIEntry
getAlignmentStart() - Method in class htsjdk.samtools.cram.structure.AlignmentContext
getAlignmentStart() - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
getAlignmentStart() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getAlignmentStart() - Method in class htsjdk.samtools.SAMRecord
getAlignmentType() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
  The `AbstractRecordAndOffset.AlignmentType` of this object, which classifies whether the given event is a match, insertion, or deletion when queried from a `SamLocusIterator`.
getAll() - Method in class htsjdk.samtools.util.OverlapDetector
  Gets all the objects that could be returned by the overlap detector.
getAllChunks() - Method in class htsjdk.samtools.BinningIndexContent
getAllele(byte[]) - Method in class htsjdk.variant.variantcontext.VariantContext
getAllele(int) - Method in class htsjdk.variant.variantcontext.FastGenotype
getAllele(int) - Method in class htsjdk.variant.variantcontext.Genotype
  Get the ith allele in this genotype
getAllele(String) - Method in class htsjdk.variant.variantcontext.VariantContext
getAlleleIndex(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
  Lookup the index of allele in this variant context
getAlleleIndices(Collection) - Method in class htsjdk.variant.variantcontext.VariantContext
  Return the allele index #getAlleleIndex for each allele in alleles
getAllelePair(int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  Get the diploid allele index pair for the given PL index
getAllelePairUsingDeprecatedOrdering(int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  Deprecated.
  since 2/5/13
getAlleles() - Method in class htsjdk.variant.variantcontext.FastGenotype
getAlleles() - Method in class htsjdk.variant.variantcontext.Genotype
getAlleles() - Method in class htsjdk.variant.variantcontext.VariantContext
  Gets the alleles.
getAlleles() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
getAlleles(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  Get the allele ploidy indices for the given PL index
getAlleleStrings() - Method in class htsjdk.variant.variantcontext.Genotype
  Utility that returns a list of allele strings corresponding to the alleles in this sample
getAllHistograms() - Method in class htsjdk.samtools.metrics.MetricsFile
getAltAlleleWithHighestAlleleCount() - Method in class htsjdk.variant.variantcontext.VariantContext
getAlternateAllele(int) - Method in class htsjdk.variant.variantcontext.VariantContext
getAlternateAlleles() - Method in class htsjdk.variant.variantcontext.VariantContext
  Gets the alternate alleles.
getAlternativeSequenceNames() - Method in class htsjdk.samtools.SAMSequenceRecord
  Returns unmodifiable set with alternative sequence names.
getAltHeaderLine(String, VCFHeaderVersion) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  Create and return a VCFAltHeaderLine object from a header line string that conforms to the `sourceVersion`
getAminoAcidNumber(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
getAncestors() - Method in interface htsjdk.tribble.gff.Gff3Feature
  Get set of all features this feature descends from, through chains of Parent attributes.
getAncestors() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
  Get set of all features this feature descends from, through chains of Parent attributes.
getAnyAttribute(String) - Method in class htsjdk.variant.variantcontext.Genotype
  A totally generic getter, that allows you to get specific keys that correspond to even inline values (GQ, for example).
getAsMap(boolean) - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
getAsPLs() - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
getAssembly() - Method in class htsjdk.samtools.SAMSequenceRecord
getAsString() - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
getAsTags() - Method in class htsjdk.samtools.cram.digest.ContentDigests
getAsVector() - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  The genotypes likelihoods in -10log10(x) vector format.
getAsyncOutputBufferSize() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Get the async output buffer size used for these options.
getAttribute(short) - Method in class htsjdk.samtools.BAMRecord
getAttribute(short) - Method in class htsjdk.samtools.SAMRecord
getAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
  Get the value for a SAM tag.
getAttribute(String) - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
getAttribute(String) - Method in class htsjdk.samtools.SAMRecord
  Get the value for a SAM tag.
getAttribute(String) - Method in class htsjdk.tribble.gff.Gff3BaseData
  get the values as List for the `key`, or an empty list if this `key` is not present
getAttribute(String) - Method in interface htsjdk.tribble.gff.Gff3Feature
getAttribute(String) - Method in class htsjdk.variant.variantcontext.CommonInfo
getAttribute(String) - Method in class htsjdk.variant.variantcontext.VariantContext
getAttribute(String, Object) - Method in class htsjdk.variant.variantcontext.CommonInfo
getAttribute(String, Object) - Method in class htsjdk.variant.variantcontext.VariantContext
getAttributeAsBoolean(String, boolean) - Method in class htsjdk.variant.variantcontext.CommonInfo
getAttributeAsBoolean(String, boolean) - Method in class htsjdk.variant.variantcontext.VariantContext
getAttributeAsDouble(String, double) - Method in class htsjdk.variant.variantcontext.CommonInfo
getAttributeAsDouble(String, double) - Method in class htsjdk.variant.variantcontext.Genotype
  Deprecated.
getAttributeAsDouble(String, double) - Method in class htsjdk.variant.variantcontext.VariantContext
getAttributeAsDoubleList(String, double) - Method in class htsjdk.variant.variantcontext.VariantContext
getAttributeAsDoubleList(String, Double) - Method in class htsjdk.variant.variantcontext.CommonInfo
getAttributeAsInt(String, int) - Method in class htsjdk.variant.variantcontext.CommonInfo
getAttributeAsInt(String, int) - Method in class htsjdk.variant.variantcontext.Genotype
  Deprecated.
getAttributeAsInt(String, int) - Method in class htsjdk.variant.variantcontext.VariantContext
getAttributeAsIntList(String, int) - Method in class htsjdk.variant.variantcontext.VariantContext
getAttributeAsIntList(String, Integer) - Method in class htsjdk.variant.variantcontext.CommonInfo
getAttributeAsList(String) - Method in class htsjdk.variant.variantcontext.CommonInfo
  Gets the attributes from a key as a list.
getAttributeAsList(String) - Method in class htsjdk.variant.variantcontext.VariantContext
  returns the value as an empty list if the key was not found, as a java.util.List if the value is a List or an Array, as a Collections.singletonList if there is only one value
getAttributeAsString(String, String) - Method in class htsjdk.variant.variantcontext.CommonInfo
getAttributeAsString(String, String) - Method in class htsjdk.variant.variantcontext.Genotype
  Deprecated.
getAttributeAsString(String, String) - Method in class htsjdk.variant.variantcontext.VariantContext
getAttributeAsStringList(String, String) - Method in class htsjdk.variant.variantcontext.CommonInfo
getAttributeAsStringList(String, String) - Method in class htsjdk.variant.variantcontext.VariantContext
getAttributes() - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
  Returns the Set of attributes.
getAttributes() - Method in class htsjdk.samtools.SAMRecord
getAttributes() - Method in class htsjdk.tribble.gff.Gff3BaseData
getAttributes() - Method in interface htsjdk.tribble.gff.Gff3Feature
getAttributes() - Method in class htsjdk.variant.variantcontext.CommonInfo
getAttributes() - Method in class htsjdk.variant.variantcontext.VariantContext
getAttributes() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Getter for attributes (DANGEROUS!!! DOES NOT MAKE A COPY!!!)
getAttributesBinarySize() - Method in class htsjdk.samtools.BAMRecord
  Depending on the concrete implementation, the binary file size of attributes may be known without computing them all.
getAttributesBinarySize() - Method in class htsjdk.samtools.SAMRecord
  Depending on the concrete implementation, the binary file size of attributes may be known without computing them all.
getAuxData() - Method in class htsjdk.samtools.CSIIndex
getAverageFeatureSize() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
getBAIEntries(CompressorCache) - Method in class htsjdk.samtools.cram.structure.Container
  Retrieve the list of BAIEntry Index entries corresponding to this Container
getBAIEntries(CompressorCache) - Method in class htsjdk.samtools.cram.structure.Slice
  Generate a BAIEntry Index entry from this Slice and other container parameters, splitting Multiple Reference slices into constituent reference sequence entries.
getBAMDecoderOptions() - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Get the `BAMDecoderOptions` for these options.
getBamDictionary() - Method in class htsjdk.samtools.AbstractBAMFileIndex
getBAMEncoderOptions() - Method in class htsjdk.beta.plugin.reads.ReadsEncoderOptions
  Get the `BAMEncoderOptions` for these ReadsEncoderOptions.
getBamFlags() - Method in class htsjdk.samtools.cram.structure.CRAMCodecModelContext
getBAMFlags() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getBamReadBaseLookup() - Static method in class htsjdk.samtools.util.SequenceUtil
  Returns a defensive copy of the BAM read base lookup table.
getBarcodes() - Method in class htsjdk.samtools.SAMReadGroupRecord
getBase() - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
getBase() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
getBase() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
getBase() - Method in enum class htsjdk.samtools.SQTagUtil.SQBase
  Deprecated.
getBaseCount() - Method in class htsjdk.samtools.cram.structure.ContainerHeader
getBaseCount() - Method in class htsjdk.samtools.cram.structure.Slice
getBaseCount() - Method in class htsjdk.samtools.util.IntervalList
  Gets the (potentially redundant) sum of the length of the intervals in the list.
getBaseData() - Method in interface htsjdk.tribble.gff.Gff3Feature
  Get BaseData object which contains all the basic information of the feature
getBaseData() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
getBaseName() - Method in interface htsjdk.io.IOPath
getBaseQualities() - Method in class htsjdk.samtools.BAMRecord
getBaseQualities() - Method in class htsjdk.samtools.fastq.FastqRecord
  Get the base qualities as binary PHRED scores (not ASCII)
getBaseQualities() - Method in class htsjdk.samtools.SAMRecord
  Do not modify the value returned by this method.
getBaseQualities() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
getBaseQuality() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
getBaseQuality(int) - Method in class htsjdk.samtools.util.EdgingRecordAndOffset
getBaseQualityHeader() - Method in class htsjdk.samtools.fastq.FastqRecord
  Get the base quality header
getBaseQualityString() - Method in class htsjdk.samtools.fastq.FastqRecord
  Get the base qualities encoded as a FASTQ string
getBaseQualityString() - Method in class htsjdk.samtools.SAMRecord
getBases() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getBases() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
getBases() - Method in class htsjdk.samtools.reference.ReferenceSequence
  Gets the array of bases that define this sequence.
getBases() - Method in interface htsjdk.variant.variantcontext.Allele
getBases() - Method in class htsjdk.variant.variantcontext.SimpleAllele
  Return the DNA bases segregating in this allele.
getBasesPerLine() - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
  Gets the number of bases in a given line.
getBasesPerSlice() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getBaseString() - Method in class htsjdk.samtools.reference.ReferenceSequence
  Returns the bases represented by this ReferenceSequence as a String.
getBaseString() - Method in interface htsjdk.variant.variantcontext.Allele
getBaseString() - Method in class htsjdk.variant.variantcontext.SimpleAllele
  Return the DNA bases segregating in this allele in String format.
getBestExternalCompressor(byte[], CRAMEncodingStrategy) - Method in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  Return the best external compressor to use for the provided byte array (compressor that results in the smallest compressed size).
getBin(int) - Method in class htsjdk.samtools.BinningIndexContent.BinList
getBinaryAttributes() - Method in class htsjdk.samtools.BAMRecord
getBinaryAttributes() - Method in class htsjdk.samtools.SAMRecord
getBinaryTag() - Method in enum class htsjdk.samtools.SAMTag
  Get the binary representation of this tag name.
getBinDepth() - Method in class htsjdk.samtools.CSIIndex
  Bin depth is the number of levels of the index.
getBinLabel() - Method in class htsjdk.samtools.util.Histogram
getBinNumber() - Method in class htsjdk.samtools.Bin
getBins() - Method in class htsjdk.samtools.BinList
  Retrieves the bins stored in this list.
getBins() - Method in class htsjdk.samtools.BinningIndexContent
getBinSize() - Method in class htsjdk.tribble.index.linear.LinearIndexCreator
getBinsOverlapping(int, int, int) - Method in interface htsjdk.samtools.BrowseableBAMIndex
  Get a list of bins in the BAM file that may contain SAMRecords for the given range.
getBinsOverlapping(int, int, int) - Method in class htsjdk.samtools.CSIIndex
getBinSummaryString(int) - Static method in class htsjdk.samtools.GenomicIndexUtil
  Return a summary string describing the bin level, level size, and genomic territory covered by the bin.
getBitCodeWithPrefix() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanBitCode
getBlock() - Method in class htsjdk.tribble.index.interval.Interval
getBlockAddress(long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
getBlockCount() - Method in class htsjdk.samtools.cram.structure.ContainerHeader
getBlockOffset(long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
getBlocks() - Method in class htsjdk.samtools.util.htsget.HtsgetResponse
getBlocks() - Method in interface htsjdk.tribble.index.ChrIndex
getBlocks() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
getBlocks() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
getBlocks(int, int) - Method in interface htsjdk.tribble.index.ChrIndex
getBlocks(int, int) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
getBlocks(int, int) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
getBlocks(String) - Method in class htsjdk.tribble.index.AbstractIndex
getBlocks(String, int, int) - Method in class htsjdk.tribble.index.AbstractIndex
getBlocks(String, int, int) - Method in interface htsjdk.tribble.index.Index
  Query the index.
getBlocks(String, int, int) - Method in class htsjdk.tribble.index.tabix.TabixIndex
getBlockSize() - Method in class htsjdk.variant.bcf2.BCF2Decoder
  The size of the current block in bytes
getBlockStats(boolean) - Method in class htsjdk.tribble.index.AbstractIndex
getBrowseableIndex() - Method in class htsjdk.samtools.CRAMFileReader
getBrowseableIndex() - Method in interface htsjdk.samtools.SamReader.Indexing
  Gets an index tagged with the BrowseableBAMIndex interface.
getBrowseableIndex() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
getBuffer() - Method in class htsjdk.samtools.cram.io.CRAMByteReader
  Return a reference to the underlying byte array.
getBufferedStream(SeekableStream) - Method in interface htsjdk.samtools.seekablestream.ISeekableStreamFactory
  Return a buffered `SeekableStream` which wraps the input `stream` using the default buffer size
getBufferedStream(SeekableStream, int) - Method in interface htsjdk.samtools.seekablestream.ISeekableStreamFactory
  Return a buffered `SeekableStream` which wraps the input `stream`
getBufferSize() - Method in class htsjdk.beta.plugin.variants.VariantsEncoderOptions
  Get the buffer size used when writing to an `IOPathResource`.
getByte() - Method in class htsjdk.samtools.util.FastLineReader
getByteArrayAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
  Will work for signed byte array, unsigned byte array, or old-style hex array
getByteArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
  Will work for signed byte array, unsigned byte array, or old-style hex array
getByteAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
  Get the tag value and attempt to coerce it into the requested type.
getByteAttribute(String) - Method in class htsjdk.samtools.SAMRecord
  Get the tag value and attempt to coerce it into the requested type.
getByteOffsetOfSliceHeaderBlock() - Method in class htsjdk.samtools.cram.structure.Slice
  The Slice's offset in bytes from the beginning of the Container's Compression Header (or the end of the Container Header), equal to `ContainerHeader.getLandmarks()` Used by BAI and CRAI indexing
getByteSizeOfSliceBlocks() - Method in class htsjdk.samtools.cram.structure.Slice
  The Slice's size in bytes Used by CRAI indexing only
getByteSizeRangeOfTagValues(List, int) - Static method in class htsjdk.samtools.cram.build.CompressionHeaderFactory
getBytesPerLine() - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
  How many bytes (bases + whitespace) are consumed by the given line?
getCachedPath() - Method in class htsjdk.io.HtsPath
getCachedString(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  Return a cached copy of the supplied string.
getCalledChrCount() - Method in class htsjdk.variant.variantcontext.VariantContext
  Returns the number of chromosomes carrying any allele in the genotypes (i.e., excluding NO_CALLS)
getCalledChrCount(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
  Returns the number of chromosomes carrying allele A in the genotypes
getCalledChrCount(Allele, Set) - Method in class htsjdk.variant.variantcontext.VariantContext
  Returns the number of chromosomes carrying allele A in the genotypes
getCalledChrCount(Set) - Method in class htsjdk.variant.variantcontext.VariantContext
  Returns the number of chromosomes carrying any allele in the genotypes (i.e., excluding NO_CALLS)
getCanonicalCodeWords() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanCanoncialCodeGenerator
  Return the canonical code words for this helper's `HuffmanParams` as a list of HuffmanBitCodes.
getCanonicalName() - Method in enum class htsjdk.samtools.cram.structure.DataSeries
getCanonicalRecordName(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  Returns a string that is the the read group ID and read name separated by a colon.
getCdEnd() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
  Method description
getCdEnd() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
  Method description
getCdStart() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
  Method description
getCdStart() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
  Method description
getCharacterAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
getCharacterAttribute(String) - Method in class htsjdk.samtools.SAMRecord
getChecksum() - Method in class htsjdk.samtools.cram.structure.ContainerHeader
getChildren() - Method in interface htsjdk.tribble.gff.Gff3Feature
  Gets set of features for which this feature is a parent
getChildren() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
  Gets set of features for which this feature is a parent
getChr() - Method in interface htsjdk.tribble.Feature
  Deprecated.
  on 03/2015. Use getContig() instead.
getChrIndexClass() - Method in class htsjdk.tribble.index.AbstractIndex
  returns the class for the index type
getChrIndexClass() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex
getChrIndexClass() - Method in class htsjdk.tribble.index.linear.LinearIndex
getChromosomes() - Method in class htsjdk.tribble.readers.TabixReader
  return the chromosomes in that tabix file
getChunk() - Method in interface htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
getChunk(long, long) - Method in class htsjdk.samtools.SBIIndex
  Return a chunk that corresponds to the given range in the data file.
getChunkEnd() - Method in class htsjdk.samtools.Chunk
getChunkList() - Method in class htsjdk.samtools.Bin
  Gets the list of chunks associated with this bin.
getChunks() - Method in class htsjdk.samtools.BAMFileSpan
  Gets the constituent chunks stored in this span.
getChunksOverlapping(int, int) - Method in class htsjdk.samtools.BinningIndexContent
getChunkStart() - Method in class htsjdk.samtools.Chunk
getCigar() - Method in class htsjdk.samtools.BAMRecord
getCigar() - Method in class htsjdk.samtools.SAMRecord
  Do not modify the value returned by this method.
getCigarElement(int) - Method in class htsjdk.samtools.Cigar
getCigarElements() - Method in class htsjdk.samtools.Cigar
getCigarForReadFeatures(int) - Method in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
  Build a `Cigar` from these read features and the given read length.
getCigarLength() - Method in class htsjdk.samtools.BAMRecord
  Avoids decoding CIGAR in order to get length.
getCigarLength() - Method in class htsjdk.samtools.SAMRecord
  This method is preferred over getCigar().getNumElements(), because for BAMRecord it may be faster.
getCigarString() - Method in class htsjdk.samtools.SAMRecord
getClasses() - Method in class htsjdk.utils.ClassFinder
  Fetches the set of classes discovered so far.
getCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
getCode() - Method in class htsjdk.samtools.util.ftp.FTPReply
  Gets server reply code from the control port after an ftp command has been executed.
getCodecs() - Method in class htsjdk.beta.plugin.registry.HtsCodecResolver
  Get a list of all codecs of the type `C` managed by this resolver.
getCodeWord() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanBitCode
getCodeWordBitLength() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanBitCode
getCodeWordLenForValue(T) - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanCanoncialCodeGenerator
getCodeWordLengths() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParams
getCodingLength() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
  Method description
getCodingLength() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
  Method description
getCoFeatures() - Method in interface htsjdk.tribble.gff.Gff3Feature
  Get set of co-features.
getCoFeatures() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
  Get set of co-features.
getColor() - Method in interface htsjdk.tribble.bed.BEDFeature
getColor() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getColumnCount() - Method in class htsjdk.variant.vcf.VCFHeader
getCommandLine() - Method in class htsjdk.samtools.SAMProgramRecord
getComments() - Method in class htsjdk.samtools.SAMFileHeader
getCommentsWithLineNumbers() - Method in class htsjdk.tribble.gff.Gff3Codec
  Gets map from line number to comment found on that line.
getCommentTexts() - Method in class htsjdk.tribble.gff.Gff3Codec
  Gets list of comments parsed by the codec.
getCommonInfo() - Method in class htsjdk.variant.variantcontext.VariantContext
getComparator() - Method in enum class htsjdk.samtools.SAMFileHeader.SortOrder
  Deprecated.
  since 7/2018, use `SAMFileHeader.SortOrder.getComparatorInstance()` with `Object.getClass()` instead
getComparatorInstance() - Method in enum class htsjdk.samtools.SAMFileHeader.SortOrder
getCompressedContent() - Method in class htsjdk.samtools.cram.structure.block.Block
getCompressedContentSize() - Method in class htsjdk.samtools.cram.structure.block.Block
getCompressedOffset() - Method in class htsjdk.samtools.util.GZIIndex.IndexEntry
  Returns the compressed offset (block-offset).
getCompressionHeader() - Method in class htsjdk.samtools.cram.structure.Container
getCompressionHeader() - Method in class htsjdk.samtools.cram.structure.Slice
getCompressionLevel() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Set the compression level for these options.
getCompressionLevel() - Method in class htsjdk.samtools.SAMFileWriterFactory
getCompressionLevel() - Static method in class htsjdk.samtools.util.IOUtil
getCompressionMethod() - Method in class htsjdk.samtools.cram.structure.block.Block
getCompressorForMethod(BlockCompressionMethod, int) - Static method in class htsjdk.samtools.cram.compression.ExternalCompressor
  Return an ExternalCompressor subclass based on the BlockCompressionMethod.
getCompressorForMethod(BlockCompressionMethod, int) - Method in class htsjdk.samtools.cram.structure.CompressorCache
  Return a compressor if it's in our cache, otherwise spin one up and cache it and return it.
getCompressorMap() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getConcreteClasses() - Method in class htsjdk.utils.ClassFinder
  Fetches the set of classes discovered so far, subsetted down to concrete (non-abstract/interface) classes only
getConnection() - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
getConnection() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
getContained(Locatable) - Method in class htsjdk.samtools.util.IntervalTreeMap
getContainerBlocksByteSize() - Method in class htsjdk.samtools.cram.structure.ContainerHeader
getContainerByteOffset() - Method in class htsjdk.samtools.cram.structure.Container
getContainerHeader() - Method in class htsjdk.samtools.cram.structure.Container
getContainerStartByteOffset() - Method in class htsjdk.samtools.cram.BAIEntry
getContainerStartByteOffset() - Method in class htsjdk.samtools.cram.CRAIEntry
getContentId() - Method in class htsjdk.samtools.cram.structure.block.Block
  Return the External Content ID for this block.
getContentIDs() - Method in class htsjdk.samtools.cram.structure.Slice
getContentLength() - Method in class htsjdk.tribble.util.FTPHelper
getContentLength() - Method in class htsjdk.tribble.util.HTTPHelper
getContentLength() - Method in class htsjdk.tribble.util.RemoteURLHelper
getContentLength() - Method in interface htsjdk.tribble.util.URLHelper
getContentLength(URL) - Static method in class htsjdk.samtools.util.ftp.FTPUtils
getContentsFollowing() - Method in class htsjdk.samtools.BAMFileSpan
  Gets a file span over the data immediately following this span.
getContentsFollowing() - Method in interface htsjdk.samtools.SAMFileSpan
  Gets a pointer over the data immediately following this span.
getContentType() - Method in interface htsjdk.beta.io.bundle.BundleResource
  Get the content type for this resource.
getContentType() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
getContentType() - Method in interface htsjdk.beta.plugin.hapref.HaploidReferenceCodec
getContentType() - Method in interface htsjdk.beta.plugin.HtsCodec
  Get the `HtsContentType` for this codec.
getContentType() - Method in interface htsjdk.beta.plugin.reads.ReadsCodec
getContentType() - Method in interface htsjdk.beta.plugin.variants.VariantsCodec
getContentType() - Method in class htsjdk.samtools.cram.structure.block.Block
  Identifies whether this is a header or data block, and which kind
getContentTypeId() - Method in enum class htsjdk.samtools.cram.structure.block.BlockContentType
getContext() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getContext() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getContig() - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
  Gets the contig associated with this entry.
getContig() - Method in class htsjdk.samtools.SAMRecord
getContig() - Method in class htsjdk.samtools.SAMSequenceRecord
  always returns `getSequenceName()`
getContig() - Method in class htsjdk.samtools.util.AbstractLocusInfo
getContig() - Method in class htsjdk.samtools.util.Interval
getContig() - Method in interface htsjdk.samtools.util.Locatable
  Gets the contig name for the contig this is mapped to.
getContig() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getContig() - Method in class htsjdk.tribble.gff.Gff3BaseData
getContig() - Method in interface htsjdk.tribble.gff.Gff3Feature
getContig() - Method in class htsjdk.tribble.gff.SequenceRegion
getContig() - Method in class htsjdk.tribble.MutableFeature
getContig() - Method in class htsjdk.tribble.SimpleFeature
getContig() - Method in class htsjdk.variant.variantcontext.VariantContext
getContig() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Getter for contig
getContigIndex() - Method in class htsjdk.samtools.reference.ReferenceSequence
  Gets the 0-based index of this contig in the source file from which it came.
getContigIndex() - Method in class htsjdk.variant.vcf.VCFContigHeaderLine
getContigLines() - Method in class htsjdk.variant.vcf.VCFHeader
getContigMap() - Method in class htsjdk.samtools.liftover.LiftOver
getCoreBlock() - Method in class htsjdk.samtools.cram.structure.SliceBlocks
  Return the core block for this Slice.
getCoreBlockInputStream() - Method in class htsjdk.samtools.cram.structure.SliceBlocksReadStreams
  Get the `BitInputStream` for this `SliceBlocks` core block.
getCoreOutputStream() - Method in class htsjdk.samtools.cram.structure.SliceBlocksWriteStreams
getCount() - Method in class htsjdk.samtools.cram.io.CountingInputStream
getCount() - Method in class htsjdk.samtools.util.AbstractProgressLogger
  Returns the count of records processed.
getCount() - Method in class htsjdk.samtools.util.Histogram
getCount() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
getCount(VariantContext) - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
  Get the number of values expected for this header field, given the properties of VariantContext vc If the count is a fixed count, return that.
getCountType() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
getCountType() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
getCRAIEntries() - Method in class htsjdk.samtools.cram.CRAIIndex
getCRAIEntries(CompressorCache) - Method in class htsjdk.samtools.cram.structure.Container
  Retrieve the list of CRAI Index entries corresponding to this Container
getCRAIEntries(CompressorCache) - Method in class htsjdk.samtools.cram.structure.Slice
  Generate a CRAI Index entry from this Slice and other container parameters, splitting Multiple Reference slices into constituent reference sequence entries.
getCRAMDecoderOptions() - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Get the `CRAMDecoderOptions` for these options.
getCRAMEncoderOptions() - Method in class htsjdk.beta.plugin.reads.ReadsEncoderOptions
  Get the `CRAMEncoderOptions` for this ReadsEncoderOptions.
getCRAMEncodingStrategy() - Method in class htsjdk.samtools.SAMFileWriterFactory
getCRAMFlags() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getCramHeader() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
getCramHeader() - Method in class htsjdk.samtools.CRAMIterator
getCRAMRecordsForAllSlices() - Method in class htsjdk.samtools.cram.build.SliceFactory
  Get all CRAM records accumulated by the factory.
getCRAMReferenceSource(CRAMDecoderOptions) - Static method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
getCRAMReferenceSource(CRAMEncoderOptions) - Static method in class htsjdk.beta.codecs.reads.cram.CRAMEncoder
  Return a `CRAMReferenceSource` using the `ReadsEncoderOptions`, or a default source.
getCramVersion() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getCramVersion() - Method in class htsjdk.samtools.cram.structure.Slice
getCRAMVersion() - Method in class htsjdk.samtools.cram.structure.CramHeader
getCRC32() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
getCrc32_BigEndian() - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
getCrc32_LittleEndian() - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
getCreator() - Method in class htsjdk.samtools.SAMFileHeader
getCumulativeProbability(double) - Method in class htsjdk.samtools.util.Histogram
  Returns the cumulative probability of observing a value `<=` v when sampling the distribution represented by this histogram.
getCurrent() - Method in class htsjdk.samtools.SecondaryAlignmentSkippingIterator
getCurrent() - Method in class htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
getCurrentReferenceBases() - Method in class htsjdk.samtools.cram.build.CRAMReferenceRegion
getCustomCompressionHeaderEncodingMap() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getCycle(boolean, int, int) - Static method in class htsjdk.samtools.util.CoordMath
  Determines the read cycle number for the base
getData() - Method in class htsjdk.samtools.util.htsget.HtsgetResponse.Block
  Gets data from this block either from its base64 encoded data url or by making an http request
getDataClass() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
getDataClass() - Method in class htsjdk.samtools.util.htsget.HtsgetResponse.Block
getDataStream() - Method in class htsjdk.samtools.util.ftp.FTPClient
getDataStream() - Method in class htsjdk.samtools.util.htsget.HtsgetResponse
  Lazily generates an InputStream over this response's data from the concatenation of the InputStreams from each of the response's data blocks
getDate() - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
getDay() - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
getDecoder(Bundle, D) - Method in interface htsjdk.beta.plugin.HtsCodec
  Get an `HtsDecoder` to decode the provided inputs.
getDecoder(Bundle, HaploidReferenceDecoderOptions) - Method in class htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0
getDecoder(Bundle, ReadsDecoderOptions) - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMCodecV1_0
getDecoder(Bundle, ReadsDecoderOptions) - Method in class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMCodecV2_1
getDecoder(Bundle, ReadsDecoderOptions) - Method in class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMCodecV3_0
getDecoder(Bundle, ReadsDecoderOptions) - Method in class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMCodecV3_1
getDecoder(Bundle, ReadsDecoderOptions) - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMCodecV1_2
getDecoder(Bundle, ReadsDecoderOptions) - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMCodecV1_0
getDecoder(Bundle, VariantsDecoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFCodecV3_2
getDecoder(Bundle, VariantsDecoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFCodecV3_3
getDecoder(Bundle, VariantsDecoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFCodecV4_0
getDecoder(Bundle, VariantsDecoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFCodecV4_1
getDecoder(Bundle, VariantsDecoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFCodecV4_2
getDecoder(Bundle, VariantsDecoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFCodecV4_3
getDecoder(String) - Method in class htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders
  Return decoder appropriate for field, or the generic decoder if no specialized one is bound
getDecodingSymbols() - Method in class htsjdk.samtools.cram.compression.rans.RANSDecode
getDefaultBinSize() - Method in enum class htsjdk.tribble.index.IndexFactory.IndexType
getDefaultCompressionLevel() - Static method in class htsjdk.samtools.util.BlockCompressedOutputStream
getDefaultCRAMReferenceSource() - Static method in class htsjdk.samtools.cram.ref.ReferenceSource
  Attempts to construct a default CRAMReferenceSource for use with CRAM files when one has not been explicitly provided.
getDefaultCreateIndexWhileWriting() - Static method in class htsjdk.samtools.SAMFileWriterFactory
  Gets the default for subsequent SAMFileWriterFactories that do not specify whether to create an index.
getDefaultCreateMd5File() - Static method in class htsjdk.samtools.SAMFileWriterFactory
  Gets the default for whether to create md5Files for BAM files this factory.
getDefaultDeflaterFactory() - Static method in class htsjdk.samtools.util.BlockCompressedOutputStream
getDefaultDictionaryForReferenceSequence(File) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Returns the default dictionary name for a FASTA file.
getDefaultDictionaryForReferenceSequence(Path) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Returns the default dictionary name for a FASTA file.
getDefaultInflaterFactory() - Static method in class htsjdk.samtools.util.BlockGunzipper
getDefaultMaxRecordsInRam() - Static method in class htsjdk.samtools.SAMFileWriterImpl
  When writing records that are not presorted, this number determines the number of records stored in RAM before spilling to disk.
getDefaultTmpDir() - Static method in class htsjdk.samtools.util.IOUtil
  Returns a default tmp directory.
getDefaultTmpDirPath() - Static method in class htsjdk.samtools.util.IOUtil
  Returns a default tmp directory as a Path.
getDeflaterFactory() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Get the `DeflaterFactory` for these options.
getDeletedInRecord() - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo
getDelta() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getDeltaContextLocation() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getDeltaContextTable() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getDescendents() - Method in interface htsjdk.tribble.gff.Gff3Feature
  Get set of all features descended from this features, through chains of Parent attributes.
getDescendents() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
  Get set of all features descended from this features, through chains of Parent attributes.
getDescription() - Method in enum class htsjdk.samtools.DownsamplingIteratorFactory.Strategy
  Gets the description of the strategy.
getDescription() - Method in enum class htsjdk.samtools.SAMFlag
getDescription() - Method in class htsjdk.samtools.SAMReadGroupRecord
getDescription() - Method in class htsjdk.samtools.SAMSequenceRecord
getDescription() - Method in interface htsjdk.tribble.bed.BEDFeature
getDescription() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getDescription() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
getDescription() - Method in class htsjdk.variant.vcf.VCFFilterHeaderLine
  get the "Description" field
getDictionaryString(int) - Method in class htsjdk.variant.bcf2.BCF2Codec
getDiscardedCount() - Method in class htsjdk.samtools.DownsamplingIterator
  Returns the number of records discarded since creation of the last call to resetStatistics.
getDiscardedFraction() - Method in class htsjdk.samtools.DownsamplingIterator
  Gets the fraction of records discarded since creation or the last call to resetStatistics().
getDisplayBases() - Method in interface htsjdk.variant.variantcontext.Allele
getDisplayBases() - Method in class htsjdk.variant.variantcontext.SimpleAllele
  Same as #getDisplayString() but returns the result as byte[].
getDisplayName() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
getDisplayName() - Method in class htsjdk.beta.codecs.reads.bam.BAMDecoder
getDisplayName() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoder
getDisplayName() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
getDisplayName() - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoder
getDisplayName() - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder
getDisplayName() - Method in class htsjdk.beta.codecs.reads.sam.SAMCodec
getDisplayName() - Method in class htsjdk.beta.codecs.reads.sam.SAMDecoder
getDisplayName() - Method in class htsjdk.beta.codecs.reads.sam.SAMEncoder
getDisplayName() - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
getDisplayName() - Method in class htsjdk.beta.codecs.variants.vcf.VCFEncoder
getDisplayName() - Method in interface htsjdk.beta.io.bundle.BundleResource
  Get the display name for this resource.
getDisplayName() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
getDisplayName() - Method in interface htsjdk.beta.plugin.HtsCodec
  Get a user-friendly display name for this codec.
getDisplayName() - Method in interface htsjdk.beta.plugin.HtsDecoder
  Get a user-friendly display name for this decoder.
getDisplayName() - Method in interface htsjdk.beta.plugin.HtsEncoder
  Get a user-friendly display name for this encoder.
getDisplayString() - Method in interface htsjdk.variant.variantcontext.Allele
getDisplayString() - Method in class htsjdk.variant.variantcontext.SimpleAllele
  Return the printed representation of this allele.
getDownloadTriesBeforeFailing() - Method in class htsjdk.samtools.cram.ref.ReferenceSource
getDP() - Method in class htsjdk.variant.variantcontext.FastGenotype
getDP() - Method in class htsjdk.variant.variantcontext.Genotype
getDuplicate() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZModels
getDuplicateReadFlag() - Method in class htsjdk.samtools.SAMRecord
  the read is either a PCR duplicate or an optical duplicate.
getDynamicType(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.AtomicInt
getDynamicType(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.GenericInts
getDynamicType(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
getDynamicType(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.IntArray
getElapsedSeconds() - Method in class htsjdk.samtools.util.AbstractProgressLogger
  Returns the number of seconds since progress tracking began.
getElapsedTime() - Method in class htsjdk.samtools.util.StopWatch
  Returns the cumulative time between all the start() and stop() calls made to this object.
getElapsedTimeSecs() - Method in class htsjdk.samtools.util.StopWatch
getEmbeddedReferenceBlock() - Method in class htsjdk.samtools.cram.structure.Slice
  Return the embedded reference block, if any.
getEmbeddedReferenceContentID() - Method in class htsjdk.samtools.cram.structure.Slice
  Get the content ID of the embedded reference block.
getEmitMd5() - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
getEncodedMatrix() - Method in class htsjdk.samtools.cram.structure.SubstitutionMatrix
  Return this substitution matrix as a byte array in a form suitable for serialization.
getEncoder(Bundle, E) - Method in interface htsjdk.beta.plugin.HtsCodec
  Get an `HtsEncoder` to encode to the provided outputs.
getEncoder(Bundle, HaploidReferenceEncoderOptions) - Method in class htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0
getEncoder(Bundle, ReadsEncoderOptions) - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMCodecV1_0
getEncoder(Bundle, ReadsEncoderOptions) - Method in class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMCodecV2_1
getEncoder(Bundle, ReadsEncoderOptions) - Method in class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMCodecV3_0
getEncoder(Bundle, ReadsEncoderOptions) - Method in class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMCodecV3_1
getEncoder(Bundle, ReadsEncoderOptions) - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMCodecV1_2
getEncoder(Bundle, ReadsEncoderOptions) - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMCodecV1_0
getEncoder(Bundle, VariantsEncoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFCodecV3_2
getEncoder(Bundle, VariantsEncoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFCodecV3_3
getEncoder(Bundle, VariantsEncoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFCodecV4_0
getEncoder(Bundle, VariantsEncoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFCodecV4_1
getEncoder(Bundle, VariantsEncoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFCodecV4_2
getEncoder(Bundle, VariantsEncoderOptions) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFCodecV4_3
getEncodingDescriptorForDataSeries(DataSeries) - Method in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  Get the encoding params that should be used for a given DataSeries.
getEncodingID() - Method in class htsjdk.samtools.cram.structure.EncodingDescriptor
getEncodingMap() - Method in class htsjdk.samtools.cram.structure.CompressionHeader
  Get the `CompressionHeaderEncodingMap` for this compression header.
getEncodingParameters() - Method in class htsjdk.samtools.cram.structure.EncodingDescriptor
getEncodingStrategy() - Method in class htsjdk.samtools.cram.build.CompressionHeaderFactory
getEncodingSymbols() - Method in class htsjdk.samtools.cram.compression.rans.RANSEncode
getEnd() - Method in interface htsjdk.beta.plugin.interval.HtsInterval
  Get the inclusive end coordinate for this interval.
getEnd() - Method in class htsjdk.beta.plugin.interval.HtsQueryInterval
getEnd() - Method in interface htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
getEnd() - Method in class htsjdk.samtools.SAMRecord
  an alias of `SAMRecord.getAlignmentEnd()`
getEnd() - Method in class htsjdk.samtools.SAMSequenceRecord
  always returns `getSequenceLength()`
getEnd() - Method in class htsjdk.samtools.util.AbstractLocusInfo
getEnd() - Method in class htsjdk.samtools.util.Interval
getEnd() - Method in class htsjdk.samtools.util.IntervalTree.Node
getEnd() - Method in interface htsjdk.samtools.util.Locatable
getEnd() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getEnd() - Method in class htsjdk.tribble.gff.Gff3BaseData
getEnd() - Method in interface htsjdk.tribble.gff.Gff3Feature
getEnd() - Method in class htsjdk.tribble.gff.SequenceRegion
getEnd() - Method in class htsjdk.tribble.MutableFeature
getEnd() - Method in class htsjdk.tribble.SimpleFeature
getEnd() - Method in class htsjdk.variant.variantcontext.VariantContext
getEnd(int, int) - Static method in class htsjdk.samtools.util.CoordMath
getEndpoint() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
getEndPosition() - Method in class htsjdk.tribble.index.Block
getError() - Method in class htsjdk.samtools.util.htsget.HtsgetErrorResponse
getErrorProbabilityFromPhredScore(int) - Static method in class htsjdk.samtools.util.QualityUtil
  Given a phred score between 0 and 100 returns the probability of error.
getETag(URL) - Static method in class htsjdk.samtools.util.HttpUtils
getExons() - Method in interface htsjdk.tribble.bed.BEDFeature
getExons() - Method in class htsjdk.tribble.bed.FullBEDFeature
getExons() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getExtendedAttribute(String) - Method in class htsjdk.variant.variantcontext.Genotype
  Same as #getExtendedAttribute with a null default
getExtendedAttribute(String, Object) - Method in class htsjdk.variant.variantcontext.Genotype
  Get the extended attribute value associated with key, if possible
getExtendedAttributes() - Method in class htsjdk.variant.variantcontext.FastGenotype
getExtendedAttributes() - Method in class htsjdk.variant.variantcontext.Genotype
  Returns the extended attributes for this object
getExtension() - Method in interface htsjdk.io.IOPath
getExtension() - Method in enum class htsjdk.samtools.fastq.FastqConstants.FastqExtensions
getExternalBlock(Integer) - Method in class htsjdk.samtools.cram.structure.SliceBlocks
  Get the external block corresponding to a contentID.
getExternalBlockContentId() - Method in enum class htsjdk.samtools.cram.structure.DataSeries
  The content id for a data series is not prescribed by the CrAM spec, so the ids used here represent the ID used by this implementation on write.
getExternalContentIDs() - Method in class htsjdk.samtools.cram.structure.SliceBlocks
  Return a list of external content IDs.
getExternalIDs() - Method in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  Get a list of all external IDs for this encoding map
getExternalReader(Integer) - Method in class htsjdk.samtools.cram.structure.SliceBlocksReadStreams
  Get the `CRAMByteReader` for the given content ID.
getExternalWriter(Integer) - Method in class htsjdk.samtools.cram.structure.SliceBlocksWriteStreams
  Get the `CRAMByteWriter` corresponding to the requested content ID.
getFailedIntervalsBelowThreshold() - Method in class htsjdk.samtools.liftover.LiftOver
getFastaExtension(Path) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Returns the FASTA extension for the path.
getFastaIndexFileName(Path) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Returns the index name for a FASTA file.
getFeatureCodec(File) - Static method in class htsjdk.tribble.example.CountRecords
  Return a `FeatureCodec` instance appropriate for the given `featureFile`.
getFeatureReader(String, FeatureCodec) - Static method in class htsjdk.tribble.AbstractFeatureReader
  Calls `AbstractFeatureReader.getFeatureReader(String, FeatureCodec, boolean)` with `requireIndex` = true
getFeatureReader(String, FeatureCodec, boolean) - Static method in class htsjdk.tribble.AbstractFeatureReader
  `AbstractFeatureReader.getFeatureReader(String, String, FeatureCodec, boolean, Function, Function)` with `null` for indexResource, wrapper, and indexWrapper
getFeatureReader(String, FeatureCodec, Index) - Static method in class htsjdk.tribble.AbstractFeatureReader
  Return a reader with a supplied index.
getFeatureReader(String, String, FeatureCodec, boolean) - Static method in class htsjdk.tribble.AbstractFeatureReader
  `AbstractFeatureReader.getFeatureReader(String, String, FeatureCodec, boolean, Function, Function)` with `null` for wrapper, and indexWrapper
getFeatureReader(String, String, FeatureCodec, boolean, Function, Function) - Static method in class htsjdk.tribble.AbstractFeatureReader
getFeaturesPerBlock() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
getFeaturesPerInterval() - Method in class htsjdk.tribble.index.interval.IntervalIndexCreator
getFeatureType() - Method in class htsjdk.tribble.AbstractFeatureCodec
getFeatureType() - Method in class htsjdk.tribble.example.ExampleBinaryCodec
getFeatureType() - Method in interface htsjdk.tribble.FeatureCodec
  This function returns the object the codec generates.
getFeatureType() - Method in class htsjdk.variant.bcf2.BCF2Codec
getField() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
getField() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
getFieldEncoder() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
getFields() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
getFile() - Method in class htsjdk.samtools.fastq.FastqReader
getFileBlock(long) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
getFileFormat() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0
getFileFormat() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
getFileFormat() - Method in class htsjdk.beta.codecs.reads.bam.BAMCodec
getFileFormat() - Method in class htsjdk.beta.codecs.reads.bam.BAMDecoder
getFileFormat() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoder
getFileFormat() - Method in class htsjdk.beta.codecs.reads.cram.CRAMCodec
getFileFormat() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
getFileFormat() - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoder
getFileFormat() - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec
getFileFormat() - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder
getFileFormat() - Method in class htsjdk.beta.codecs.reads.sam.SAMCodec
getFileFormat() - Method in class htsjdk.beta.codecs.reads.sam.SAMDecoder
getFileFormat() - Method in class htsjdk.beta.codecs.reads.sam.SAMEncoder
getFileFormat() - Method in class htsjdk.beta.codecs.variants.vcf.VCFCodec
getFileFormat() - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
getFileFormat() - Method in class htsjdk.beta.codecs.variants.vcf.VCFEncoder
getFileFormat() - Method in interface htsjdk.beta.io.bundle.BundleResource
  Get the file format for this resource.
getFileFormat() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
getFileFormat() - Method in interface htsjdk.beta.plugin.HtsCodec
  Get the name of the file format supported by this codec.
getFileFormat() - Method in interface htsjdk.beta.plugin.HtsDecoder
  Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (see `BundleResourceType` and `BundleResource.getFileFormat()`).
getFileFormat() - Method in interface htsjdk.beta.plugin.HtsEncoder
  Get the name of the file format supported by this encoder.
getFileHeader() - Method in class htsjdk.samtools.BAMFileReader
getFileHeader() - Method in class htsjdk.samtools.CRAMFileReader
getFileHeader() - Method in class htsjdk.samtools.HtsgetBAMFileReader
getFileHeader() - Method in interface htsjdk.samtools.SAMFileWriter
getFileHeader() - Method in class htsjdk.samtools.SAMFileWriterImpl
getFileHeader() - Method in class htsjdk.samtools.SAMLineParser
  Get the File header.
getFileHeader() - Method in interface htsjdk.samtools.SamReader
getFileHeader() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
getFileHeader() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
getFileHeader() - Method in class htsjdk.variant.vcf.VCFFileReader
  Synonym of `VCFFileReader.getHeader()`
getFileHeader(File) - Method in class htsjdk.samtools.SamReaderFactory
  Utility method to open the file get the header and close the file
getFileHeader(Path) - Method in class htsjdk.samtools.SamReaderFactory
  Utility method to open the file get the header and close the file
getFileLength() - Method in class htsjdk.samtools.SBIIndex.Header
getFilename() - Method in class htsjdk.samtools.BAMFileWriter
getFilename() - Method in class htsjdk.samtools.CRAMFileWriter
getFilename() - Method in class htsjdk.samtools.SAMFileWriterImpl
  For producing error messages.
getFilename() - Method in class htsjdk.samtools.SAMTextWriter
  For producing error messages.
getFilePointer() - Method in class htsjdk.samtools.SAMFileSource
  A pointer to the region on disk from which the read originated.
getFilePointer() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
getFilePointer() - Method in class htsjdk.samtools.util.BlockCompressedOutputStream
  Encode virtual file pointer Upper 48 bits is the byte offset into the compressed stream of a block.
getFilePointerSpanningReads() - Method in class htsjdk.samtools.BAMFileReader
  Gets an unbounded pointer to the first record in the BAM file.
getFilePointerSpanningReads() - Method in class htsjdk.samtools.CRAMFileReader
getFilePointerSpanningReads() - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Generally gets a pointer to the first read in the file.
getFilePointerSpanningReads() - Method in interface htsjdk.samtools.SamReader.Indexing
  Gets a pointer spanning all reads in the BAM file.
getFilePointerSpanningReads() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
getFilePointerSpanningReads() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
getFilesMatchingRegexp(File, String) - Static method in class htsjdk.samtools.util.IOUtil
getFilesMatchingRegexp(File, Pattern) - Static method in class htsjdk.samtools.util.IOUtil
getFileSource() - Method in class htsjdk.samtools.CRAMIterator
getFileSource() - Method in class htsjdk.samtools.SAMRecord
  Gets the source of this SAM record -- both the reader that retrieved the record and the position on disk from whence it came.
getFileSpan(QueryInterval[], BAMIndex) - Static method in class htsjdk.samtools.BAMFileReader
  Use the index to determine the chunk boundaries for the required intervals.
getFilterHeaderLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
getFilterLines() - Method in class htsjdk.variant.vcf.VCFHeader
getFilters() - Method in class htsjdk.variant.variantcontext.CommonInfo
getFilters() - Method in class htsjdk.variant.variantcontext.Genotype
  Returns the filter string associated with this Genotype.
getFilters() - Method in class htsjdk.variant.variantcontext.VariantContext
getFilters() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Getter for filters (DANGEROUS!!! DOES NOT MAKE A COPY!!!)
getFiltersMaybeNull() - Method in class htsjdk.variant.variantcontext.CommonInfo
getFiltersMaybeNull() - Method in class htsjdk.variant.variantcontext.VariantContext
getFinalContainer(long) - Method in class htsjdk.samtools.cram.build.ContainerFactory
  Obtain a `Container` from any remaining accumulated SAMRecords, if any.
getFirstBinInLevel(int) - Static method in class htsjdk.samtools.AbstractBAMFileIndex
  Gets the first bin in the given level.
getFirstBinInLevelForCSI(int) - Method in class htsjdk.samtools.CSIIndex
  Extends the functionality of `AbstractBAMFileIndex.getFirstBinInLevel(int)` , which cannot be overridden due to its static nature.
getFirstCigarElement() - Method in class htsjdk.samtools.Cigar
  returns the first cigar element
getFirstContainerOffset() - Method in class htsjdk.samtools.CRAMIterator
getFirstLocusInBin(Bin) - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Gets the first locus that this bin can index into.
getFirstLocusInBin(Bin) - Method in interface htsjdk.samtools.BrowseableBAMIndex
  Gets the first locus that this bin can index into.
getFirstLocusInBin(Bin) - Method in class htsjdk.samtools.CSIIndex
getFirstOffset() - Method in class htsjdk.samtools.BAMFileSpan
  Find the first offset in the chunk list
getFirstOfPairFlag() - Method in class htsjdk.samtools.SAMRecord
  the read is the first read in a pair.
getFixedLen() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getFlags() - Method in class htsjdk.samtools.SAMRecord
  It is preferable to use the get*Flag() methods that handle the flag word symbolically.
getFlags() - Method in class htsjdk.tribble.index.AbstractIndex
getFlags(int) - Static method in enum class htsjdk.samtools.SAMFlag
getFloatArrayAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
getFloatArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
getFloatAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
getFloatAttribute(String) - Method in class htsjdk.samtools.SAMRecord
getFlowOrder() - Method in class htsjdk.samtools.SAMReadGroupRecord
getFormat() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
getFormat() - Method in class htsjdk.samtools.util.htsget.HtsgetResponse
getFormatFlags() - Method in class htsjdk.samtools.cram.compression.range.RangeParams
getFormatFlags() - Method in class htsjdk.samtools.cram.compression.rans.RANS4x8Params
getFormatFlags() - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
getFormatFlags() - Method in interface htsjdk.samtools.cram.compression.rans.RANSParams
getFormatHeaderLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
getFormatHeaderLines() - Method in class htsjdk.variant.vcf.VCFHeader
  Returns the FORMAT HeaderLines in their original ordering
getFormatLine(String) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
  Returns the standard format line for `ID`.
getFormatLine(String, boolean) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
  Returns the standard format line for `ID`.
getFormatSpec() - Method in class htsjdk.tribble.index.tabix.TabixIndex
getFormatString() - Method in enum class htsjdk.variant.vcf.VCFHeaderVersion
getFQZFlags() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParams
getFQZParamList() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParams
getFrequencies() - Method in class htsjdk.samtools.cram.compression.rans.RANSDecode
getFullCanonicalPath(File) - Static method in class htsjdk.samtools.util.IOUtil
  Returns the full path to the file with all symbolic links resolved
getFullContigLength() - Method in class htsjdk.samtools.cram.build.CRAMReferenceRegion
getGenericFields() - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
getGenotype(int) - Method in class htsjdk.variant.variantcontext.VariantContext
getGenotype(String) - Method in class htsjdk.variant.variantcontext.VariantContext
getGenotypeFieldDecoder(String) - Method in class htsjdk.variant.bcf2.BCF2Codec
getGenotypeFieldWriter(String) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager
  Get a genotypes writer specialized to encode values for genotypes field
getGenotypes() - Method in class htsjdk.variant.variantcontext.GenotypesContext
getGenotypes() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
  Overrides the genotypes accessor.
getGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContext
getGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Getter for genotypes (DANGEROUS!!! DOES NOT MAKE A COPY!!!)
getGenotypes(String) - Method in class htsjdk.variant.variantcontext.VariantContext
  Returns a map from sampleName -> Genotype for the genotype associated with sampleName.
getGenotypes(Collection) - Method in class htsjdk.variant.variantcontext.VariantContext
  Returns a map from sampleName -> Genotype for each sampleName in sampleNames.
getGenotypes(Set) - Method in class htsjdk.variant.variantcontext.VariantContext
getGenotypeSamples() - Method in class htsjdk.variant.vcf.VCFHeader
  get the genotyping sample names
getGenotypesOrderedBy(Iterable) - Method in class htsjdk.variant.variantcontext.VariantContext
getGenotypesOrderedByName() - Method in class htsjdk.variant.variantcontext.VariantContext
getGenotypeString() - Method in class htsjdk.variant.variantcontext.Genotype
  Return a VCF-like string representation for the alleles of this genotype.
getGenotypeString(boolean) - Method in class htsjdk.variant.variantcontext.Genotype
  Return a VCF-like string representation for the alleles of this genotype.
getGeometricMean() - Method in class htsjdk.samtools.util.Histogram
  Gets the geometric mean of the distribution.
getGLIndecesOfAlternateAllele(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
  Deprecated.
  7/18 use `VariantContext.getGLIndicesOfAlternateAllele(Allele)` instead
getGLIndicesOfAlternateAllele(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
getGlobalLogLevel() - Static method in class htsjdk.samtools.util.Log
  Get the log level.
getGlobalPrintStream() - Static method in class htsjdk.samtools.util.Log
  Get the `PrintStream` for writing.
getGlobalRecordCounter() - Method in class htsjdk.samtools.cram.structure.ContainerHeader
getGlobalRecordCounter() - Method in class htsjdk.samtools.cram.structure.Slice
getGQ() - Method in class htsjdk.variant.variantcontext.FastGenotype
getGQ() - Method in class htsjdk.variant.variantcontext.Genotype
  Returns a phred-scaled quality score, or -1 if none is available
getGQLog10FromLikelihoods(int, double[]) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
getGranularity() - Method in class htsjdk.samtools.SBIIndex
  Returns the granularity of the index, that is the number of alignments between subsequent entries in the index, or zero if not specified.
getGranularity() - Method in class htsjdk.samtools.SBIIndex.Header
getGroupOrder() - Method in class htsjdk.samtools.SAMFileHeader
getGZIPCompressionLevel() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getHaploidReferenceDecoder(Bundle) - Method in class htsjdk.beta.plugin.registry.HaploidReferenceResolver
  Get a `HaploidReferenceDecoder` for the given input Bundle.
getHaploidReferenceDecoder(Bundle, HaploidReferenceDecoderOptions) - Method in class htsjdk.beta.plugin.registry.HaploidReferenceResolver
  Get a `HaploidReferenceDecoder` suitable for decoding `inputBundle` using options in `HaploidReferenceDecoderOptions`.
getHaploidReferenceDecoder(IOPath) - Method in class htsjdk.beta.plugin.registry.HaploidReferenceResolver
  Get a `HaploidReferenceDecoder` for the given inputPath.
getHaploidReferenceDecoder(IOPath, HaploidReferenceDecoderOptions) - Method in class htsjdk.beta.plugin.registry.HaploidReferenceResolver
  Get a `HaploidReferenceDecoder` suitable for decoding `inputPath` using options in `HaploidReferenceDecoderOptions`.
getHaploidReferenceResolver() - Method in class htsjdk.beta.plugin.registry.HtsCodecRegistry
  Get the `HaploidReferenceResolver` for this registry.
getHaploidReferenceResolver() - Static method in class htsjdk.beta.plugin.registry.HtsDefaultRegistry
  Grt the `HaploidReferenceResolver` resolver for this registry.
getHeader() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
getHeader() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
getHeader() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
getHeader() - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
getHeader() - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0
getHeader() - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
getHeader() - Method in interface htsjdk.beta.plugin.HtsDecoder
  Get the file header for this decoder.
getHeader() - Method in class htsjdk.samtools.SAMRecord
getHeader() - Method in class htsjdk.samtools.SAMRecordSetBuilder
getHeader() - Method in class htsjdk.samtools.SBIIndex
  Returns the index header.
getHeader() - Method in class htsjdk.samtools.util.AbstractLocusIterator
getHeader() - Method in class htsjdk.samtools.util.IntervalList
  Gets the header (if there is one) for the interval list.
getHeader() - Method in class htsjdk.samtools.util.IntervalListReferenceSequenceMask
getHeader() - Method in class htsjdk.tribble.AbstractFeatureReader
  get the header
getHeader() - Method in interface htsjdk.tribble.FeatureReader
  Provide access to the header of the reader
getHeader() - Method in class htsjdk.variant.bcf2.BCF2Codec
getHeader() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
getHeader() - Method in class htsjdk.variant.vcf.AbstractVCFCodec
getHeader() - Method in class htsjdk.variant.vcf.VCFFileReader
  Returns the VCFHeader associated with this VCF/BCF file.
getHeader() - Method in interface htsjdk.variant.vcf.VCFIterator
  Returns the VCFHeader associated with this VCF/BCF file.
getHeader() - Method in interface htsjdk.variant.vcf.VCFReader
  Returns the VCFHeader associated with this VCFReader.
getHeaderEnd() - Method in class htsjdk.tribble.FeatureCodecHeader
getHeaderField(URL, String) - Static method in class htsjdk.samtools.util.HttpUtils
getHeaderFields() - Method in class htsjdk.variant.vcf.VCFHeader
  get the header fields in order they're presented in the input file (which is now required to be the order presented in the spec).
getHeaderKey() - Method in class htsjdk.samtools.filter.AbstractJavascriptFilter
  returns key used for header binding
getHeaders() - Method in class htsjdk.samtools.metrics.MetricsFile
  Returns the list of headers.
getHeaders() - Method in class htsjdk.samtools.SamFileHeaderMerger
  Returns the collection of readers that this header merger is working with.
getHeaders() - Method in class htsjdk.samtools.util.htsget.HtsgetResponse.Block
getHeaders(Class) - Method in class htsjdk.samtools.metrics.MetricsFile
  Returns the list of headers with the specified type.
getHeaderValue() - Method in class htsjdk.tribble.FeatureCodecHeader
getHeaderVersion(String) - Static method in enum class htsjdk.variant.vcf.VCFHeaderVersion
getHelper(URL) - Method in interface htsjdk.tribble.util.URLHelperFactory
getHetCount() - Method in class htsjdk.variant.variantcontext.VariantContext
  Genotype-specific functions -- how many het calls are there in the genotypes?
getHistogram() - Method in class htsjdk.samtools.metrics.MetricsFile
  Returns the histogram contained in the metrics file if any.
getHistogramString() - Method in enum class htsjdk.samtools.SAMValidationError.Type
getHomRefCount() - Method in class htsjdk.variant.variantcontext.VariantContext
  Genotype-specific functions -- how many hom ref calls are there in the genotypes?
getHomVarCount() - Method in class htsjdk.variant.variantcontext.VariantContext
  Genotype-specific functions -- how many hom var calls are there in the genotypes?
getHours() - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
getHuffmanParams() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParamsCalculator
getId() - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
  Returns the ID tag (or equivalent) for this header record.
getId() - Method in class htsjdk.samtools.cram.structure.CramHeader
getId() - Method in enum class htsjdk.samtools.cram.structure.EncodingID
getId() - Method in class htsjdk.samtools.SAMProgramRecord
getId() - Method in class htsjdk.samtools.SAMReadGroupRecord
getId() - Method in class htsjdk.samtools.util.Histogram.Bin
  Gets the ID of this bin.
getId() - Method in class htsjdk.tribble.gff.Gff3BaseData
getID() - Method in interface htsjdk.tribble.gff.Gff3Feature
getID() - Method in enum class htsjdk.variant.bcf2.BCF2Type
  The ID according to the BCF2 specification
getID() - Method in class htsjdk.variant.variantcontext.VariantContext
getID() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Getter for id of variant
getID() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
getID() - Method in interface htsjdk.variant.vcf.VCFIDHeaderLine
getID() - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
getIDHeaderLines() - Method in class htsjdk.variant.vcf.VCFHeader
getIdValue() - Method in class htsjdk.samtools.util.Histogram.Bin
getIndelLengths() - Method in class htsjdk.variant.variantcontext.VariantContext
  Gets the sizes of the alternate alleles if they are insertion/deletion events, and returns a list of their sizes
getIndex() - Method in class htsjdk.beta.plugin.reads.ReadsBundle
  Get the optional `BundleResourceType.CT_READS_INDEX` resource for this `ReadsBundle`.
getIndex() - Method in class htsjdk.beta.plugin.variants.VariantsBundle
  Get the optional `BundleResourceType.CT_VARIANTS_INDEX` resource for this `VariantsBundle`.
getIndex() - Method in class htsjdk.samtools.BAMFileReader
  Retrieves the index for the given file type.
getIndex() - Method in class htsjdk.samtools.cram.structure.ReadTag
getIndex() - Method in class htsjdk.samtools.CRAMFileReader
getIndex() - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Always null as htsget sources do not have indices
getIndex() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
getIndex() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
getIndex() - Method in interface htsjdk.samtools.SamReader.Indexing
  Retrieves the index for the given file type.
getIndex() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
getIndex() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
getIndex(int, int) - Method in class htsjdk.samtools.util.IntervalTree
  Find the rank of the specified interval.
getIndexChannelTransformer() - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Get the channel transformer for the index resource.
getIndexChannelTransformer() - Method in class htsjdk.beta.plugin.variants.VariantsDecoderOptions
  Get the channel transformer for the index resource.
getIndexedFile() - Method in class htsjdk.tribble.index.AbstractIndex
  Deprecated.
  on 03/2017. Use `AbstractIndex.getIndexedPath()` instead.
getIndexedFileMD5() - Method in class htsjdk.tribble.index.AbstractIndex
getIndexedFileSize() - Method in class htsjdk.tribble.index.AbstractIndex
getIndexedFileTS() - Method in class htsjdk.tribble.index.AbstractIndex
getIndexedPath() - Method in class htsjdk.tribble.index.AbstractIndex
getIndexEntries() - Method in class htsjdk.samtools.LinearIndex
  Direct access to the array.
getIndexEntries() - Method in class htsjdk.samtools.util.GZIIndex
  Gets an unmodifiable list with the index entries.
getIndexEntry(String) - Method in class htsjdk.samtools.reference.FastaSequenceIndex
  Retrieve the index entry associated with the given contig.
getIndexingBin() - Method in interface htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
getIndexStart() - Method in class htsjdk.samtools.LinearIndex
getIndexStats(BAMFileReader) - Static method in class htsjdk.samtools.BAMIndexMetaData
  Prints meta-data statistics from BAM index (.bai or .csi) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate
getIndexType() - Method in class htsjdk.samtools.BAMFileReader
  Return the type of the BAM index, BAI or CSI.
getIndexType(BufferedInputStream) - Static method in enum class htsjdk.tribble.index.IndexFactory.IndexType
getIndices() - Method in class htsjdk.tribble.index.tabix.TabixIndex
getInferredInsertSize() - Method in class htsjdk.samtools.SAMRecord
getInflaterFactory() - Method in class htsjdk.beta.codecs.reads.bam.BAMDecoderOptions
  Get the `InflaterFactory` used for these options.
getInfoHeaderLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
getInfoHeaderLines() - Method in class htsjdk.variant.vcf.VCFHeader
  Returns the INFO HeaderLines in their original ordering
getInfoLine(String) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
  Returns the standard info line for `ID`.
getInfoLine(String, boolean) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
  Returns the standard info line for `ID`.
getInputBundle() - Method in class htsjdk.beta.codecs.reads.bam.BAMDecoder
  Get the input `Bundle` for this decoder.
getInputBundle() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
  Get the input `Bundle` for this decoder.
getInputBundle() - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder
  Get the input `Bundle` for this decoder.
getInputBundle() - Method in class htsjdk.beta.codecs.reads.sam.SAMDecoder
  Get the input `Bundle` for this decoder.
getInputBundle() - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
  Get the input `Bundle` for this decoder.
getInputFileName() - Method in class htsjdk.samtools.util.BinaryCodec
  ///////////////////////////////////////////////
getInputStream() - Method in interface htsjdk.beta.io.bundle.BundleResource
  Get an `InputStream` for this resource, or Optional.empty.
getInputStream() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
getInputStream() - Method in class htsjdk.beta.io.bundle.InputStreamResource
getInputStream() - Method in class htsjdk.beta.io.bundle.IOPathResource
  Get an `InputStream` for this resource, or Optional.empty.
getInputStream() - Method in class htsjdk.beta.io.bundle.SeekableStreamResource
  Get the `SeekableStream` managed by this resource as an `InputStream`.
getInputStream() - Method in class htsjdk.io.HtsPath
getInputStream() - Method in interface htsjdk.io.IOPath
  Get a `InputStream` for this URI if a provider is for the URI's scheme is available.
getInputStream() - Method in class htsjdk.samtools.util.BinaryCodec
getInsertedInRecord() - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo
getInstance() - Static method in class htsjdk.samtools.CustomReaderFactory
getInstance() - Static method in class htsjdk.samtools.DefaultSAMRecordFactory
getInstance() - Static method in class htsjdk.samtools.seekablestream.SeekableStreamFactory
getInstance(Class) - Static method in class htsjdk.samtools.util.Log
  Get a Log instance to perform logging within the Class specified.
getIntegerAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
  Get the tag value and attempt to coerce it into the requested type.
getIntegerAttribute(String) - Method in class htsjdk.samtools.SAMRecord
  Get the tag value and attempt to coerce it into the requested type.
getIntersectionLength(Interval) - Method in class htsjdk.samtools.util.Interval
getInterval() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
getIntervals() - Method in class htsjdk.samtools.util.AbstractLocusIterator
getIntervals() - Method in class htsjdk.samtools.util.IntervalList
  Gets the set of intervals as held internally.
getIntervals() - Method in class htsjdk.tribble.index.interval.IntervalTree
  Return all intervals in tree.
getIOPath() - Method in interface htsjdk.beta.io.bundle.BundleResource
  Get the `IOPath` backing this resource, or Optional.empty.
getIOPath() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
getIOPath() - Method in class htsjdk.beta.io.bundle.IOPathResource
getIsDuplicate() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getIsoDate(Date) - Static method in class htsjdk.samtools.util.DateParser
  Generate a ISO 8601 date
getIterator() - Method in class htsjdk.samtools.BAMFileReader
  Prepare to iterate through the SAMRecords in file order.
getIterator() - Method in class htsjdk.samtools.CRAMFileReader
getIterator() - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Prepare to iterate through the SAMRecords in file order.
getIterator() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
getIterator(SAMFileSpan) - Method in class htsjdk.samtools.BAMFileReader
getIterator(SAMFileSpan) - Method in class htsjdk.samtools.CRAMFileReader
  Note: the resolution of this iterator is the Slice, so the records returned are all of the records in all the slices that overlap these spans.
getIterator(SAMFileSpan) - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Generally loads data at a given point in the file.
getIterator(SAMFileSpan) - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
getIUPACCodesString() - Static method in class htsjdk.samtools.util.SequenceUtil
  Returns all IUPAC codes as a string
getKey() - Method in class htsjdk.samtools.cram.structure.ReadTag
getKey() - Method in class htsjdk.variant.vcf.VCFHeaderLine
  Get the key
getKeyAndType() - Method in class htsjdk.samtools.cram.structure.ReadTag
getKeySequence() - Method in class htsjdk.samtools.SAMReadGroupRecord
getLabel() - Method in enum class htsjdk.samtools.SAMFlag
getLandmarkIndex() - Method in class htsjdk.samtools.cram.BAIEntry
getLandmarks() - Method in class htsjdk.samtools.cram.structure.ContainerHeader
getLastChunk() - Method in class htsjdk.samtools.Bin
  Warning: Currently only valid during index building, not when reading existing index, (AbstractBAMFileIndex.optimizeChunkList doesn't maintain this)
getLastCigarElement() - Method in class htsjdk.samtools.Cigar
  returns the last cigar element
getLastLocusInBin(Bin) - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Gets the last locus that this bin can index into.
getLastLocusInBin(Bin) - Method in interface htsjdk.samtools.BrowseableBAMIndex
  Gets the last locus that this bin can index into.
getLastLocusInBin(Bin) - Method in class htsjdk.samtools.CSIIndex
getLeftmost(List) - Static method in class htsjdk.samtools.cram.CRAIIndex
  Currently unused, but retained for the native rai query implementation
getLength() - Method in class htsjdk.samtools.AlignmentBlock
  The number of contiguous bases aligned to the reference.
getLength() - Method in class htsjdk.samtools.CigarElement
getLength() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZModels
getLength() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
getLength() - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
getLength() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
getLength() - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
getLength() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
getLength() - Method in class htsjdk.samtools.util.IntervalTree.Node
getLength(int, int) - Static method in class htsjdk.samtools.util.CoordMath
getLengthOnReference() - Method in interface htsjdk.samtools.util.Locatable
getLevelForBin(Bin) - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Gets the level associated with the given bin number.
getLevelForBin(Bin) - Method in interface htsjdk.samtools.BrowseableBAMIndex
  Gets the level associated with the given bin number.
getLevelForBin(Bin) - Method in class htsjdk.samtools.CSIIndex
getLevelSize(int) - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Gets the number of bins in the given level.
getLevelSize(int) - Method in interface htsjdk.samtools.BrowseableBAMIndex
  Gets the size (number of bins in) a given level of a BAM index.
getLevelSize(int) - Method in class htsjdk.samtools.CSIIndex
  Computes the number of bins on the given level.
getLibrary() - Method in class htsjdk.samtools.SAMReadGroupRecord
getLiftOverMinMatch() - Method in class htsjdk.samtools.liftover.LiftOver
  Get minimum fraction of bases that must remap.
getLikelihoods() - Method in class htsjdk.variant.variantcontext.Genotype
  Returns the GenotypesLikelihoods data associated with this Genotype, or null if missing
getLikelihoodsString() - Method in class htsjdk.variant.variantcontext.Genotype
  Convenience function that returns a string representation of the PL field of this genotype, or .
getLinearIndex() - Method in class htsjdk.samtools.BinningIndexContent
getLineNumber() - Method in class htsjdk.samtools.fastq.FastqReader
getLineNumber() - Method in interface htsjdk.samtools.util.LineReader
getLineTerminatorLength() - Method in class htsjdk.tribble.readers.AsciiLineReader
  Returns the length of the line terminator read after the last read line.
getLink() - Method in interface htsjdk.tribble.bed.BEDFeature
getLink() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getLocation() - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
  Gets the location of this contig within the fasta.
getLocus() - Method in class htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference
getlOffset() - Method in class htsjdk.samtools.BinWithOffset
getLog10GQ(Genotype, VariantContext) - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
getLog10GQ(Genotype, List) - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
getLog10GQ(GenotypeType) - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  Deprecated.
  since 2/5/13 use `GenotypeLikelihoods.getLog10GQ(Genotype, VariantContext)` or `GenotypeLikelihoods.getLog10GQ(Genotype, List)`
getLog10PError() - Method in class htsjdk.variant.variantcontext.CommonInfo
getLog10PError() - Method in class htsjdk.variant.variantcontext.Genotype
  Deprecated.
getLog10PError() - Method in class htsjdk.variant.variantcontext.VariantContext
getLongCrc32() - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
getMagicNumber() - Method in enum class htsjdk.tribble.index.IndexFactory.IndexType
getMajor() - Method in class htsjdk.samtools.cram.common.CRAMVersion
getMajorVersion() - Method in class htsjdk.beta.plugin.HtsVersion
  Get the major version integer for this version.
getMajorVersion() - Method in class htsjdk.variant.bcf2.BCFVersion
getMappedCount() - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
getMappedReadsCount() - Method in class htsjdk.samtools.cram.BAIEntry
getMappingQuality() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getMappingQuality() - Method in class htsjdk.samtools.SAMRecord
getMappingQualityScoreCutoff() - Method in class htsjdk.samtools.util.AbstractLocusIterator
getMateAlignmentBlocks(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
getMateAlignmentEnd(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  This method uses the MateCigar value as determined from the attribute MC.
getMateAlignmentStart() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getMateAlignmentStart() - Method in class htsjdk.samtools.SAMRecord
getMateCigar(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  Returns the Mate Cigar or null if there is none.
getMateCigar(SAMRecord, boolean) - Static method in class htsjdk.samtools.SAMUtils
  Returns the Mate Cigar or null if there is none.
getMateCigarLength(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
getMateCigarString(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  Returns the Mate Cigar String as stored in the attribute 'MC'.
getMateFlags() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getMateNegativeStrandFlag() - Method in class htsjdk.samtools.SAMRecord
  strand of the mate (false for forward; true for reverse strand).
getMateReferenceIndex() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getMateReferenceIndex() - Method in class htsjdk.samtools.SAMRecord
  Returns the mate reference index for this record.
getMateReferenceName() - Method in class htsjdk.samtools.SAMRecord
getMateUnclippedEnd(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
getMateUnclippedStart(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
getMateUnmappedFlag() - Method in class htsjdk.samtools.SAMRecord
  the mate is unmapped.
getMax() - Method in class htsjdk.samtools.util.Histogram
  Returns the key with the highest count.
getMaxAddressibleGenomicLocation() - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Gets the possible number of bins for a given reference sequence.
getMaxBins() - Method in class htsjdk.samtools.CSIIndex
getMaxPloidy(int) - Method in class htsjdk.variant.variantcontext.GenotypesContext
  What is the max ploidy among all samples? Returns defaultPloidy if no genotypes are present
getMaxPloidy(int) - Method in class htsjdk.variant.variantcontext.VariantContext
  Returns the maximum ploidy of all samples in this VC, or default if there are no genotypes This function is caching, so it's only expensive on the first call
getMaxPosition() - Method in class htsjdk.samtools.util.IntervalListReferenceSequenceMask
getMaxPosition() - Method in interface htsjdk.samtools.util.ReferenceSequenceMask
getMaxPosition() - Method in class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
getMaxReadsToAccumulatePerLocus() - Method in class htsjdk.samtools.util.AbstractLocusIterator
getMaxRecordsInRam() - Method in class htsjdk.samtools.SAMFileWriterFactory
  Gets the maximum number of records held in RAM before spilling to disk during sorting.
getMaxRecordsInRam() - Method in class htsjdk.samtools.SAMFileWriterImpl
getMaxRecordsInRAM() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Set the maximum records kept in RAM before spilling to disk for these options.
getMaxSelector() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParams
getMaxSequenceIndex() - Method in class htsjdk.samtools.util.IntervalListReferenceSequenceMask
getMaxSequenceIndex() - Method in interface htsjdk.samtools.util.ReferenceSequenceMask
getMaxSequenceIndex() - Method in class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
getMaxSpan() - Method in class htsjdk.samtools.CSIIndex
getMaxSymbol() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParams
getMaxSymbols() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getMd5() - Method in exception class htsjdk.samtools.cram.ref.GaveUpException
getMd5() - Method in class htsjdk.samtools.SAMSequenceRecord
getMd5() - Method in class htsjdk.samtools.SBIIndex.Header
getMd5() - Method in class htsjdk.samtools.util.htsget.HtsgetResponse
getMean() - Method in class htsjdk.samtools.util.Histogram
  Assuming that the key type for the histogram is a Number type, returns the mean of all the items added to the histogram.
getMeanBinSize() - Method in class htsjdk.samtools.util.Histogram
  Calculates the mean bin size
getMedian() - Method in class htsjdk.samtools.util.Histogram
getMedianAbsoluteDeviation() - Method in class htsjdk.samtools.util.Histogram
  Gets the median absolute deviation of the distribution.
getMedianBinSize() - Method in class htsjdk.samtools.util.Histogram
  Calculates the median bin size
getMergedHeader() - Method in class htsjdk.samtools.MergingSamRecordIterator
  Returns the merged header that the merging iterator is working from.
getMergedHeader() - Method in class htsjdk.samtools.SamFileHeaderMerger
  Returns the merged header that should be written to any output merged file.
getMergedSequenceIndex(SAMFileHeader, Integer) - Method in class htsjdk.samtools.SamFileHeaderMerger
  Another mechanism for getting the new sequence index, for situations in which the reader is not available.
getMergedSequenceIndex(SamReader, Integer) - Method in class htsjdk.samtools.SamFileHeaderMerger
  Deprecated.
  replaced by `SamFileHeaderMerger.getMergedSequenceIndex(SAMFileHeader, Integer)`
getMessage() - Method in class htsjdk.samtools.SAMValidationError
getMessage() - Method in class htsjdk.samtools.util.htsget.HtsgetErrorResponse
getMessage() - Method in exception class htsjdk.tribble.TribbleException
  override the default message with ours, which attaches the source file in question
getMetaData(int) - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Return meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
getMetaData(int) - Method in interface htsjdk.samtools.BAMIndex
  Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
getMetaData(int) - Method in class htsjdk.samtools.CSIIndex
  Return meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
getMetaDataForField(VCFHeader, String) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
getMetaDataInInputOrder() - Method in class htsjdk.variant.vcf.VCFHeader
  get the meta data, associated with this header, in sorted order
getMetaDataInSortedOrder() - Method in class htsjdk.variant.vcf.VCFHeader
getMetaDataLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
  Get the VCFHeaderLine whose key equals key.
getMetaHeaderLine(String, VCFHeaderVersion) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  Create and return a VCFMetaHeaderLine object from a header line string that conforms to the `sourceVersion`
getMethod() - Method in class htsjdk.samtools.cram.compression.ExternalCompressor
getMethodId() - Method in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
getMetrics() - Method in class htsjdk.samtools.metrics.MetricsFile
  Returns the list of headers.
getMetricsColumnLabels() - Method in class htsjdk.samtools.metrics.MetricsFile
getMin() - Method in class htsjdk.samtools.util.Histogram
  Returns the key with the lowest count.
getMinimumOffset(int) - Method in class htsjdk.samtools.LinearIndex
  Gets the minimum offset of any alignment start appearing in this index, according to the linear index.
getMinimumSingleReferenceSliceSize() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getMinor() - Method in class htsjdk.samtools.cram.common.CRAMVersion
getMinorVersion() - Method in class htsjdk.beta.plugin.HtsVersion
  Get the minor version integer for this version.
getMinorVersion() - Method in class htsjdk.variant.bcf2.BCFVersion
getMinShift() - Method in class htsjdk.samtools.CSIIndex
  2^(min shift) is the smallest width of a bin
getMinutes() - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
getMissingBytes() - Method in enum class htsjdk.variant.bcf2.BCF2Type
  The bytes (encoded as an int) that are used to represent a missing value for this type in BCF2
getMissingJavaValue() - Method in enum class htsjdk.variant.bcf2.BCF2Type
  Return the java object (aka null) that is used to represent a missing value for this type in Java
getMixedCount() - Method in class htsjdk.variant.variantcontext.VariantContext
  Genotype-specific functions -- how many mixed calls are there in the genotypes?
getMode() - Method in class htsjdk.samtools.util.Histogram
  Returns id of the Bin that's the mode of the distribution (i.e.
getMonth() - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
getMultiRefAlignmentSpans(CompressorCache, ValidationStringency) - Method in class htsjdk.samtools.cram.structure.Slice
  Uses a Multiple Reference Slice Alignment Reader to determine the reference spans of a MULTI_REF Slice.
getNAlleles() - Method in class htsjdk.variant.variantcontext.VariantContext
getName() - Method in class htsjdk.samtools.reference.ReferenceSequence
  Gets the set of names given to this sequence in the source file.
getName() - Method in class htsjdk.samtools.util.Interval
  Returns the name of the interval, possibly null.
getName() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getName() - Method in class htsjdk.tribble.gff.Gff3BaseData
getName() - Method in interface htsjdk.tribble.gff.Gff3Feature
getName() - Method in interface htsjdk.tribble.index.ChrIndex
getName() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
getName() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
getName() - Method in interface htsjdk.tribble.NameAwareCodec
getName() - Method in interface htsjdk.tribble.NamedFeature
getName() - Method in class htsjdk.variant.variantcontext.CommonInfo
getName() - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  get the name of this codec
getNBlocks() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
getNext() - Method in class htsjdk.samtools.SAMBinaryTagAndValue
getNextContainer(SAMRecord, long) - Method in class htsjdk.samtools.cram.build.ContainerFactory
  Add a new `SAMRecord` object to the factory, obtaining a `Container` if one is returned.
getNextSegment() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getNFeatures() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
getNGenotypeSamples() - Method in class htsjdk.variant.vcf.VCFHeader
getNoCallCount() - Method in class htsjdk.variant.variantcontext.VariantContext
  Genotype-specific functions -- how many no-calls are there in the genotypes?
getNoCoordinateCount() - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Returns count of records unassociated with any reference.
getNoCoordinateCount() - Method in class htsjdk.samtools.CSIIndex
  Returns count of records unassociated with any reference.
getNonCollidingId(String) - Method in class htsjdk.samtools.SAMFileHeader.PgIdGenerator
getNoTags() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
getNotPrimaryAlignmentFlag() - Method in class htsjdk.samtools.SAMRecord
  Deprecated.
  use `SAMRecord.isSecondaryAlignment()` instead.
getNSamples() - Method in class htsjdk.variant.variantcontext.VariantContext
getNumAttributes() - Method in class htsjdk.variant.variantcontext.CommonInfo
getNumber() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
getNumber() - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
getNumberOfBlocks() - Method in class htsjdk.samtools.cram.structure.Slice
getNumberOfBlocks() - Method in class htsjdk.samtools.util.GZIIndex
  Gets the number of blocks on the file.
getNumberOfExternalBlocks() - Method in class htsjdk.samtools.cram.structure.SliceBlocks
  Number of external locks present in this SliceBlocks object (does not include the core block).
getNumberOfNonNullBins() - Method in class htsjdk.samtools.BinningIndexContent.BinList
getNumberOfRecords() - Method in class htsjdk.samtools.cram.structure.ContainerHeader
getNumberOfRecords() - Method in class htsjdk.samtools.cram.structure.Slice
getNumberOfReferences() - Method in class htsjdk.samtools.AbstractBAMFileIndex
getNumberOfReferences() - Method in class htsjdk.samtools.CSIIndex
getNumberOfSliceEntries() - Method in class htsjdk.samtools.cram.build.SliceFactory
getNumErrors() - Method in class htsjdk.samtools.SamFileValidator
  Number of errors during SAM file validation
getNumHistograms() - Method in class htsjdk.samtools.metrics.MetricsFile
  Returns the number of histograms added to the metrics file.
getNumIndexLevels() - Static method in class htsjdk.samtools.AbstractBAMFileIndex
  Get the number of levels employed by this index.
getNumInterleavedRANSStates() - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
getNumMateCigarsAdded() - Method in class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
getNumOverlappingAlignedBasesToClip(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  Returns the number of bases that need to be clipped due to overlapping pairs.
getNumRecords() - Method in class htsjdk.samtools.cram.structure.CRAMCodecModelContext
getNumRecordsOnDisk() - Method in class htsjdk.samtools.util.DiskBackedQueue
getNumWarnings() - Method in class htsjdk.samtools.SamFileValidator
  Number of warnings during SAM file validation
getOffset() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
getOperator() - Method in class htsjdk.samtools.CigarElement
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
getOperator() - Method in interface htsjdk.samtools.cram.encoding.readfeatures.ReadFeature
  Read features are distinguished by operator, similar to cigar operator.
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
getOperator() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
getOrder() - Method in class htsjdk.samtools.cram.compression.range.RangeParams
getOrder() - Method in class htsjdk.samtools.cram.compression.rans.RANS4x8Params
getOrder() - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
getOrder() - Method in interface htsjdk.samtools.cram.compression.rans.RANSParams
getOrElse(T, T) - Static method in class htsjdk.samtools.util.CodeUtil
  Mimic of Oracle's nvl() - returns the first value if not null, otherwise the second value.
getOriginalBaseQualities() - Method in class htsjdk.samtools.SAMRecord
  If the original base quality scores have been store in the "OQ" tag will return the numeric score as a byte[]
getOrThrow(String) - Method in class htsjdk.beta.io.bundle.Bundle
  Get the BundleResource for the provided targetContentType string, or throw if no such resource exists.
getOtherCanonicalAlignments(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  Extract a List of 'other canonical alignments' from a SAM record.
getOtherHeaderLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
getOtherHeaderLines() - Method in class htsjdk.variant.vcf.VCFHeader
  Returns the other HeaderLines in their original ordering
getOutputBufferSize() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Get the output buffer size for these options.
getOutputBundle() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoder
  Get the output `Bundle` for this encoder.
getOutputBundle() - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoder
  Get the output `Bundle` for this encoder.
getOutputBundle() - Method in class htsjdk.beta.codecs.reads.sam.SAMEncoder
  Get the output `Bundle` for this encoder.
getOutputBundle() - Method in class htsjdk.beta.codecs.variants.vcf.VCFEncoder
  Get the output `Bundle` for this encoder.
getOutputFileName() - Method in class htsjdk.samtools.util.BinaryCodec
getOutputPosition() - Method in class htsjdk.samtools.cram.compression.range.RangeCoder
  Return the current write position in the output buffer.
getOutputStream() - Method in interface htsjdk.beta.io.bundle.BundleResource
  Get an `OutputStream` for this resource, or Optional.empty.
getOutputStream() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
getOutputStream() - Method in class htsjdk.beta.io.bundle.IOPathResource
getOutputStream() - Method in class htsjdk.beta.io.bundle.OutputStreamResource
getOutputStream() - Method in class htsjdk.io.HtsPath
getOutputStream() - Method in interface htsjdk.io.IOPath
  Get an `OutputStream` for this URI if a provider is for the URI's scheme.
getOutputStream() - Method in class htsjdk.samtools.util.BinaryCodec
getOverlap(int, int, int, int) - Static method in class htsjdk.samtools.util.CoordMath
  Determines the amount of overlap between two coordinate ranges.
getOverlapping(Locatable) - Method in class htsjdk.samtools.util.IntervalTreeMap
getOverlaps(Locatable) - Method in class htsjdk.samtools.util.OverlapDetector
  Gets the Set of objects that overlap the provided locatable.
getPaddedReferenceLength() - Method in class htsjdk.samtools.Cigar
getPairedReadName() - Method in class htsjdk.samtools.SAMRecord
getPairOrientation(SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil
  Computes the pair orientation of the given SAMRecord.
getParentBinNumber(int) - Method in class htsjdk.samtools.CSIIndex
getParentBinNumber(Bin) - Method in class htsjdk.samtools.CSIIndex
getParents() - Method in interface htsjdk.tribble.gff.Gff3Feature
  Gets set of parent features
getParents() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
  Gets set of parent features
getPartition(V) - Method in class htsjdk.samtools.util.CollectionUtil.Partitioner
  Deprecated.
getPassword() - Method in interface htsjdk.samtools.seekablestream.UserPasswordInput
getPatchVersion() - Method in class htsjdk.beta.plugin.HtsVersion
  Get the patch version integer for this version.
getPath() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Returns the path to the reference file.
getPath() - Method in class htsjdk.samtools.reference.FastaSequenceFile
  Returns the path to the reference file.
getPath() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Returns the path to the reference file.
getPath(String) - Static method in class htsjdk.samtools.util.IOUtil
  Converts the given URI to a `Path` object.
getPaths(List) - Static method in class htsjdk.samtools.util.IOUtil
getPathToDataFile(String) - Method in interface htsjdk.tribble.FeatureCodec
  Codecs may override this method if the file that they recognize with `FeatureCodec.canDecode(String)` is different than the file that contains the data they parse.
getPedigreeHeaderLine(String, VCFHeaderVersion) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  Create and return a VCFPedigreeHeaderLine object from a header line string that conforms to the `sourceVersion`
getPercentile(double) - Method in class htsjdk.samtools.util.Histogram
  Gets the bin in which the given percentile falls.
getPGLine(SAMProgramRecord) - Method in class htsjdk.samtools.SAMTextHeaderCodec
getPhase() - Method in class htsjdk.tribble.gff.Gff3BaseData
getPhase() - Method in interface htsjdk.tribble.gff.Gff3Feature
getPhredScaledQual() - Method in class htsjdk.variant.variantcontext.CommonInfo
  Floating-point arithmetic allows signed zeros such as +0.0 and -0.0.
getPhredScaledQual() - Method in class htsjdk.variant.variantcontext.Genotype
  Deprecated.
getPhredScaledQual() - Method in class htsjdk.variant.variantcontext.VariantContext
getPhredScoreFromErrorProbability(double) - Static method in class htsjdk.samtools.util.QualityUtil
  Gets the phred score for any given probability of error.
getPhredScoreFromObsAndErrors(double, double) - Static method in class htsjdk.samtools.util.QualityUtil
  Gets the phred score given the specified observations and errors.
getPL() - Method in class htsjdk.variant.variantcontext.FastGenotype
getPL() - Method in class htsjdk.variant.variantcontext.Genotype
  Unsafe low-level accessor the PL field itself, may be null.
getPlatform() - Method in class htsjdk.samtools.SAMReadGroupRecord
getPlatformModel() - Method in class htsjdk.samtools.SAMReadGroupRecord
getPlatformUnit() - Method in class htsjdk.samtools.SAMReadGroupRecord
getPLIndecesOfAlleles(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  Deprecated.
  7/18 use `GenotypeLikelihoods.getPLIndicesOfAlleles(int, int)` instead
getPLIndicesOfAlleles(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  get the PL indices (AA, AB, BB) for the given allele pair; assumes allele1Index <= allele2Index.
getPloidy() - Method in class htsjdk.variant.variantcontext.Genotype
  What is the ploidy of this sample?
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
getPosition() - Method in interface htsjdk.samtools.cram.encoding.readfeatures.ReadFeature
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
getPosition() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
getPosition() - Method in class htsjdk.samtools.cram.io.CRAMByteReader
  Return the current read position within the buffer.
getPosition() - Method in class htsjdk.samtools.cram.io.CRAMByteWriter
  Return the current write position (alias for `CRAMByteWriter.size()`).
getPosition() - Method in class htsjdk.samtools.util.AbstractLocusInfo
getPosition() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
getPosition() - Method in class htsjdk.samtools.util.BlockCompressedOutputStream
getPosition() - Method in interface htsjdk.samtools.util.LocationAware
  The current offset, in bytes, of this stream/writer/file.
getPosition() - Method in interface htsjdk.samtools.util.Locus
getPosition() - Method in class htsjdk.samtools.util.LocusImpl
getPosition() - Method in class htsjdk.samtools.util.PositionalOutputStream
getPosition() - Method in class htsjdk.tribble.readers.AsciiLineReader
getPosition() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
  Returns the byte position at the end of the most-recently-read line (a.k.a., the beginning of the next line) from `AsciiLineReaderIterator.next()` in the underlying `AsciiLineReader`.
getPosition() - Method in class htsjdk.tribble.readers.PositionalBufferedStream
getPositionContextLocation() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getPositionContextTable() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getPredictedMedianInsertSize() - Method in class htsjdk.samtools.SAMReadGroupRecord
getPreviousProgramGroupId() - Method in class htsjdk.samtools.SAMProgramRecord
getPreviousQuality() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getPreviousRecord() - Method in class htsjdk.samtools.SAMSortOrderChecker
getPreviousSegment() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getPrimaryContentType() - Method in class htsjdk.beta.io.bundle.Bundle
  Get the primary content type for this bundle.
getPrimaryResource() - Method in class htsjdk.beta.io.bundle.Bundle
  Get the primary `BundleResource` for this bundle.
getProgramGroup() - Method in class htsjdk.samtools.SAMReadGroupRecord
getProgramGroupId() - Method in class htsjdk.samtools.SAMProgramRecord
getProgramGroupId(SAMFileHeader, String) - Method in class htsjdk.samtools.SamFileHeaderMerger
getProgramGroupId(SamReader, String) - Method in class htsjdk.samtools.SamFileHeaderMerger
  Deprecated.
  replaced by `SamFileHeaderMerger.getProgramGroupId(SAMFileHeader, String)`
getProgramName() - Method in class htsjdk.samtools.SAMProgramRecord
getProgramRecord(String) - Method in class htsjdk.samtools.SAMFileHeader
getProgramRecords() - Method in class htsjdk.samtools.SAMFileHeader
getProgramVersion() - Method in class htsjdk.samtools.SAMProgramRecord
getProperPairFlag() - Method in class htsjdk.samtools.SAMRecord
  the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
getProperties() - Method in class htsjdk.tribble.index.AbstractIndex
  return a mapping of name to property value
getProperties() - Method in interface htsjdk.tribble.index.Index
getProperties() - Method in class htsjdk.tribble.index.tabix.TabixIndex
  No arbitrary properties in Tabix
getQuality() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZModels
getQualityContext() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getQualityContextBits() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getQualityContextLocation() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getQualityContextShift() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getQualityContextTable() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getQualityLengthArray() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getQualityMap() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getQualityScore() - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
getQualityScore() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
getQualityScoreCutoff() - Method in class htsjdk.samtools.util.AbstractLocusIterator
getQualityScoreLengths() - Method in class htsjdk.samtools.cram.structure.CRAMCodecModelContext
getQualityScores() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getQueryName() - Method in interface htsjdk.beta.plugin.interval.HtsInterval
  Get the name part of this interval query.
getQueryName() - Method in class htsjdk.beta.plugin.interval.HtsQueryInterval
getQueryResults(int) - Method in class htsjdk.samtools.AbstractBAMFileIndex
getQueryResults(int) - Method in class htsjdk.samtools.CSIIndex
getQueryResults(int) - Method in class htsjdk.samtools.DiskBasedBAMFileIndex
getRandomBases(Random, int) - Static method in class htsjdk.samtools.util.SequenceUtil
  Returns an array of bytes containing random DNA bases
getRandomBases(Random, int, byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
  Fills an array of bytes with random DNA bases.
getRawContent() - Method in class htsjdk.samtools.cram.structure.block.Block
  Return the raw (uncompressed) content from a block.
getRawInputString() - Method in class htsjdk.io.HtsPath
  Return the raw input string provided to the constructor.
getRawInputString() - Method in interface htsjdk.io.IOPath
  Return the raw input string that was provided to the constructor.
getReadBase() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
getReadBases() - Method in class htsjdk.samtools.BAMRecord
getReadBases() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getReadBases() - Method in class htsjdk.samtools.fastq.FastqRecord
  Get the DNA sequence.
getReadBases() - Method in class htsjdk.samtools.SAMRecord
  Do not modify the value returned by this method.
getReader() - Method in class htsjdk.samtools.SAMFileSource
  Retrieves the reader from which this read was initially retrieved.
getReaders() - Method in class htsjdk.samtools.SamFileHeaderMerger
  Deprecated.
  replaced by `SamFileHeaderMerger.getHeaders()`
getReadFailsVendorQualityCheckFlag() - Method in class htsjdk.samtools.SAMRecord
  the read fails platform/vendor quality checks.
getReadFeatures() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getReadFeaturesList() - Method in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
  Return the list of read features for this record.
getReadGroup() - Method in class htsjdk.samtools.SAMRecord
  Get the SAMReadGroupRecord for this SAMRecord.
getReadGroup(String) - Method in class htsjdk.samtools.SAMFileHeader
  Look up read group record by name.
getReadGroupId() - Method in class htsjdk.samtools.SAMReadGroupRecord
getReadGroupId(SAMFileHeader, String) - Method in class htsjdk.samtools.SamFileHeaderMerger
  Returns the read group id that should be used for the input read and RG id.
getReadGroupId(SamReader, String) - Method in class htsjdk.samtools.SamFileHeaderMerger
  Deprecated.
  replaced by `SamFileHeaderMerger.getReadGroupId(SAMFileHeader, String)`
getReadGroupID() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getReadGroups() - Method in class htsjdk.samtools.SAMFileHeader
getReadHeader() - Method in class htsjdk.samtools.fastq.FastqRecord
  Deprecated.
  since 02/2017. Use `FastqRecord.getReadName()` instead
getReadLength() - Method in class htsjdk.samtools.BAMRecord
  Avoids decoding binary block to get read length.
getReadLength() - Method in class htsjdk.samtools.Cigar
getReadLength() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getReadLength() - Method in class htsjdk.samtools.fastq.FastqRecord
  Get the read length
getReadLength() - Method in class htsjdk.samtools.SAMRecord
  This method is preferred over getReadBases().length, because for BAMRecord it may be faster.
getReadLength(List) - Static method in class htsjdk.samtools.Cigar
getReadName() - Method in class htsjdk.samtools.BAMRecord
getReadName() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getReadName() - Method in class htsjdk.samtools.fastq.FastqRecord
  Get the read name
getReadName() - Method in class htsjdk.samtools.SAMRecord
getReadName() - Method in class htsjdk.samtools.SAMValidationError
  may be null
getReadName() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
getReadNameLength() - Method in class htsjdk.samtools.BAMRecord
  Avoids decoding read name to get read name length.
getReadNameLength() - Method in class htsjdk.samtools.SAMRecord
  This method is preferred over getReadName().length(), because for BAMRecord it may be faster.
getReadNegativeStrandFlag() - Method in class htsjdk.samtools.SAMRecord
  strand of the query (false for forward; true for reverse strand).
getReadOrdinal() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getReadPairedFlag() - Method in class htsjdk.samtools.SAMRecord
  the read is paired in sequencing, no matter whether it is mapped in a pair.
getReadPositionAtReferencePosition(int) - Method in class htsjdk.samtools.SAMRecord
  Returns the 1-based position in the read of the 1-based reference position provided.
getReadPositionAtReferencePosition(int, boolean) - Method in class htsjdk.samtools.SAMRecord
  Non-static version of static function with the same name.
getReadPositionAtReferencePosition(SAMRecord, int, boolean) - Static method in class htsjdk.samtools.SAMRecord
  Returns the 1-based position in the read of the provided reference position, or 0 if no such position exists.
getReads() - Method in class htsjdk.beta.plugin.reads.ReadsBundle
  return the `BundleResourceType.CT_ALIGNED_READS` `BundleResource` for this `ReadsBundle`
getReadsBundleFromPath(IOPath) - Static method in class htsjdk.beta.plugin.reads.ReadsBundle
  Create a `ReadsBundle` from a JSON string contained in jsonPath.
getReadsBundleFromString(String) - Static method in class htsjdk.beta.plugin.reads.ReadsBundle
  Create a `ReadsBundle` from a JSON string.
getReadsBundleFromString(String, Function) - Static method in class htsjdk.beta.plugin.reads.ReadsBundle
  Create a `ReadsBundle` from a JSON string with all IOPathResources using an IOPath-derived class of type `T`.
getReadsChannelTransformer() - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Get the channel transformer for the reads resource.
getReadsDecoder(Bundle) - Method in class htsjdk.beta.plugin.registry.ReadsResolver
  Get a `ReadsDecoder` suitable for decoding `inputBundle`.
getReadsDecoder(Bundle, ReadsDecoderOptions) - Method in class htsjdk.beta.plugin.registry.ReadsResolver
  Get a `ReadsDecoder` suitable for decoding `inputBundle` using options in `readsDecoderOptions`.
getReadsDecoder(IOPath) - Method in class htsjdk.beta.plugin.registry.ReadsResolver
  Get a `ReadsDecoder` suitable for decoding `inputPath`.
getReadsDecoder(IOPath, ReadsDecoderOptions) - Method in class htsjdk.beta.plugin.registry.ReadsResolver
  Grt a `ReadsDecoder` suitable for decoding `inputPath` using options in `readsDecoderOptions`.
getReadsDecoderOptions() - Method in class htsjdk.beta.codecs.reads.bam.BAMDecoder
  Get the `ReadsDecoderOptions` for this decoder.
getReadsDecoderOptions() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
  Get the `ReadsDecoderOptions` for this decoder.
getReadsDecoderOptions() - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder
  Get the `ReadsDecoderOptions` for this decoder.
getReadsDecoderOptions() - Method in class htsjdk.beta.codecs.reads.sam.SAMDecoder
  Get the `ReadsDecoderOptions` for this decoder.
getReadsDecoderOptions() - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
  Get the `VariantsDecoderOptions` for this decoder.
getReadsEncoder(Bundle, ReadsEncoderOptions) - Method in class htsjdk.beta.plugin.registry.ReadsResolver
  Get a `ReadsEncoder` suitable for encoding to `outputBundle`, using the options in `readsEncoderOptions`.
getReadsEncoder(Bundle, ReadsEncoderOptions, String, HtsVersion) - Method in class htsjdk.beta.plugin.registry.ReadsResolver
  Get a `ReadsEncoder` suitable for encoding to `outputBundle`, using the options in `readsEncoderOptions`, and the file format and version specified in readsFormat and formatVersion.
getReadsEncoder(IOPath) - Method in class htsjdk.beta.plugin.registry.ReadsResolver
  Get a `ReadsEncoder` suitable for encoding to `outputPath`.
getReadsEncoder(IOPath, ReadsEncoderOptions) - Method in class htsjdk.beta.plugin.registry.ReadsResolver
  Get a `ReadsEncoder` suitable for encoding to `outputPath`, using the options in `readsEncoderOptions`.
getReadsEncoderOptions() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoder
  Get the `ReadsEncoderOptions` for this encoder.
getReadsEncoderOptions() - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoder
  Get the `ReadsEncoderOptions` for this encoder.
getReadsEncoderOptions() - Method in class htsjdk.beta.codecs.reads.sam.SAMEncoder
  Get the `ReadsEncoderOptions` for this encoder.
getReadsPerSlice() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getReadsResolver() - Method in class htsjdk.beta.plugin.registry.HtsCodecRegistry
  Get the `ReadsResolver` for this registry.
getReadsResolver() - Static method in class htsjdk.beta.plugin.registry.HtsDefaultRegistry
  Gt the `ReadsResolver` resolver for this registry.
getReadStart() - Method in class htsjdk.samtools.AlignmentBlock
  The first, 1-based, base in the read that is aligned to the reference reference.
getReadString() - Method in class htsjdk.samtools.fastq.FastqRecord
  Get the DNA sequence
getReadString() - Method in class htsjdk.samtools.SAMRecord
getReadUnmappedFlag() - Method in class htsjdk.samtools.SAMRecord
  the query sequence itself is unmapped.
getRecord() - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
getRecord() - Method in class htsjdk.samtools.util.SamRecordWithOrdinal
getRecordAndOffsets() - Method in class htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference
  Getter
getRecordAndOffsets() - Method in class htsjdk.samtools.util.AbstractLocusInfo
getRecordAndPositions() - Method in class htsjdk.samtools.util.AbstractLocusInfo
  Deprecated.
  since name of the method can be confusing, new implementation should be used `getRecordAndOffsets()`
getRecordBytes() - Method in class htsjdk.variant.bcf2.BCF2Decoder
  Returns the byte[] for the block of data we are currently decoding
getRecordBytes() - Method in class htsjdk.variant.variantcontext.writer.BCF2Encoder
getRecordKey() - Method in class htsjdk.samtools.filter.AbstractJavascriptFilter
  returns key used for record binding
getRecordKey() - Method in class htsjdk.samtools.filter.JavascriptSamRecordFilter
getRecordKey() - Method in class htsjdk.variant.variantcontext.filter.JavascriptVariantFilter
getRecordLength() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getRecordNumber() - Method in class htsjdk.samtools.SAMValidationError
  1-based.
getRecordOrdinal() - Method in class htsjdk.samtools.util.SamRecordWithOrdinal
getRecords() - Method in class htsjdk.samtools.DuplicateSet
  Gets the list of records from this set.
getRecords() - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Returns the accumulated list of sam records.
getRecords(boolean) - Method in class htsjdk.samtools.DuplicateSet
  Gets the list of records from this set.
getRecordsToNextFragment() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getReference() - Method in class htsjdk.variant.variantcontext.VariantContext
getReferenceBase() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
getReferenceBase() - Method in class htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference
getReferenceBases(SAMSequenceRecord, boolean) - Method in class htsjdk.samtools.cram.ref.CRAMLazyReferenceSource
getReferenceBases(SAMSequenceRecord, boolean) - Method in interface htsjdk.samtools.cram.ref.CRAMReferenceSource
  Get the reference bases for an entire reference contig.
getReferenceBases(SAMSequenceRecord, boolean) - Method in class htsjdk.samtools.cram.ref.ReferenceSource
getReferenceBasesByRegion(SAMSequenceRecord, int, int) - Method in class htsjdk.samtools.cram.ref.CRAMLazyReferenceSource
getReferenceBasesByRegion(SAMSequenceRecord, int, int) - Method in interface htsjdk.samtools.cram.ref.CRAMReferenceSource
  Get the reference bases for a region of a reference contig.
getReferenceBasesByRegion(SAMSequenceRecord, int, int) - Method in class htsjdk.samtools.cram.ref.ReferenceSource
getReferenceContext() - Method in class htsjdk.samtools.cram.BAIEntry
getReferenceContext() - Method in class htsjdk.samtools.cram.structure.AlignmentContext
getReferenceContextID() - Method in class htsjdk.samtools.cram.ref.ReferenceContext
  Get the ReferenceContext sequence ID, or, for unmapped or multiple context, a sentinel value suitable for serialization: 0 or greater for single reference -1 for unmapped -2 for multiple reference
getReferenceIndex() - Method in class htsjdk.samtools.cram.build.CRAMReferenceRegion
getReferenceIndex() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getReferenceIndex() - Method in class htsjdk.samtools.SAMRecord
  Returns the reference index for this record.
getReferenceLength() - Method in class htsjdk.samtools.Cigar
getReferenceLength() - Method in class htsjdk.samtools.SAMSequenceDictionary
getReferenceMD5() - Method in class htsjdk.samtools.cram.structure.Slice
getReferenceName() - Method in class htsjdk.samtools.SAMRecord
getReferencePath() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoderOptions
  Get the reference path for these options.
getReferencePath() - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoderOptions
  Get the reference path for these options.
getReferencePositionAtReadPosition(int) - Method in class htsjdk.samtools.SAMRecord
  Non static version of the static function with the same name.
getReferencePositionAtReadPosition(SAMRecord, int) - Static method in class htsjdk.samtools.SAMRecord
  Returns the 1-based reference position for the provided 1-based position in read.
getReferenceSequence() - Method in class htsjdk.samtools.Bin
getReferenceSequence() - Method in class htsjdk.samtools.BinList
  Get the reference sequence to which this bin belongs.
getReferenceSequence() - Method in class htsjdk.samtools.BinningIndexContent
  Reference for this Content
getReferenceSequence() - Method in class htsjdk.samtools.LinearIndex
getReferenceSequence(int) - Method in class htsjdk.samtools.util.AbstractLocusIterator
getReferenceSequenceFile() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
getReferenceSequenceFile(File) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
getReferenceSequenceFile(File, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
getReferenceSequenceFile(File, boolean, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
getReferenceSequenceFile(String, SeekableStream, FastaSequenceIndex) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Return an instance of ReferenceSequenceFile using the given fasta sequence file stream, optional index stream, and no sequence dictionary
getReferenceSequenceFile(String, SeekableStream, FastaSequenceIndex, SAMSequenceDictionary, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Return an instance of ReferenceSequenceFile using the given fasta sequence file stream and optional index stream and sequence dictionary.
getReferenceSequenceFile(Path) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
getReferenceSequenceFile(Path, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
getReferenceSequenceFile(Path, boolean, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
getReferenceSequenceFile(Path, Function, boolean, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
getReferenceSequenceFileFromBundle(Bundle, boolean, boolean) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Attempts to determine the type of the reference file specified in the bundle, and return an instance of ReferenceSequenceFile that is appropriate to use to read the reference.
getReferenceSequenceID() - Method in class htsjdk.samtools.cram.ref.ReferenceContext
  Get the valid reference sequence ID.
getReferenceSource() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoderOptions
  Get the `CRAMReferenceSource` for these options.
getReferenceSource() - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoderOptions
  Get the `CRAMReferenceSource` for these options.
getReferenceStart() - Method in class htsjdk.samtools.AlignmentBlock
  The first, 1-based, position in the reference to which the read is aligned.
getRefPos() - Method in class htsjdk.samtools.util.EdgingRecordAndOffset
getRegionLength() - Method in class htsjdk.samtools.cram.build.CRAMReferenceRegion
getRegionStart() - Method in class htsjdk.samtools.cram.build.CRAMReferenceRegion
getRelationship(IntervalTree.Node) - Method in class htsjdk.samtools.util.IntervalTree.Node
getRelativeValue() - Method in class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken.EndToken
getRelativeValue() - Method in class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken
getRelativeValueAsInt() - Method in class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken
  Get the relative value as an int, parsing from string only on first call.
getReply() - Method in class htsjdk.samtools.util.ftp.FTPClient
getReplyString() - Method in class htsjdk.samtools.util.ftp.FTPReply
  Gets server reply string from the control port after an ftp command has been executed.
getRepresentative() - Method in class htsjdk.samtools.DuplicateSet
  Gets the representative record according to the duplicate comparator.
getResourceDescription() - Method in interface htsjdk.samtools.SamReader
getResourceDescription() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
getResources() - Method in class htsjdk.beta.io.bundle.Bundle
  Get the collection of resources from this `Bundle`.
getResponse() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
  Attempt to make htsget request and return response if there are no errors
getReverse() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZModels
getReverseArray() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getReverseLookup() - Method in class htsjdk.samtools.cram.compression.rans.RANSDecode
getRGLine(SAMReadGroupRecord) - Method in class htsjdk.samtools.SAMTextHeaderCodec
getRunDate() - Method in class htsjdk.samtools.SAMReadGroupRecord
getSamFileHeader() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
getSAMFileHeader() - Method in class htsjdk.samtools.CRAMIterator
getSAMFlags() - Method in class htsjdk.samtools.SAMRecord
  shortcut to
getSAMIndexTypeFromStream(SeekableStream) - Static method in enum class htsjdk.samtools.SamIndexes
getSample() - Method in class htsjdk.samtools.SAMReadGroupRecord
getSampleHeaderLine(String, VCFHeaderVersion) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  Create and return a VCFSampleHeaderLine object from a header line string that conforms to the `sourceVersion`
getSampleName() - Method in class htsjdk.variant.variantcontext.Genotype
  Returns the name associated with this sample.
getSampleNames() - Method in class htsjdk.variant.variantcontext.GenotypesContext
getSampleNames() - Method in class htsjdk.variant.variantcontext.VariantContext
getSampleNamesInOrder() - Method in class htsjdk.variant.vcf.VCFHeader
  Get the genotype sample names, sorted in ascending order.
getSampleNamesOrderedByName() - Method in class htsjdk.variant.variantcontext.GenotypesContext
getSampleNamesOrderedByName() - Method in class htsjdk.variant.variantcontext.VariantContext
getSampleNameToOffset() - Method in class htsjdk.variant.vcf.VCFHeader
getSamReader() - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Creates samFileReader from the data in instance of this class
getSamReader(Bundle, ReadsDecoderOptions, SamReaderFactory) - Static method in class htsjdk.beta.codecs.reads.ReadsCodecUtils
  Propagate all reads decoder options and all bam decoder options to either a SamReaderFactory or a SamInputResource, and return the resulting SamReader
getSamReadNameFromFastqHeader(String) - Static method in class htsjdk.samtools.util.SequenceUtil
  Returns a read name from a FASTQ header string suitable for use in a SAM/BAM file.
getSAMRecords(ValidationStringency, CRAMReferenceRegion, CompressorCache, SAMFileHeader) - Method in class htsjdk.samtools.cram.structure.Container
  Get SAMRecords from all Slices in this container.
getSAMSequenceRecord() - Method in class htsjdk.variant.vcf.VCFContigHeaderLine
  Get the SAMSequenceRecord that corresponds to this VCF header line.
getSAMString() - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
  Returns the record in the SAM line-based text format.
getSAMString() - Method in class htsjdk.samtools.SAMFileHeader
getSAMString() - Method in class htsjdk.samtools.SAMProgramRecord
getSAMString() - Method in class htsjdk.samtools.SAMReadGroupRecord
getSAMString() - Method in class htsjdk.samtools.SAMRecord
  Returns the record in the SAM line-based text format.
getSAMString() - Method in class htsjdk.samtools.SAMSequenceRecord
getScheme() - Method in interface htsjdk.io.IOPath
  Return the scheme for this `IOPath`.
getScore() - Method in interface htsjdk.tribble.bed.BEDFeature
getScore() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getScore() - Method in class htsjdk.tribble.gff.Gff3BaseData
getScore() - Method in interface htsjdk.tribble.gff.Gff3Feature
getScores() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
getSecondOfPairFlag() - Method in class htsjdk.samtools.SAMRecord
  the read is the second read in a pair.
getSeconds() - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
getSeekableStream() - Method in interface htsjdk.beta.io.bundle.BundleResource
  Get a `SeekableStream` for this resource, or Optional.empty.
getSeekableStream() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
getSeekableStream() - Method in class htsjdk.beta.io.bundle.IOPathResource
getSeekableStream() - Method in class htsjdk.beta.io.bundle.SeekableStreamResource
getSeenCount() - Method in class htsjdk.samtools.DownsamplingIterator
  Returns the number of records seen, including accepted and discarded, since creation of the last call to resetStatistics.
getSelector() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZModels
getSelector() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getSelectorContextLocation() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
getSelectorTable() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParams
getSelectorTable() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
getSentinel() - Method in class htsjdk.samtools.util.IntervalTree
  Get the special sentinel value that will be used to signal novelty when putting a new interval into the tree, or to signal "not found" when removing an interval.
getSequence() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
getSequence() - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
getSequence() - Method in class htsjdk.samtools.util.Interval
  Deprecated.
  use getContig() instead
getSequence(int) - Method in class htsjdk.samtools.SAMFileHeader
  Look up a sequence record by index.
getSequence(int) - Method in class htsjdk.samtools.SAMSequenceDictionary
getSequence(String) - Method in class htsjdk.samtools.reference.FastaSequenceFile
  default implementation -- override if index is supported
getSequence(String) - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Retrieves the complete sequence described by this contig.
getSequence(String) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Retrieves the complete sequence described by this contig.
getSequence(String) - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
  Retrieves the complete sequence described by this contig.
getSequence(String) - Method in class htsjdk.samtools.SAMFileHeader
  Look up sequence record by name.
getSequence(String) - Method in class htsjdk.samtools.SAMSequenceDictionary
getSequenceDictionary() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Returns the list of sequence records associated with the reference sequence if found otherwise null.
getSequenceDictionary() - Method in class htsjdk.samtools.reference.FastaSequenceFile
  Returns the list of sequence records associated with the reference sequence if found otherwise null.
getSequenceDictionary() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Returns the list of sequence records associated with the reference sequence if found otherwise null.
getSequenceDictionary() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
  Must return a sequence dictionary with at least the following fields completed for each sequence: name, length.
getSequenceDictionary() - Method in class htsjdk.samtools.reference.ReferenceSequenceFileWalker
getSequenceDictionary() - Method in class htsjdk.samtools.SAMFileHeader
getSequenceDictionary() - Method in class htsjdk.variant.vcf.VCFHeader
  Returns the contigs in this VCF file as a SAMSequenceDictionary.
getSequenceDictionary(File) - Static method in class htsjdk.tribble.util.TabixUtils
  Generates the SAMSequenceDictionary from the given tabix index file
getSequenceDictionary(File) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Returns the SAMSequenceDictionary from the provided VCF file.
getSequenceDictionary(Path) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Returns the SAMSequenceDictionary from the provided VCF file.
getSequenceId() - Method in class htsjdk.samtools.cram.CRAIEntry
getSequenceIndex() - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
getSequenceIndex() - Method in class htsjdk.samtools.SAMSequenceRecord
getSequenceIndex() - Method in class htsjdk.samtools.util.AbstractLocusInfo
getSequenceIndex() - Method in interface htsjdk.samtools.util.Locus
getSequenceIndex() - Method in class htsjdk.samtools.util.LocusImpl
getSequenceIndex(String) - Method in class htsjdk.samtools.SAMFileHeader
getSequenceIndex(String) - Method in class htsjdk.samtools.SAMSequenceDictionary
getSequenceLength() - Method in class htsjdk.samtools.SAMSequenceRecord
getSequenceLength() - Method in class htsjdk.samtools.util.AbstractLocusInfo
getSequenceName() - Method in class htsjdk.samtools.SAMSequenceRecord
getSequenceName() - Method in class htsjdk.samtools.util.AbstractLocusInfo
getSequenceNameList(SAMSequenceDictionary) - Static method in class htsjdk.variant.variantcontext.VariantContextComparator
getSequenceNames() - Method in interface htsjdk.tribble.FeatureReader
  Provides the list of sequenceNames if known.
getSequenceNames() - Method in class htsjdk.tribble.index.AbstractIndex
getSequenceNames() - Method in interface htsjdk.tribble.index.Index
getSequenceNames() - Method in class htsjdk.tribble.index.linear.LinearIndex
getSequenceNames() - Method in class htsjdk.tribble.index.tabix.TabixIndex
getSequenceNames() - Method in class htsjdk.tribble.TabixFeatureReader
getSequenceNames() - Method in class htsjdk.tribble.TribbleIndexedFeatureReader
  Return the sequence (chromosome/contig) names in this file, if known.
getSequenceRegions() - Method in class htsjdk.tribble.gff.Gff3Codec
  Get list of sequence regions parsed by the codec.
getSequences() - Method in class htsjdk.samtools.SAMSequenceDictionary
getSequencingCenter() - Method in class htsjdk.samtools.SAMReadGroupRecord
getSequentialIndex() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getShortAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
  Get the tag value and attempt to coerce it into the requested type.
getShortAttribute(String) - Method in class htsjdk.samtools.SAMRecord
  Get the tag value and attempt to coerce it into the requested type.
getSignatureLength() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0
getSignatureLength() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMCodecV1_0
getSignatureLength() - Method in class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMCodecV2_1
getSignatureLength() - Method in class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMCodecV3_0
getSignatureLength() - Method in class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMCodecV3_1
getSignatureLength() - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec
getSignatureLength() - Method in class htsjdk.beta.codecs.reads.sam.SAMCodec
getSignatureLength() - Method in class htsjdk.beta.codecs.variants.vcf.VCFCodec
getSignatureLength() - Method in interface htsjdk.beta.plugin.HtsCodec
  Get the number of bytes in the format and version signature used by the file format supported by this codec.
getSignaturePrefixLength() - Method in class htsjdk.beta.io.bundle.SignatureStream
  Get the maximum number of bytes that can be consumed from this stream.
getSignatureProbeLength() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMCodecV1_0
getSignatureProbeLength() - Method in class htsjdk.beta.codecs.reads.sam.SAMCodec
getSignatureProbeLength() - Method in class htsjdk.beta.codecs.variants.vcf.VCFCodec
getSignatureProbeLength() - Method in interface htsjdk.beta.plugin.HtsCodec
  Get the number of bytes of needed by this codec to probe an input stream for a format/version signature, and determine if it can supply a decoder for the stream.
getSignatureStream(int) - Method in interface htsjdk.beta.io.bundle.BundleResource
  Get a `SignatureStream` for this resource.
getSignatureStream(int) - Method in class htsjdk.beta.io.bundle.InputStreamResource
getSignatureStream(int) - Method in class htsjdk.beta.io.bundle.IOPathResource
getSignatureStream(int) - Method in class htsjdk.beta.io.bundle.OutputStreamResource
getSignatureStream(int) - Method in class htsjdk.beta.io.bundle.SeekableStreamResource
  Get a `SignatureStream` for this resource.
getSignatureString() - Method in class htsjdk.beta.codecs.reads.cram.CRAMCodec
  Get the signature string for this codec.
getSignatureString() - Method in class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMCodecV2_1
getSignatureString() - Method in class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMCodecV3_0
getSignatureString() - Method in class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMCodecV3_1
getSignatureString() - Method in class htsjdk.beta.codecs.variants.vcf.VCFCodec
  Get the signature string for this codec.
getSignatureString() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFCodecV3_2
getSignatureString() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFCodecV3_3
getSignatureString() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFCodecV4_0
getSignatureString() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFCodecV4_1
getSignatureString() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFCodecV4_2
getSignatureString() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFCodecV4_3
getSignedByteArrayAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
  Will work for signed byte array or old-style hex array
getSignedByteArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
  Will work for signed byte array or old-style hex array
getSignedIntArrayAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
getSignedIntArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
getSignedShortArrayAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
getSignedShortArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
getSingleChunk() - Method in class htsjdk.samtools.BAMFileSpan
  Checks that there is only a single chunk for this span and returns it.
getSingleton() - Static method in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use the static methods in `SAMTag` instead
getSingleton() - Static method in class htsjdk.samtools.util.SolexaQualityConverter
getSiteFieldWriter(String) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager
  Get a site writer specialized to encode values for site info field
getSize() - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
  Gets the size, in bytes, of the data in the contig.
getSize() - Method in class htsjdk.tribble.index.Block
getSize() - Method in class htsjdk.tribble.index.interval.IntervalTree
  The estimated size of the tree.
getSize(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.Accessor
getSize(VariantContext) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
getSizeInBytes() - Method in enum class htsjdk.variant.bcf2.BCF2Type
  How many bytes are used to represent this type on disk?
getSkipMateValidation() - Method in class htsjdk.samtools.SamFileValidator
getSliceBlocks() - Method in class htsjdk.samtools.cram.structure.Slice
getSliceByteOffsetFromCompressionHeaderStart() - Method in class htsjdk.samtools.cram.BAIEntry
getSliceByteOffsetFromCompressionHeaderStart() - Method in class htsjdk.samtools.cram.CRAIEntry
getSliceByteSize() - Method in class htsjdk.samtools.cram.CRAIEntry
getSliceHeaderBlock() - Method in class htsjdk.samtools.cram.structure.Slice
getSlices() - Method in class htsjdk.samtools.cram.structure.Container
getSlicesPerContainer() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getSliceTags() - Method in class htsjdk.samtools.cram.structure.Slice
getSoleElement(Collection) - Static method in class htsjdk.samtools.util.CollectionUtil
getSolexaToPhredConversionTable() - Method in class htsjdk.samtools.util.SolexaQualityConverter
getSortKey(SAMRecord) - Method in class htsjdk.samtools.SAMSortOrderChecker
  Return the sort key used for the given sort order.
getSortOrder() - Method in class htsjdk.samtools.SAMFileHeader
getSortOrder() - Method in class htsjdk.samtools.SAMFileWriterImpl
  Must be called after calling setHeader().
getSortOrder() - Method in class htsjdk.samtools.SAMSortOrderChecker
getSource() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Returns the named source of the reference file.
getSource() - Method in class htsjdk.samtools.reference.FastaSequenceFile
  Returns the named source of the reference file.
getSource() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Returns the named source of the reference file.
getSource() - Method in class htsjdk.samtools.SAMValidationError
getSource() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
getSource() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
getSource() - Method in class htsjdk.samtools.seekablestream.SeekableStream
getSource() - Method in class htsjdk.tribble.gff.Gff3BaseData
getSource() - Method in interface htsjdk.tribble.gff.Gff3Feature
getSource() - Method in class htsjdk.tribble.readers.TabixReader
  return the source (filename/URL) of that reader
getSource() - Method in class htsjdk.variant.variantcontext.VariantContext
getSource() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
getSpanOverlapping(int, int, int) - Method in interface htsjdk.samtools.BAMIndex
  Gets the compressed chunks which should be searched for the contents of records contained by the span referenceIndex:startPos-endPos, inclusive.
getSpanOverlapping(int, int, int) - Method in class htsjdk.samtools.CSIIndex
getSpanOverlapping(int, int, int) - Method in class htsjdk.samtools.DiskBasedBAMFileIndex
  Get list of regions of BAM file that may contain SAMRecords for the given range
getSpanOverlapping(Bin) - Method in interface htsjdk.samtools.BrowseableBAMIndex
  Perform an overlapping query of all bins bounding the given location.
getSpanOverlapping(Bin) - Method in class htsjdk.samtools.CSIIndex
getSpecies() - Method in class htsjdk.samtools.SAMSequenceRecord
getSQLine(SAMSequenceRecord) - Method in class htsjdk.samtools.SAMTextHeaderCodec
getStandardDeviation() - Method in class htsjdk.samtools.util.Histogram
getStandardDeviationBinSize(double) - Method in class htsjdk.samtools.util.Histogram
  Calculates the standard deviation of the bin size
getStart() - Method in interface htsjdk.beta.plugin.interval.HtsInterval
  Get the 1-based inclusive start coordinate for this interval.
getStart() - Method in class htsjdk.beta.plugin.interval.HtsQueryInterval
getStart() - Method in interface htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
getStart() - Method in class htsjdk.samtools.SAMRecord
  an alias of `SAMRecord.getAlignmentStart()`
getStart() - Method in class htsjdk.samtools.SAMSequenceRecord
  always returns 1
getStart() - Method in class htsjdk.samtools.util.AbstractLocusInfo
getStart() - Method in class htsjdk.samtools.util.EdgingRecordAndOffset
getStart() - Method in class htsjdk.samtools.util.Interval
getStart() - Method in class htsjdk.samtools.util.IntervalTree.Node
getStart() - Method in interface htsjdk.samtools.util.Locatable
getStart() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getStart() - Method in class htsjdk.tribble.gff.Gff3BaseData
getStart() - Method in interface htsjdk.tribble.gff.Gff3Feature
getStart() - Method in class htsjdk.tribble.gff.SequenceRegion
getStart() - Method in class htsjdk.tribble.MutableFeature
getStart() - Method in class htsjdk.tribble.SimpleFeature
getStart() - Method in class htsjdk.variant.variantcontext.VariantContext
  Returns 1-based inclusive start position of the variant.
getStart() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Getter for start position
getStart(int, int) - Static method in class htsjdk.samtools.util.CoordMath
getStartOffset() - Method in class htsjdk.tribble.bed.BEDCodec
getStartOfLastLinearBin() - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Use to get close to the unmapped reads at the end of a BAM file.
getStartOfLastLinearBin() - Method in interface htsjdk.samtools.BAMIndex
  Gets the start of the last linear bin in the index.
getStartOfLastLinearBin() - Method in class htsjdk.samtools.CSIIndex
getStartPosition() - Method in class htsjdk.tribble.index.Block
getStaticType() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
getStop() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Getter for stop position
getStoreMD() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getStoreNM() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getStrand() - Method in class htsjdk.samtools.util.Interval
  Return the `Strand` this interval is on.
getStrand() - Method in interface htsjdk.tribble.bed.BEDFeature
getStrand() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getStrand() - Method in class htsjdk.tribble.gff.Gff3BaseData
getStrand() - Method in interface htsjdk.tribble.gff.Gff3Feature
getStream(int, int) - Method in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
  Return the token stream for a specific position and token type.
getStreamFor(String) - Method in interface htsjdk.samtools.seekablestream.ISeekableStreamFactory
getStreamFor(String, Function) - Method in interface htsjdk.samtools.seekablestream.ISeekableStreamFactory
  Open a stream from the input path, applying the wrapper to the stream.
getStreamFor(URL) - Method in interface htsjdk.samtools.seekablestream.ISeekableStreamFactory
getStreamsForPos(int) - Method in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
  Return the array of token streams for a given column position.
getStringAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
getStringAttribute(String) - Method in class htsjdk.samtools.SAMRecord
getStringFromPath(IOPath) - Static method in class htsjdk.beta.io.IOPathUtils
  Get the entire contents of an IOPath file as a string.
getStringFromPath(IOPath) - Static method in class htsjdk.beta.plugin.IOUtils
  Get the entire contents of an IOPath as a string.
getStripeNumStreams() - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
getStructuralVariantType() - Method in class htsjdk.variant.variantcontext.VariantContext
  Search for the INFO=SVTYPE and return the type of Structural Variant
getSubsequenceAt(Locatable) - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
  Gets the subsequence of the contig in the locatable.
getSubsequenceAt(String, long, long) - Method in class htsjdk.samtools.reference.FastaSequenceFile
  default implementation -- override if index is supported
getSubsequenceAt(String, long, long) - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Gets the subsequence of the contig in the range [start,stop]
getSubsequenceAt(String, long, long) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Gets the subsequence of the contig in the range [start,stop]
getSubsequenceAt(String, long, long) - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
  Gets the subsequence of the contig in the range [start,stop]
getSubstitutionMatrix() - Method in class htsjdk.samtools.cram.structure.CompressionHeader
getSum() - Method in class htsjdk.samtools.util.Histogram
  Returns the sum of the products of the histgram bin ids and the number of entries in each bin.
getSumOfValues() - Method in class htsjdk.samtools.util.Histogram
  Returns the sum of the number of entries in each bin.
getSupplementaryAlignmentFlag() - Method in class htsjdk.samtools.SAMRecord
getSymbol() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanBitCode
getSymbols() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParams
getTabixFormat() - Method in class htsjdk.tribble.bed.BEDCodec
getTabixFormat() - Method in class htsjdk.tribble.BinaryFeatureCodec
  Marked as final because binary features could not be tabix indexed
getTabixFormat() - Method in interface htsjdk.tribble.FeatureCodec
  Define the tabix format for the feature, used for indexing.
getTabixFormat() - Method in class htsjdk.tribble.gff.Gff3Codec
getTabixFormat() - Method in class htsjdk.variant.vcf.AbstractVCFCodec
getTagEncodingMap() - Method in class htsjdk.samtools.cram.structure.CompressionHeader
getTagIDDictionary() - Method in class htsjdk.samtools.cram.structure.CompressionHeader
getTagIdsIndex() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getTagKeyCache() - Method in class htsjdk.samtools.cram.structure.CompressionHeader
  Returns the `TagKeyCache` for looking up pre-computed tag key metadata.
getTags() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getTags() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
getTargetProportion() - Method in class htsjdk.samtools.DownsamplingIterator
  Gets the target proportion of records that should be retained during downsampling.
getTempDirecory(String, String) - Static method in class htsjdk.samtools.util.TestUtil
  Deprecated.
  Use properly spelled method. `TestUtil.getTempDirectory(String, String)`
getTempDirectory() - Method in class htsjdk.samtools.SAMFileWriterFactory
  Gets the temporary directory that will be used when sorting data.
getTempDirectory() - Method in class htsjdk.samtools.SAMFileWriterImpl
getTempDirectory(String, String) - Static method in class htsjdk.samtools.util.TestUtil
getTemplateSize() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
getTemporaryDirectory() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Get the temporary directory path used for these options.
getTextHeader() - Method in class htsjdk.samtools.SAMFileHeader
  Deprecated.
  since May 1st 2019 - text version of header is no longer stored.
getThreadNamePrefix() - Method in class htsjdk.samtools.fastq.AsyncFastqWriter
getThreadNamePrefix() - Method in class htsjdk.samtools.util.AbstractAsyncWriter
  Returns the prefix to use when naming threads.
getThreadNamePrefix() - Method in class htsjdk.samtools.util.AsyncBufferedIterator
getThreadNamePrefix() - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
getTime() - Method in class htsjdk.samtools.util.RelativeIso8601Date
getTimeoutSeconds() - Method in class htsjdk.io.AsyncWriterPool
  Get the `timeoutSeconds` value.
getTimestamp() - Method in class htsjdk.samtools.util.Log
  Creates a date string for insertion into the log.
getTimezoneOffset() - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
getTokenType() - Method in class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken
getToPathFailureReason() - Method in class htsjdk.io.HtsPath
getToPathFailureReason() - Method in interface htsjdk.io.IOPath
  Return a string message describing why this URI cannot be converted to a `java.nio.file.Path` (`#isPath()` returns false).
getTopLevelFeatures() - Method in interface htsjdk.tribble.gff.Gff3Feature
  Get the set of top level features from which this feature is descended.
getTopLevelFeatures() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
  Get the set of top level features from which this feature is descended
getTotalNumberOfRecords() - Method in class htsjdk.samtools.SBIIndex.Header
getTotalSize() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
getTransientAttribute(Object) - Method in class htsjdk.samtools.SAMRecord
  Fetches the value of a transient attribute on the SAMRecord, of null if not set.
getTrialCandidatesMap() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
getTribbleIndexType() - Method in enum class htsjdk.tribble.index.IndexFactory.IndexType
getType() - Method in class htsjdk.samtools.cram.ref.ReferenceContext
  Get the ReferenceContext type: SINGLE_REFERENCE_TYPE, UNMAPPED_UNPLACED_TYPE, or MULTIPLE_REFERENCE_TYPE
getType() - Method in enum class htsjdk.samtools.cram.structure.DataSeries
getType() - Method in class htsjdk.samtools.SAMValidationError
getType() - Method in class htsjdk.samtools.util.EdgingRecordAndOffset
getType() - Method in interface htsjdk.tribble.bed.BEDFeature
getType() - Method in class htsjdk.tribble.bed.SimpleBEDFeature
getType() - Method in class htsjdk.tribble.gff.Gff3BaseData
getType() - Method in interface htsjdk.tribble.gff.Gff3Feature
getType() - Method in class htsjdk.tribble.index.AbstractIndex
  get the index type
getType() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex
getType() - Method in class htsjdk.tribble.index.linear.LinearIndex
getType() - Method in class htsjdk.variant.variantcontext.Genotype
getType() - Method in class htsjdk.variant.variantcontext.VariantContext
  Determines (if necessary) and returns the type of this variation by examining the alleles it contains.
getType() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
getType(boolean) - Method in class htsjdk.variant.variantcontext.VariantContext
  Determines (if necessary) and returns the type of this variation by examining the alleles it contains.
getType(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
  Get the BCF2 type for this field, either from the static type of the field itself or by inspecting the value itself.
getUnalignedRecordCount() - Method in class htsjdk.samtools.BAMIndexMetaData
getUnclippedEnd() - Method in class htsjdk.samtools.SAMRecord
getUnclippedEnd(int, Cigar) - Static method in class htsjdk.samtools.SAMUtils
getUnclippedStart() - Method in class htsjdk.samtools.SAMRecord
getUnclippedStart(int, Cigar) - Static method in class htsjdk.samtools.SAMUtils
getUncompressedContent(CompressorCache) - Method in class htsjdk.samtools.cram.structure.block.Block
  Uncompress the stored block content (if not RAW) and return the uncompressed content.
getUncompressedContentSize() - Method in class htsjdk.samtools.cram.structure.block.Block
getUncompressedOffset() - Method in class htsjdk.samtools.util.GZIIndex.IndexEntry
  Returns the uncompressed offset.
getUnderlyingIterator() - Method in class htsjdk.samtools.util.PeekIterator
getUniqueAttribute(String) - Method in class htsjdk.tribble.gff.Gff3BaseData
  Most attributes in a GFF file are present just one time in a line, e.g.
getUniqueAttribute(String) - Method in interface htsjdk.tribble.gff.Gff3Feature
  Most attributes in a GFF file are present just one time in a line, e.g.
getUniqueBaseCount() - Method in class htsjdk.samtools.util.IntervalList
  Gets the count of unique bases represented by the intervals in the list.
getUniqueIntervals() - Method in class htsjdk.samtools.util.IntervalList
  Deprecated.
  use `IntervalList.uniqued()`.`IntervalList.getIntervals()` instead.
getUniqueIntervals(boolean) - Method in class htsjdk.samtools.util.IntervalList
  Deprecated.
  use `IntervalList.uniqued(boolean)`.`IntervalList.getIntervals()` or `IntervalList.getUniqueIntervals(IntervalList, boolean)` instead.
getUniqueIntervals(IntervalList, boolean) - Static method in class htsjdk.samtools.util.IntervalList
  Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()
getUniqueIntervals(IntervalList, boolean, boolean) - Static method in class htsjdk.samtools.util.IntervalList
  Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()
getUniqueIntervals(IntervalList, boolean, boolean, boolean) - Static method in class htsjdk.samtools.util.IntervalList
  Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()
getUnmappedCount() - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
getUnmappedReadsCount() - Method in class htsjdk.samtools.cram.BAIEntry
getUnmappedUnplacedCount() - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
getUnmappedUnplacedReadsCount() - Method in class htsjdk.samtools.cram.BAIEntry
getUnparsedGenotypeData() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
getUnsignedByteArrayAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
getUnsignedByteArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
getUnsignedIntArrayAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
getUnsignedIntArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
getUnsignedIntegerAttribute(short) - Method in class htsjdk.samtools.SAMRecord
  A convenience method that will return a valid unsigned integer as a Long, or fail with an exception if the tag value is invalid.
getUnsignedIntegerAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
  A convenience method that will return a valid unsigned integer as a Long, or fail with an exception if the tag value is invalid.
getUnsignedIntegerAttribute(String) - Method in class htsjdk.samtools.SAMRecord
  A convenience method that will return a valid unsigned integer as a Long, or fail with an exception if the tag value is invalid.
getUnsignedShortArrayAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
getUnsignedShortArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
getUpdatedReferenceContext(int, int, int, long) - Method in class htsjdk.samtools.cram.build.SliceFactory
  Decide if the current records should be flushed based on the current reference context, the reference context for the next record to be written, the number of records seen so far, and the accumulated number of bases.
getUri() - Method in class htsjdk.samtools.util.htsget.HtsgetResponse.Block
getURI() - Method in class htsjdk.io.HtsPath
getURI() - Method in interface htsjdk.io.IOPath
  Get a `java.net.URI` object for this `IOPath`.
getURIString() - Method in class htsjdk.io.HtsPath
getURIString() - Method in interface htsjdk.io.IOPath
  Returns the string from which this `IOPath` was originally created.
getUrl() - Method in class htsjdk.tribble.util.FTPHelper
getUrl() - Method in class htsjdk.tribble.util.HTTPHelper
getUrl() - Method in class htsjdk.tribble.util.RemoteURLHelper
getUrl() - Method in interface htsjdk.tribble.util.URLHelper
getURLHelper(URL) - Static method in class htsjdk.tribble.util.ParsingUtils
  Return a URLHelper from the current URLHelperFactory
getURLHelperFactory() - Static method in class htsjdk.tribble.util.ParsingUtils
getUser() - Method in interface htsjdk.samtools.seekablestream.UserPasswordInput
getUuid() - Method in class htsjdk.samtools.SBIIndex.Header
getValidationErrors() - Method in class htsjdk.samtools.SAMFileHeader
getValidationStringency() - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Get the `ValidationStringency` used for these options.
getValidationStringency() - Method in class htsjdk.samtools.BAMFileReader
getValidationStringency() - Method in class htsjdk.samtools.CRAMFileReader
getValidationStringency() - Method in class htsjdk.samtools.CRAMIterator
getValidationStringency() - Method in class htsjdk.samtools.HtsgetBAMFileReader
getValidationStringency() - Method in class htsjdk.samtools.SAMLineParser
  Get validation stringency.
getValidationStringency() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
getValidationStringency() - Method in class htsjdk.samtools.SAMRecord
getValue() - Method in class htsjdk.samtools.cram.structure.ReadTag
getValue() - Method in class htsjdk.samtools.metrics.StringHeader
getValue() - Method in class htsjdk.samtools.util.Histogram.Bin
  Gets the value in the bin.
getValue() - Method in class htsjdk.samtools.util.IntervalTree.Node
getValue() - Method in class htsjdk.variant.vcf.VCFHeaderLine
  Get the value
getValue(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.DPAccessor
getValue(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.GQAccessor
getValueAsByteArray() - Method in class htsjdk.samtools.cram.structure.ReadTag
  Serialize this tag's value to a byte array using CRAM/BAM binary encoding.
getValueLabel() - Method in class htsjdk.samtools.util.Histogram
getValues(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.Accessor
getValues(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.ADAccessor
getValues(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.DPAccessor
getValues(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.GQAccessor
getValues(Genotype) - Method in class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.PLAccessor
getValueString(double) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
getValueString(double) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
  Method description
getVariableBinaryRepresentation() - Method in class htsjdk.samtools.BAMRecord
  If this record has a valid binary representation of the variable-length portion of a binary record stored, return that byte array, otherwise return null.
getVariableBinaryRepresentation() - Method in class htsjdk.samtools.SAMRecord
  If this record has a valid binary representation of the variable-length portion of a binary record stored, return that byte array, otherwise return null.
getVariants() - Method in class htsjdk.beta.plugin.variants.VariantsBundle
getVariantsBundleFromPath(IOPath) - Static method in class htsjdk.beta.plugin.variants.VariantsBundle
  Create a `VariantsBundle` from a JSON string contained in jsonPath.
getVariantsBundleFromPath(IOPath, Function) - Static method in class htsjdk.beta.plugin.variants.VariantsBundle
  Create a `VariantsBundle` from a JSON string contained in jsonPath.
getVariantsBundleFromString(String) - Static method in class htsjdk.beta.plugin.variants.VariantsBundle
  Create a `VariantsBundle` from a JSON string.
getVariantsBundleFromString(String, Function) - Static method in class htsjdk.beta.plugin.variants.VariantsBundle
  Create a `VariantsBundle` from a JSON string with all IOPathResources using an IOPath-derived class of type `T`.
getVariantsChannelTransformer() - Method in class htsjdk.beta.plugin.variants.VariantsDecoderOptions
  Get the channel transformer for the variants resource.
getVariantsDecoder(Bundle) - Method in class htsjdk.beta.plugin.registry.VariantsResolver
  Get a `VariantsDecoder` suitable for decoding `inputBundle`.
getVariantsDecoder(Bundle, VariantsDecoderOptions) - Method in class htsjdk.beta.plugin.registry.VariantsResolver
  Get a `VariantsDecoder` suitable for decoding `inputBundle` using `variantsDecoderOptions`.
getVariantsDecoder(IOPath) - Method in class htsjdk.beta.plugin.registry.VariantsResolver
  Get a `VariantsDecoder` suitable for decoding `inputPath`.
getVariantsDecoder(IOPath, VariantsDecoderOptions) - Method in class htsjdk.beta.plugin.registry.VariantsResolver
  Get a `VariantsDecoder` suitable for decoding `inputPath` using `variantsDecoderOptions`.
getVariantsEncoder(Bundle, VariantsEncoderOptions) - Method in class htsjdk.beta.plugin.registry.VariantsResolver
  Get a `VariantsEncoder` suitable for encoding to `outputBundle` using `variantsEncoderOptions`.
getVariantsEncoder(Bundle, VariantsEncoderOptions, String, HtsVersion) - Method in class htsjdk.beta.plugin.registry.VariantsResolver
  Get a `VariantsEncoder` suitable for encoding to `outputBundle` using `variantsEncoderOptions`, specifying a version and output format.
getVariantsEncoder(IOPath) - Method in class htsjdk.beta.plugin.registry.VariantsResolver
  Get a `VariantsEncoder` suitable for encoding to `outputPath`.
getVariantsEncoder(IOPath, VariantsEncoderOptions) - Method in class htsjdk.beta.plugin.registry.VariantsResolver
  Get a `VariantsEncoder` suitable for encoding to `outputPath` using `variantsEncoderOptions`.
getVariantsEncoderOptions() - Method in class htsjdk.beta.codecs.variants.vcf.VCFEncoder
  Get the `VariantsEncoderOptions` for this encoder.
getVariantsResolver() - Method in class htsjdk.beta.plugin.registry.HtsCodecRegistry
  Get the `VariantsResolver` for this registry.
getVariantsResolver() - Static method in class htsjdk.beta.plugin.registry.HtsDefaultRegistry
  Get the `VariantsResolver` resolver for this registry.
getVCFHeaderVersion() - Method in class htsjdk.variant.vcf.VCFHeader
getVCFRecordComparator() - Method in class htsjdk.variant.vcf.VCFHeader
getVersion() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0
getVersion() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
getVersion() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMCodecV1_0
getVersion() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
getVersion() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMEncoderV1_0
getVersion() - Method in class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMCodecV2_1
getVersion() - Method in class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMDecoderV2_1
getVersion() - Method in class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMEncoderV2_1
getVersion() - Method in class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMCodecV3_0
getVersion() - Method in class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMDecoderV3_0
getVersion() - Method in class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMEncoderV3_0
getVersion() - Method in class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMCodecV3_1
getVersion() - Method in class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMDecoderV3_1
getVersion() - Method in class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMEncoderV3_1
getVersion() - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec
getVersion() - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder
getVersion() - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMCodecV1_0
getVersion() - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0
getVersion() - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMEncoderV1_0
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFCodecV3_2
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFDecoderV3_2
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFEncoderV3_2
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFCodecV3_3
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFDecoderV3_3
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFEncoderV3_3
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFCodecV4_0
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFDecoderV4_0
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFEncoderV4_0
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFCodecV4_1
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFDecoderV4_1
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFEncoderV4_1
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFCodecV4_2
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFDecoderV4_2
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFEncoderV4_2
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFCodecV4_3
getVersion() - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFDecoderV4_3
getVersion() - Method in interface htsjdk.beta.plugin.HtsCodec
  Get the version of the file format returned by `HtsCodec.getFileFormat()` that is supported by this codec.
getVersion() - Method in interface htsjdk.beta.plugin.HtsDecoder
  Get the version of the file format supported by this decoder.
getVersion() - Method in interface htsjdk.beta.plugin.HtsEncoder
  Get the version of the file format supported by this encoder.
getVersion() - Method in class htsjdk.samtools.SAMFileHeader
getVersion() - Method in class htsjdk.tribble.index.AbstractIndex
getVersion() - Method in class htsjdk.variant.vcf.AbstractVCFCodec
getVersion() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
getVersionedItem() - Method in class htsjdk.samtools.metrics.VersionHeader
getVersionString() - Method in class htsjdk.samtools.metrics.VersionHeader
getVersionString() - Method in enum class htsjdk.variant.vcf.VCFHeaderVersion
getVirtualFilePointer() - Method in class htsjdk.samtools.BAMFileReader
getVirtualOffsetForSeek(long) - Method in class htsjdk.samtools.util.GZIIndex
  Gets the virtual offset for seek with `BlockCompressedInputStream.seek(long)`.
getVirtualOffsets() - Method in class htsjdk.samtools.SBIIndex
  Returns the entries in the index.
getWriteCompressionLevel() - Method in class htsjdk.samtools.cram.compression.GZIPExternalCompressor
getWriter() - Method in class htsjdk.samtools.SAMTextWriter
  Returns the Writer used by this instance.
getWriter(String, Map) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager
getWrittenCount() - Method in class htsjdk.tribble.util.LittleEndianOutputStream
getYear() - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
GFF - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
  Predefined headers for known formats
GFF3 - Static variable in class htsjdk.samtools.util.FileExtensions
Gff3BaseData - Class in htsjdk.tribble.gff
Gff3BaseData(String, String, String, int, int, Double, Strand, int, Map) - Constructor for class htsjdk.tribble.gff.Gff3BaseData
Gff3Codec - Class in htsjdk.tribble.gff
  Codec for parsing Gff3 files, as defined in https://github.com/The-Sequence-Ontology/Specifications/blob/31f62ad469b31769b43af42e0903448db1826925/gff3.md Note that while spec states that all feature types must be defined in sequence ontology, this implementation makes no check on feature types, and allows any string as feature type Each feature line in the Gff3 file will be emitted as a separate feature.
Gff3Codec() - Constructor for class htsjdk.tribble.gff.Gff3Codec
Gff3Codec(Gff3Codec.DecodeDepth) - Constructor for class htsjdk.tribble.gff.Gff3Codec
Gff3Codec(Gff3Codec.DecodeDepth, Predicate) - Constructor for class htsjdk.tribble.gff.Gff3Codec
Gff3Codec.DecodeDepth - Enum Class in htsjdk.tribble.gff
Gff3Codec.Gff3Directive - Enum Class in htsjdk.tribble.gff
  Enum for parsing directive lines.
Gff3Constants - Class in htsjdk.tribble.gff
Gff3Constants() - Constructor for class htsjdk.tribble.gff.Gff3Constants
Gff3Feature - Interface in htsjdk.tribble.gff
  Gff3 format spec is defined at https://github.com/The-Sequence-Ontology/Specifications/blob/31f62ad469b31769b43af42e0903448db1826925/gff3.md Discontinuous features which are split between multiple lines in the gff files are implemented as separate features linked as "co-features"
Gff3FeatureImpl - Class in htsjdk.tribble.gff
  Gff3 format spec is defined at https://github.com/The-Sequence-Ontology/Specifications/blob/31f62ad469b31769b43af42e0903448db1826925/gff3.md Discontinuous features which are split between multiple lines in the gff files are implemented as separate features linked as "co-features"
Gff3FeatureImpl(Gff3BaseData) - Constructor for class htsjdk.tribble.gff.Gff3FeatureImpl
Gff3FeatureImpl(String, String, String, int, int, Double, Strand, int, Map) - Constructor for class htsjdk.tribble.gff.Gff3FeatureImpl
Gff3Writer - Class in htsjdk.tribble.gff
  A class to write out gff3 files.
Gff3Writer(OutputStream) - Constructor for class htsjdk.tribble.gff.Gff3Writer
Gff3Writer(Path) - Constructor for class htsjdk.tribble.gff.Gff3Writer
GOLOMB - Enum constant in enum class htsjdk.samtools.cram.structure.EncodingID
  EXPERIMENTAL: This encoding is untested and scheduled for removal from the CRAM spec.
GOLOMB_RICE - Enum constant in enum class htsjdk.samtools.cram.structure.EncodingID
  EXPERIMENTAL: This encoding is untested and scheduled for removal from the CRAM spec.
GolombIntegerEncoding - Class in htsjdk.samtools.cram.encoding.core.experimental
GolombLongEncoding - Class in htsjdk.samtools.cram.encoding.core.experimental
GolombLongEncoding(int, int) - Constructor for class htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding
GolombRiceIntegerEncoding - Class in htsjdk.samtools.cram.encoding.core.experimental
GolombRiceIntegerEncoding(int, int) - Constructor for class htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding
GQ - Enum constant in enum class htsjdk.samtools.SAMTag
  Deprecated.
  for backwards compatibility only
GQ - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
GQ(int) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
GQAccessor() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.GQAccessor
GROUP_ORDER_TAG - Static variable in class htsjdk.samtools.SAMFileHeader
GS - Enum constant in enum class htsjdk.samtools.SAMTag
  Deprecated.
  for backwards compatibility only
GS - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
GTWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GTWriter
GZI - Static variable in class htsjdk.samtools.util.FileExtensions
GZIIndex - Class in htsjdk.samtools.util
  Represents a .gzi index of a block-compressed file.
GZIIndex.GZIIndexer - Class in htsjdk.samtools.util
  Helper class for constructing the GZIindex.
GZIIndex.IndexEntry - Class in htsjdk.samtools.util
  Index entry mapping the block-offset (compressed offset) to the uncompressed offset where the block starts.
GZIIndexer(OutputStream) - Constructor for class htsjdk.samtools.util.GZIIndex.GZIIndexer
GZIIndexer(Path) - Constructor for class htsjdk.samtools.util.GZIIndex.GZIIndexer
GZIP - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
GZIP - Enum constant in enum class htsjdk.samtools.util.GzipCodec.Format
GZIP_BLOCK_PREAMBLE - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
GZIP_CM_DEFLATE - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
GZIP_FLG - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
GZIP_HEADER_READ_LENGTH - Static variable in class htsjdk.samtools.util.IOUtil
  number of bytes that will be read for the GZIP-header in the function `IOUtil.isGZIPInputStream(InputStream)`
GZIP_ID1 - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
GZIP_ID2 - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
GZIP_OS_UNKNOWN - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
GZIP_OVERHEAD - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
GZIP_XFL - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
GZIP_XLEN - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
GzipCodec - Class in htsjdk.samtools.util
  A reusable codec for compressing and decompressing GZIP and BGZF data using direct `Deflater`/`Inflater` operations on `ByteBuffer`s.
GzipCodec() - Constructor for class htsjdk.samtools.util.GzipCodec
  Create a codec with the default compression level and default strategy.
GzipCodec(int) - Constructor for class htsjdk.samtools.util.GzipCodec
  Create a codec with the specified compression level and default strategy.
GzipCodec(int, int) - Constructor for class htsjdk.samtools.util.GzipCodec
  Create a codec with the specified compression level and deflate strategy.
GzipCodec(int, int, DeflaterFactory, InflaterFactory) - Constructor for class htsjdk.samtools.util.GzipCodec
  Create a codec with full control over compression parameters and factory implementations.
GzipCodec.Format - Enum Class in htsjdk.samtools.util
  The output format for compression.
GZIPExternalCompressor - Class in htsjdk.samtools.cram.compression
GZIPExternalCompressor() - Constructor for class htsjdk.samtools.cram.compression.GZIPExternalCompressor
GZIPExternalCompressor(int) - Constructor for class htsjdk.samtools.cram.compression.GZIPExternalCompressor
GZIPExternalCompressor(int, int) - Constructor for class htsjdk.samtools.cram.compression.GZIPExternalCompressor

## H

H - Enum constant in enum class htsjdk.samtools.CigarOperator
  Hard clip.
H0 - Enum constant in enum class htsjdk.samtools.SAMTag
H0 - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
H1 - Enum constant in enum class htsjdk.samtools.SAMTag
H1 - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
H2 - Enum constant in enum class htsjdk.samtools.SAMTag
H2 - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
hammingDistance(String, String) - Static method in class htsjdk.samtools.util.StringUtil
  Calculates the Hamming distance (number of character mismatches) between two strings s1 and s2.
handleItem(String) - Method in class htsjdk.utils.ClassFinder
  Checks an item to see if it is a class and is annotated with the specified annotation.
handlesURI(IOPath) - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec
HAPLOID_REFERENCE - Enum constant in enum class htsjdk.beta.plugin.HtsContentType
  Haploid reference content type (see `HaploidReferenceFormats` for related formats)
HaploidReferenceCodec - Interface in htsjdk.beta.plugin.hapref
  Base class for all `HtsContentType.HAPLOID_REFERENCE` codecs.
HaploidReferenceDecoder - Interface in htsjdk.beta.plugin.hapref
  Base class for all `HtsContentType.HAPLOID_REFERENCE` decoders.
HaploidReferenceDecoderOptions - Class in htsjdk.beta.plugin.hapref
  Class for haploid reference decoder options.
HaploidReferenceDecoderOptions() - Constructor for class htsjdk.beta.plugin.hapref.HaploidReferenceDecoderOptions
HaploidReferenceEncoder - Interface in htsjdk.beta.plugin.hapref
  Base class for all `HtsContentType.HAPLOID_REFERENCE` encoders.
HaploidReferenceEncoderOptions - Class in htsjdk.beta.plugin.hapref
  Class for haploid reference encoder options.
HaploidReferenceEncoderOptions() - Constructor for class htsjdk.beta.plugin.hapref.HaploidReferenceEncoderOptions
HaploidReferenceFormats - Class in htsjdk.beta.plugin.hapref
  Class with string constants representing the file formats supported by haploid reference codecs.
HaploidReferenceFormats() - Constructor for class htsjdk.beta.plugin.hapref.HaploidReferenceFormats
HaploidReferenceResolver - Class in htsjdk.beta.plugin.registry
  Class with methods for resolving inputs and outputs to haploid reference encoders and decoders.
HaploidReferenceResolver() - Constructor for class htsjdk.beta.plugin.registry.HaploidReferenceResolver
  Create a new HaploidReferenceResolver.
HAPLOTYPE_QUALITY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
HAPMAP2_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
HAPMAP3_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
HapRefDecoderOptions - Class in htsjdk.beta.plugin.hapref
  Class for haploid reference decoder options.
HapRefDecoderOptions() - Constructor for class htsjdk.beta.plugin.hapref.HapRefDecoderOptions
HARD_CLIP - Static variable in enum class htsjdk.samtools.CigarOperator
HardClip - Class in htsjdk.samtools.cram.encoding.readfeatures
  A read feature representing a hard clip similar to `CigarOperator.H`.
HardClip(int, int) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.HardClip
HardyWeinbergCalculation - Class in htsjdk.tribble.util.popgen
  This class calculates a HardyWeinberg p-value given three values representing the observed frequences of homozygous and heterozygous genotypes in the test population.
has(String) - Method in class htsjdk.variant.variantcontext.GenotypeJEXLContext
HAS_GREATER_PART - Static variable in class htsjdk.samtools.util.IntervalTree.Node
HAS_HEALTHY_LAST_BLOCK - Enum constant in enum class htsjdk.samtools.util.BlockCompressedInputStream.FileTermination
HAS_LESSER_PART - Static variable in class htsjdk.samtools.util.IntervalTree.Node
HAS_OVERLAPPING_PART - Static variable in class htsjdk.samtools.util.IntervalTree.Node
HAS_TERMINATOR_BLOCK - Enum constant in enum class htsjdk.samtools.util.BlockCompressedInputStream.FileTermination
hasAD() - Method in class htsjdk.variant.variantcontext.Genotype
  Does the AD field have a value?
hasAllele(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
hasAllele(Allele, boolean) - Method in class htsjdk.variant.variantcontext.VariantContext
hasAltAllele() - Method in class htsjdk.variant.variantcontext.Genotype
hasAlternateAllele(Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
hasAlternateAllele(Allele, boolean) - Method in class htsjdk.variant.variantcontext.VariantContext
hasAlternativeSequenceNames() - Method in class htsjdk.samtools.SAMSequenceRecord
  Returns `true` if there are alternative sequence names; `false` otherwise.
hasAnyAttribute(String) - Method in class htsjdk.variant.variantcontext.Genotype
hasAttribute(SAMTag) - Method in class htsjdk.samtools.SAMRecord
hasAttribute(String) - Method in class htsjdk.samtools.SAMRecord
hasAttribute(String) - Method in class htsjdk.tribble.gff.Gff3BaseData
  Returns `true` if this record contains an attribute for the specified key.
hasAttribute(String) - Method in interface htsjdk.tribble.gff.Gff3Feature
  Returns `true` if this record contains an attribute for the specified key.
hasAttribute(String) - Method in class htsjdk.variant.variantcontext.CommonInfo
hasAttribute(String) - Method in class htsjdk.variant.variantcontext.VariantContext
hasBlockCompressedExtension(File) - Static method in class htsjdk.samtools.util.IOUtil
  Checks if a file ends in one of the `FileExtensions.BLOCK_COMPRESSED`.
hasBlockCompressedExtension(File) - Static method in class htsjdk.tribble.AbstractFeatureReader
  Deprecated.
  use `IOUtil.hasBlockCompressedExtension(File)`.
hasBlockCompressedExtension(String) - Static method in class htsjdk.samtools.util.IOUtil
  Checks if a file ends in one of the `FileExtensions.BLOCK_COMPRESSED`.
hasBlockCompressedExtension(String) - Static method in class htsjdk.tribble.AbstractFeatureReader
  Deprecated.
  use `IOUtil.hasBlockCompressedExtension(String)`.
hasBlockCompressedExtension(URI) - Static method in class htsjdk.samtools.util.IOUtil
  Checks if a file ends in one of the `FileExtensions.BLOCK_COMPRESSED`.
hasBlockCompressedExtension(URI) - Static method in class htsjdk.tribble.AbstractFeatureReader
  Deprecated.
  use `IOUtil.hasBlockCompressedExtension(URI)`.
hasBlockCompressedExtension(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Checks if a path ends in one of the `FileExtensions.BLOCK_COMPRESSED`.
hasBrowseableIndex() - Method in class htsjdk.samtools.CRAMFileReader
hasBrowseableIndex() - Method in interface htsjdk.samtools.SamReader.Indexing
  Returns true if the supported index is browseable, meaning the bins in it can be traversed and chunk data inspected and retrieved.
hasBrowseableIndex() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
hasChildren() - Method in interface htsjdk.tribble.gff.Gff3Feature
hasChildren() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
hasCoFeatures() - Method in interface htsjdk.tribble.gff.Gff3Feature
hasCoFeatures() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
hasConstantNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
hasConstantNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
hasContextDeterminedNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
hasContextDeterminedNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
hasCurrent() - Method in class htsjdk.samtools.SecondaryAlignmentSkippingIterator
hasCurrent() - Method in class htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
hasDP() - Method in class htsjdk.variant.variantcontext.Genotype
  Does the DP field have a value?
hasExtendedAttribute(String) - Method in class htsjdk.variant.variantcontext.Genotype
  Is key associated with a value (even a null one) in the extended attributes? Note this will not return true for the inline attributes DP, GQ, AD, or PL
hasExtension(String) - Method in interface htsjdk.io.IOPath
  Return true if the path component (the hierarchical part of the scheme specific part of the underlying URI) ends with the provided `extension` string.
hasFileSize() - Method in class htsjdk.tribble.index.AbstractIndex
hasFileSystemProvider() - Method in class htsjdk.io.HtsPath
hasFileSystemProvider() - Method in interface htsjdk.io.IOPath
hasFilterLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
hasForbiddenKey(Map) - Static method in class htsjdk.variant.variantcontext.Genotype
  Does the attribute map have a mapping involving a forbidden key (i.e., one that's managed inline by this Genotypes object?
hasFormatLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
hasGenotype(String) - Method in class htsjdk.variant.variantcontext.VariantContext
hasGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContext
hasGenotypes(Collection) - Method in class htsjdk.variant.variantcontext.VariantContext
hasGenotypingData() - Method in class htsjdk.variant.vcf.VCFHeader
  do we have genotyping data?
hasGQ() - Method in class htsjdk.variant.variantcontext.Genotype
  Does the GQ field have a value?
hasGzipFileExtension(Path) - Static method in class htsjdk.samtools.util.IOUtil
  check if the file name ends with .gz, .gzip, or .bfq
hashCode() - Method in class htsjdk.beta.io.bundle.Bundle
hashCode() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
hashCode() - Method in class htsjdk.beta.io.bundle.InputStreamResource
hashCode() - Method in class htsjdk.beta.io.bundle.IOPathResource
hashCode() - Method in class htsjdk.beta.io.bundle.OutputStreamResource
hashCode() - Method in class htsjdk.beta.io.bundle.SeekableStreamResource
hashCode() - Method in class htsjdk.beta.plugin.HtsVersion
hashCode() - Method in class htsjdk.io.HtsPath
hashCode() - Method in class htsjdk.samtools.Bin
  Compute a unique hash code for the given reference sequence and bin number.
hashCode() - Method in class htsjdk.samtools.BinningIndexContent.BinList
hashCode() - Method in class htsjdk.samtools.BinningIndexContent
hashCode() - Method in class htsjdk.samtools.Chunk
hashCode() - Method in class htsjdk.samtools.Cigar
hashCode() - Method in class htsjdk.samtools.CigarElement
hashCode() - Method in class htsjdk.samtools.cram.common.CRAMVersion
hashCode() - Method in class htsjdk.samtools.cram.common.MutableInt
hashCode() - Method in class htsjdk.samtools.cram.compression.ExternalCompressor
hashCode() - Method in class htsjdk.samtools.cram.compression.GZIPExternalCompressor
hashCode() - Method in class htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken
hashCode() - Method in class htsjdk.samtools.cram.compression.RANS4x8ExternalCompressor
hashCode() - Method in class htsjdk.samtools.cram.compression.RANSNx16ExternalCompressor
hashCode() - Method in class htsjdk.samtools.cram.CRAIEntry
hashCode() - Method in class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanIntegerEncoding
hashCode() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParams
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
hashCode() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
hashCode() - Method in class htsjdk.samtools.cram.ref.ReferenceContext
hashCode() - Method in class htsjdk.samtools.cram.structure.AlignmentContext
hashCode() - Method in class htsjdk.samtools.cram.structure.AlignmentSpan
hashCode() - Method in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
hashCode() - Method in record class htsjdk.samtools.cram.structure.CompressorDescriptor
  Returns a hash code value for this object.
hashCode() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
hashCode() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
hashCode() - Method in class htsjdk.samtools.cram.structure.CramHeader
hashCode() - Method in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
hashCode() - Method in class htsjdk.samtools.cram.structure.EncodingDescriptor
hashCode() - Method in class htsjdk.samtools.cram.structure.ReadTag
hashCode() - Method in class htsjdk.samtools.fastq.FastqRecord
hashCode() - Method in class htsjdk.samtools.LinearIndex
hashCode() - Method in class htsjdk.samtools.metrics.MetricBase
  Computes a hashcode by formatting each field into its on disk representation and summing the hashcodes of all the fields.
hashCode() - Method in class htsjdk.samtools.metrics.MetricsFile
hashCode() - Method in class htsjdk.samtools.metrics.StringHeader
hashCode() - Method in class htsjdk.samtools.metrics.VersionHeader
hashCode() - Method in class htsjdk.samtools.QueryInterval
hashCode() - Method in class htsjdk.samtools.reference.FastaSequenceIndex
hashCode() - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
  In general, we expect one entry per contig, so compute the hash based only on the contig.
hashCode() - Method in class htsjdk.samtools.SAMBinaryTagAndValue
hashCode() - Method in class htsjdk.samtools.SAMFileHeader
hashCode() - Method in class htsjdk.samtools.SAMProgramRecord
hashCode() - Method in class htsjdk.samtools.SAMReadGroupRecord
hashCode() - Method in class htsjdk.samtools.SAMRecord
hashCode() - Method in class htsjdk.samtools.SAMSequenceDictionary
hashCode() - Method in class htsjdk.samtools.SAMSequenceRecord
hashCode() - Method in class htsjdk.samtools.SBIIndex
hashCode() - Method in class htsjdk.samtools.SBIIndex.Header
hashCode() - Method in class htsjdk.samtools.util.GZIIndex
hashCode() - Method in class htsjdk.samtools.util.GZIIndex.IndexEntry
hashCode() - Method in class htsjdk.samtools.util.Histogram.Bin
hashCode() - Method in class htsjdk.samtools.util.Histogram
hashCode() - Method in class htsjdk.samtools.util.Interval
hashCode() - Method in class htsjdk.samtools.util.IntervalList
hashCode() - Method in class htsjdk.samtools.util.IntervalTreeMap
hashCode() - Method in class htsjdk.samtools.util.RelativeIso8601Date
hashCode() - Method in class htsjdk.samtools.util.Tuple
hashCode() - Method in class htsjdk.tribble.gff.Gff3BaseData
hashCode() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
hashCode() - Method in class htsjdk.tribble.gff.SequenceRegion
hashCode() - Method in class htsjdk.tribble.index.Block
hashCode() - Method in class htsjdk.tribble.index.interval.Interval
hashCode() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
hashCode() - Method in class htsjdk.tribble.index.tabix.TabixFormat
hashCode() - Method in class htsjdk.tribble.index.tabix.TabixIndex
hashCode() - Method in class htsjdk.variant.bcf2.BCFVersion
hashCode() - Method in interface htsjdk.variant.variantcontext.Allele
hashCode() - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
hashCode() - Method in class htsjdk.variant.variantcontext.SimpleAllele
hashCode() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
hashCode() - Method in class htsjdk.variant.vcf.VCFContigHeaderLine
hashCode() - Method in class htsjdk.variant.vcf.VCFHeaderLine
hashCode() - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
hashUnencodedChars(CharSequence) - Method in class htsjdk.samtools.util.Murmur3
  Hashes a character stream to an int using Murmur3.
hasID() - Method in class htsjdk.variant.variantcontext.VariantContext
hasIndex() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
hasIndex() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
hasIndex() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
hasIndex() - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
hasIndex() - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0
hasIndex() - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
hasIndex() - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Return true if the underlying resource has an index.
hasIndex() - Method in class htsjdk.samtools.BAMFileReader
hasIndex() - Method in class htsjdk.samtools.CRAMFileReader
hasIndex() - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Always false as htsget sources do not have indices
hasIndex() - Method in interface htsjdk.samtools.SamReader
hasIndex() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
hasIndex() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
hasIndex() - Method in class htsjdk.tribble.AbstractFeatureReader
  Whether the reader has an index or not Default implementation returns false
hasIndex() - Method in class htsjdk.tribble.TabixFeatureReader
hasIndex() - Method in class htsjdk.tribble.TribbleIndexedFeatureReader
hasIndexEntry(String) - Method in class htsjdk.samtools.reference.FastaSequenceIndex
  Does the given contig name have a corresponding entry?
hasInfoLine(String) - Method in class htsjdk.variant.vcf.VCFHeader
hasInputType() - Method in interface htsjdk.beta.io.bundle.BundleResource
  Return true if is this resource is backed by a type that can be used for input.
hasInputType() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
hasInputType() - Method in class htsjdk.beta.io.bundle.InputStreamResource
hasInputType() - Method in class htsjdk.beta.io.bundle.IOPathResource
hasInputType() - Method in class htsjdk.beta.io.bundle.SeekableStreamResource
hasLikelihoods() - Method in class htsjdk.variant.variantcontext.Genotype
hasLog10PError() - Method in class htsjdk.variant.variantcontext.CommonInfo
hasLog10PError() - Method in class htsjdk.variant.variantcontext.Genotype
  Deprecated.
hasLog10PError() - Method in class htsjdk.variant.variantcontext.VariantContext
hasMateCigar(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  Checks to see if it is valid for this record to have a mate CIGAR (MC) and then if there is a mate CIGAR available.
hasMD5() - Method in class htsjdk.tribble.index.AbstractIndex
hasMergedSequenceDictionary() - Method in class htsjdk.samtools.SamFileHeaderMerger
hasNext() - Method in class htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator
  Returns true if a next element exists; false otherwise.
hasNext() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
hasNext() - Method in class htsjdk.samtools.cram.build.CramSpanContainerIterator
hasNext() - Method in class htsjdk.samtools.CRAMIterator
hasNext() - Method in class htsjdk.samtools.DuplicateSetIterator
hasNext() - Method in class htsjdk.samtools.fastq.FastqReader
hasNext() - Method in class htsjdk.samtools.filter.FilteringSamIterator
  Returns true if the iteration has more elements.
hasNext() - Method in class htsjdk.samtools.MergingSamRecordIterator
  Returns true if any of the underlying iterators has more records, otherwise false.
hasNext() - Method in class htsjdk.samtools.reference.SamLocusAndReferenceIterator
hasNext() - Method in class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
hasNext() - Method in class htsjdk.samtools.SamReader.AssertingIterator
hasNext() - Method in class htsjdk.samtools.util.AbstractIterator
hasNext() - Method in class htsjdk.samtools.util.AbstractLocusIterator
  Returns true if there are more AbstractLocusInfo<T> objects that can be returned, due to any of the following reasons: 1) there are more aligned reads in the SAM file 2) there are AbstractLocusInfo<T>s in some stage of accumulation 3) there are loci in the target mask that have yet to be accumulated (even if there are no reads covering them)
hasNext() - Method in class htsjdk.samtools.util.AsyncBufferedIterator
hasNext() - Method in class htsjdk.samtools.util.DelegatingIterator
hasNext() - Method in class htsjdk.samtools.util.IntervalList.IntervalMergerIterator
hasNext() - Method in class htsjdk.samtools.util.IntervalTree.FwdIterator
hasNext() - Method in class htsjdk.samtools.util.IntervalTree.OverlapIterator
hasNext() - Method in class htsjdk.samtools.util.IntervalTree.RevIterator
hasNext() - Method in class htsjdk.samtools.util.IntervalTree.ValuesIterator
hasNext() - Method in class htsjdk.samtools.util.MergingIterator
hasNext() - Method in class htsjdk.samtools.util.PeekableIterator
  True if there are more items, in which case both next() and peek() will return a value.
hasNext() - Method in class htsjdk.samtools.util.PeekIterator
hasNext() - Method in class htsjdk.samtools.util.SAMRecordPrefetchingIterator
hasNext() - Method in class htsjdk.samtools.util.SortingLongCollection
  Call only after doneAddingStartIteration() has been called.
hasNext() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
hasNext() - Method in class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator
  Returns true if the iteration has more elements.
hasOriginalMappingInformation(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  See if any tags pertaining to original mapping information have been set.
hasOutputType() - Method in interface htsjdk.beta.io.bundle.BundleResource
  Return true if this resource is backed by a type that can be used for output.
hasOutputType() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
hasOutputType() - Method in class htsjdk.beta.io.bundle.IOPathResource
hasOutputType() - Method in class htsjdk.beta.io.bundle.OutputStreamResource
hasParents() - Method in interface htsjdk.tribble.gff.Gff3Feature
hasParents() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
hasPL() - Method in class htsjdk.variant.variantcontext.Genotype
  Does the PL field have a value?
hasProgramGroupCollisions() - Method in class htsjdk.samtools.SamFileHeaderMerger
  Returns true if there are program group duplicates within the merged headers.
hasReadGroupCollisions() - Method in class htsjdk.samtools.SamFileHeaderMerger
  Returns true if there are read group duplicates within the merged headers.
hasRefAllele() - Method in class htsjdk.variant.variantcontext.Genotype
hasSameAllelesAs(VariantContext) - Method in class htsjdk.variant.variantcontext.VariantContext
hasSameAlternateAllelesAs(VariantContext) - Method in class htsjdk.variant.variantcontext.VariantContext
hasScheme(String) - Static method in class htsjdk.samtools.util.IOUtil
  Check if the given URI has a scheme.
hasSeekableStream() - Method in interface htsjdk.beta.io.bundle.BundleResource
  Returns true if this resource can be rendered as a `SeekableStream`.
hasSeekableStream() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
hasSeekableStream() - Method in class htsjdk.beta.io.bundle.IOPathResource
hasSeekableStream() - Method in class htsjdk.beta.io.bundle.SeekableStreamResource
hasSelectorTable() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZGlobalFlags
hasSymbolicAlleles() - Method in class htsjdk.variant.variantcontext.VariantContext
hasSymbolicAlleles(List) - Static method in class htsjdk.variant.variantcontext.VariantContext
hasTimestamp() - Method in class htsjdk.tribble.index.AbstractIndex
hasValidFileExtension(String) - Method in class htsjdk.samtools.SamReader.Type
hasValueDeterminedNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
hasValueDeterminedNumElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
HC_HardClip - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
header - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetClass
header - Variable in class htsjdk.tribble.AbstractFeatureReader
header - Variable in class htsjdk.variant.bcf2.BCF2Codec.LazyData
header - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
Header - Interface in htsjdk.samtools.metrics
  A header for a metrics file.
Header(long, byte[], byte[], long, long) - Constructor for class htsjdk.samtools.SBIIndex.Header
HEADER_INDICATOR - Static variable in class htsjdk.variant.vcf.VCFHeader
HEADER_LINE - Static variable in class htsjdk.tribble.example.ExampleBinaryCodec
HEADER_NAME_AND_DESCRIPTION_SEPARATOR - Static variable in class htsjdk.samtools.reference.FastaReferenceWriter
  Character used to separate the sequence name and the description if any.
HEADER_RECORD_MISSING_REQUIRED_TAG - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
HEADER_START_CHAR - Static variable in class htsjdk.samtools.reference.FastaReferenceWriter
  Sequence header start character.
HEADER_TAG_INVALID_KEY - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Header tag key contains invalid characters or is not length two
HEADER_TAG_MULTIPLY_DEFINED - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Header tag appears more than once in header line with different value
HEADER_TAG_NON_CONFORMING_VALUE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Header tag contains illegal value
headerLinesAreOrderedConsistently(VCFHeader, VCFHeader) - Static method in class htsjdk.variant.bcf2.BCF2Utils
  Are the elements and their order in the output and input headers consistent so that we can write out the raw genotypes block without decoding and recoding it? If the order of INFO, FILTER, or contrig elements in the output header is different than in the input header we must decode the blocks using the input header and then recode them based on the new output order.
headRecordIsFromDisk() - Method in class htsjdk.samtools.util.DiskBackedQueue
HELICOS - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Helicos Biosciences
HET - Enum constant in enum class htsjdk.variant.variantcontext.GenotypeType
  The sample is heterozygous, with at least one ref and at least one one alt in any order
HeterozygosityFilter - Class in htsjdk.variant.variantcontext.filter
  A Predicate on VariantContexts that either returns true at heterozygous sites (invertible to false).
HeterozygosityFilter(boolean) - Constructor for class htsjdk.variant.variantcontext.filter.HeterozygosityFilter
  Constructor as above that doesn't take a sample, instead it will look at the first genotype of the variant context.
HeterozygosityFilter(boolean, String) - Constructor for class htsjdk.variant.variantcontext.filter.HeterozygosityFilter
  Constructor for a filter that will keep (or remove, if keepHets is false) VC for which the genotype of sample is heterozygous.
HEXADECIMAL - Enum constant in enum class htsjdk.samtools.SamFlagField
hexStringToBytes(String) - Static method in class htsjdk.samtools.util.StringUtil
  Convert a String containing hex characters into an array of bytes with the binary representation of the hex string
HI - Enum constant in enum class htsjdk.samtools.SAMTag
HI - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
HIGH_ACCURACY_DESCRIPTION - Static variable in class htsjdk.samtools.DownsamplingIteratorFactory
HighAccuracy - Enum constant in enum class htsjdk.samtools.DownsamplingIteratorFactory.Strategy
High-level overview - Section in class htsjdk.variant.variantcontext.VariantContext
HISTO_HEADER - Static variable in class htsjdk.samtools.metrics.MetricsFile
Histogram<K> - Class in htsjdk.samtools.util
  Class for computing and accessing histogram type data.
Histogram() - Constructor for class htsjdk.samtools.util.Histogram
  Constructs a new Histogram with default bin and value labels.
Histogram(Histogram) - Constructor for class htsjdk.samtools.util.Histogram
  Copy constructor for a histogram.
Histogram(String, String) - Constructor for class htsjdk.samtools.util.Histogram
  Constructs a new Histogram with supplied bin and value labels.
Histogram(String, String, Comparator) - Constructor for class htsjdk.samtools.util.Histogram
  Constructor that takes labels for the bin and values and a comparator to sort the bins.
Histogram(Comparator) - Constructor for class htsjdk.samtools.util.Histogram
  Constructs a new Histogram that'll use the supplied comparator to sort keys.
Histogram.Bin<K> - Class in htsjdk.samtools.util
  Represents a bin in the Histogram.
HOM_REF - Enum constant in enum class htsjdk.variant.variantcontext.GenotypeType
  The sample is homozygous reference
HOM_VAR - Enum constant in enum class htsjdk.variant.variantcontext.GenotypeType
  All alleles are non-reference
HtsCodec<D,E> - Interface in htsjdk.beta.plugin
  Base interface implemented by all `htsjdk.beta.plugin` codecs.
HtsCodecRegistry - Class in htsjdk.beta.plugin.registry
  A registry for tracking `HtsCodec` instances.
HtsCodecRegistry() - Constructor for class htsjdk.beta.plugin.registry.HtsCodecRegistry
  Create a registry.
HtsCodecResolver<C> - Class in htsjdk.beta.plugin.registry
  Base class for content-type-specific resolvers, with methods for resolving an input or output resource to a codec that can supply an encoder or decoder for that resource.
HtsCodecResolver(String) - Constructor for class htsjdk.beta.plugin.registry.HtsCodecResolver
  Create a resolver for a given `HtsCodec` type, defined by the type parameter `C`.
HtsContentType - Enum Class in htsjdk.beta.plugin
  The plugin framework defines a set of supported content types, each of which represents a type of HTS data such as "aligned reads".
HtsDecoder<H,R> - Interface in htsjdk.beta.plugin
  Base interface for decoders.
HtsDecoderOptions - Interface in htsjdk.beta.plugin
  Base tag interface for options for `HtsDecoder`s.
HtsDefaultRegistry - Class in htsjdk.beta.plugin.registry
  A global, static, immutable, public registry for `HtsCodec` instances.
HtsDefaultRegistry() - Constructor for class htsjdk.beta.plugin.registry.HtsDefaultRegistry
HtsEncoder<H,R> - Interface in htsjdk.beta.plugin
  Base interface for encoders.
HtsEncoderOptions - Interface in htsjdk.beta.plugin
  Base tag interface for options for `HtsEncoder`s.
HTSGET_BAM - Static variable in class htsjdk.beta.plugin.reads.ReadsFormats
  GA4GH htsget BAM format.
HTSGET_SCHEME - Static variable in class htsjdk.samtools.HtsgetBAMFileReader
HTSGET_VERSION - Static variable in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec
HtsgetBAMCodec - Class in htsjdk.beta.codecs.reads.htsget
  Base class for concrete implementations of reads codecs that handle `BundleResourceType.FMT_READS_HTSGET_BAM` codecs.
HtsgetBAMCodec() - Constructor for class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec
HtsgetBAMCodecV1_2 - Class in htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2
  Version 1.2 of `BundleResourceType.FMT_READS_HTSGET_BAM` codec.
HtsgetBAMCodecV1_2() - Constructor for class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMCodecV1_2
HtsgetBAMDecoder - Class in htsjdk.beta.codecs.reads.htsget
  Base class for concrete implementations of reads decoders that handle `BundleResourceType.FMT_READS_HTSGET_BAM` decoding.
HtsgetBAMDecoder(Bundle, ReadsDecoderOptions) - Constructor for class htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder
HtsgetBAMDecoderV1_2 - Class in htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2
  Version 1.2 of `BundleResourceType.FMT_READS_HTSGET_BAM` decoder.
HtsgetBAMDecoderV1_2(Bundle, ReadsDecoderOptions) - Constructor for class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
HtsgetBAMFileReader - Class in htsjdk.samtools
  Class for reading and querying BAM files from an htsget source
HtsgetBAMFileReader(URI, boolean, ValidationStringency, SAMRecordFactory, boolean) - Constructor for class htsjdk.samtools.HtsgetBAMFileReader
  Prepare to read BAM from an htsget source
HtsgetBAMFileReader(URI, boolean, ValidationStringency, SAMRecordFactory, boolean, InflaterFactory) - Constructor for class htsjdk.samtools.HtsgetBAMFileReader
  Prepare to read BAM from a htsget source
HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter - Class in htsjdk.samtools
  Filters out records that do not match any of the given intervals and query type.
HtsgetClass - Enum Class in htsjdk.samtools.util.htsget
  Classes of data that can be requested in an htsget request as defined by the spec
HtsgetErrorResponse - Class in htsjdk.samtools.util.htsget
  Class allowing deserialization from json htsget error response, as defined in https://samtools.github.io/hts-specs/htsget.html An example response could be as follows { "htsget": { "error": "NotFound", "message": "No such accession 'ENS16232164'" } }
HtsgetErrorResponse(String, String) - Constructor for class htsjdk.samtools.util.htsget.HtsgetErrorResponse
HtsgetFormat - Enum Class in htsjdk.samtools.util.htsget
  Formats currently supported by htsget as defined by spec
HtsgetMalformedResponseException - Exception Class in htsjdk.samtools.util.htsget
HtsgetMalformedResponseException() - Constructor for exception class htsjdk.samtools.util.htsget.HtsgetMalformedResponseException
HtsgetMalformedResponseException(String) - Constructor for exception class htsjdk.samtools.util.htsget.HtsgetMalformedResponseException
HtsgetMalformedResponseException(String, Throwable) - Constructor for exception class htsjdk.samtools.util.htsget.HtsgetMalformedResponseException
HtsgetMalformedResponseException(Throwable) - Constructor for exception class htsjdk.samtools.util.htsget.HtsgetMalformedResponseException
HtsgetPOSTRequest - Class in htsjdk.samtools.util.htsget
  Builder for an htsget POST request that allows opening a connection using the request after validating that it is properly formed.
HtsgetPOSTRequest(HtsgetRequest) - Constructor for class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
HtsgetPOSTRequest(URI) - Constructor for class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
  Construct an HtsgetRequest from a URI identifying a valid resource on a htsget server
HtsgetRequest - Class in htsjdk.samtools.util.htsget
  Builder for an htsget GET request that allows opening a connection using the request after validating that it is properly formed.
HtsgetRequest(URI) - Constructor for class htsjdk.samtools.util.htsget.HtsgetRequest
  Construct an HtsgetRequest from a URI identifying a valid resource on a htsget server
HtsgetRequestField - Enum Class in htsjdk.samtools.util.htsget
  Fields which can be used to filter a htsget request as defined by the spec
HtsgetResponse - Class in htsjdk.samtools.util.htsget
  Class allowing deserialization from json htsget response, as defined in https://samtools.github.io/hts-specs/htsget.html
HtsgetResponse(HtsgetFormat, List, String) - Constructor for class htsjdk.samtools.util.htsget.HtsgetResponse
HtsgetResponse.Block - Class in htsjdk.samtools.util.htsget
HtsHeader - Interface in htsjdk.beta.plugin
  Tagging interface used as a type-bound for codec/encoder/decoder header type params.
HtsInterval - Interface in htsjdk.beta.plugin.interval
  A common interface for 1-based, closed genomic intervals.
HtsIntervalUtils - Class in htsjdk.beta.plugin.interval
  Methods for interconverting between HtsQueryInterval and existing htsjdk types such as Locatable/QueryInterval
HtsIntervalUtils() - Constructor for class htsjdk.beta.plugin.interval.HtsIntervalUtils
htsjdk.annotations - package htsjdk.annotations
htsjdk.beta.codecs.hapref.fasta - package htsjdk.beta.codecs.hapref.fasta
htsjdk.beta.codecs.reads - package htsjdk.beta.codecs.reads
htsjdk.beta.codecs.reads.bam - package htsjdk.beta.codecs.reads.bam
htsjdk.beta.codecs.reads.bam.bamV1_0 - package htsjdk.beta.codecs.reads.bam.bamV1_0
htsjdk.beta.codecs.reads.cram - package htsjdk.beta.codecs.reads.cram
htsjdk.beta.codecs.reads.cram.cramV2_1 - package htsjdk.beta.codecs.reads.cram.cramV2_1
htsjdk.beta.codecs.reads.cram.cramV3_0 - package htsjdk.beta.codecs.reads.cram.cramV3_0
htsjdk.beta.codecs.reads.cram.cramV3_1 - package htsjdk.beta.codecs.reads.cram.cramV3_1
htsjdk.beta.codecs.reads.htsget - package htsjdk.beta.codecs.reads.htsget
htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2 - package htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2
htsjdk.beta.codecs.reads.sam - package htsjdk.beta.codecs.reads.sam
htsjdk.beta.codecs.reads.sam.samV1_0 - package htsjdk.beta.codecs.reads.sam.samV1_0
htsjdk.beta.codecs.variants.vcf - package htsjdk.beta.codecs.variants.vcf
htsjdk.beta.codecs.variants.vcf.vcfv3_2 - package htsjdk.beta.codecs.variants.vcf.vcfv3_2
htsjdk.beta.codecs.variants.vcf.vcfv3_3 - package htsjdk.beta.codecs.variants.vcf.vcfv3_3
htsjdk.beta.codecs.variants.vcf.vcfv4_0 - package htsjdk.beta.codecs.variants.vcf.vcfv4_0
htsjdk.beta.codecs.variants.vcf.vcfv4_1 - package htsjdk.beta.codecs.variants.vcf.vcfv4_1
htsjdk.beta.codecs.variants.vcf.vcfv4_2 - package htsjdk.beta.codecs.variants.vcf.vcfv4_2
htsjdk.beta.codecs.variants.vcf.vcfv4_3 - package htsjdk.beta.codecs.variants.vcf.vcfv4_3
htsjdk.beta.exception - package htsjdk.beta.exception
htsjdk.beta.io - package htsjdk.beta.io
htsjdk.beta.io.bundle - package htsjdk.beta.io.bundle
htsjdk.beta.plugin - package htsjdk.beta.plugin
htsjdk.beta.plugin.hapref - package htsjdk.beta.plugin.hapref
htsjdk.beta.plugin.interval - package htsjdk.beta.plugin.interval
htsjdk.beta.plugin.reads - package htsjdk.beta.plugin.reads
htsjdk.beta.plugin.registry - package htsjdk.beta.plugin.registry
htsjdk.beta.plugin.variants - package htsjdk.beta.plugin.variants
htsjdk.io - package htsjdk.io
htsjdk.samtools - package htsjdk.samtools
htsjdk.samtools.apps - package htsjdk.samtools.apps
htsjdk.samtools.cram - package htsjdk.samtools.cram
htsjdk.samtools.cram.build - package htsjdk.samtools.cram.build
htsjdk.samtools.cram.common - package htsjdk.samtools.cram.common
htsjdk.samtools.cram.compression - package htsjdk.samtools.cram.compression
htsjdk.samtools.cram.compression.fqzcomp - package htsjdk.samtools.cram.compression.fqzcomp
htsjdk.samtools.cram.compression.nametokenisation - package htsjdk.samtools.cram.compression.nametokenisation
htsjdk.samtools.cram.compression.nametokenisation.tokens - package htsjdk.samtools.cram.compression.nametokenisation.tokens
htsjdk.samtools.cram.compression.range - package htsjdk.samtools.cram.compression.range
htsjdk.samtools.cram.compression.rans - package htsjdk.samtools.cram.compression.rans
htsjdk.samtools.cram.digest - package htsjdk.samtools.cram.digest
htsjdk.samtools.cram.encoding - package htsjdk.samtools.cram.encoding
htsjdk.samtools.cram.encoding.core - package htsjdk.samtools.cram.encoding.core
htsjdk.samtools.cram.encoding.core.experimental - package htsjdk.samtools.cram.encoding.core.experimental
htsjdk.samtools.cram.encoding.core.huffmanUtils - package htsjdk.samtools.cram.encoding.core.huffmanUtils
htsjdk.samtools.cram.encoding.external - package htsjdk.samtools.cram.encoding.external
htsjdk.samtools.cram.encoding.reader - package htsjdk.samtools.cram.encoding.reader
htsjdk.samtools.cram.encoding.readfeatures - package htsjdk.samtools.cram.encoding.readfeatures
htsjdk.samtools.cram.encoding.writer - package htsjdk.samtools.cram.encoding.writer
htsjdk.samtools.cram.io - package htsjdk.samtools.cram.io
htsjdk.samtools.cram.ref - package htsjdk.samtools.cram.ref
htsjdk.samtools.cram.structure - package htsjdk.samtools.cram.structure
htsjdk.samtools.cram.structure.block - package htsjdk.samtools.cram.structure.block
htsjdk.samtools.example - package htsjdk.samtools.example
htsjdk.samtools.fastq - package htsjdk.samtools.fastq
htsjdk.samtools.filter - package htsjdk.samtools.filter
htsjdk.samtools.liftover - package htsjdk.samtools.liftover
htsjdk.samtools.metrics - package htsjdk.samtools.metrics
htsjdk.samtools.reference - package htsjdk.samtools.reference
htsjdk.samtools.seekablestream - package htsjdk.samtools.seekablestream
htsjdk.samtools.util - package htsjdk.samtools.util
htsjdk.samtools.util.ftp - package htsjdk.samtools.util.ftp
htsjdk.samtools.util.htsget - package htsjdk.samtools.util.htsget
htsjdk.samtools.util.nio - package htsjdk.samtools.util.nio
htsjdk.samtools.util.zip - package htsjdk.samtools.util.zip
htsjdk.tribble - package htsjdk.tribble
htsjdk.tribble.annotation - package htsjdk.tribble.annotation
htsjdk.tribble.bed - package htsjdk.tribble.bed
htsjdk.tribble.example - package htsjdk.tribble.example
htsjdk.tribble.exception - package htsjdk.tribble.exception
htsjdk.tribble.gff - package htsjdk.tribble.gff
htsjdk.tribble.index - package htsjdk.tribble.index
htsjdk.tribble.index.interval - package htsjdk.tribble.index.interval
htsjdk.tribble.index.linear - package htsjdk.tribble.index.linear
htsjdk.tribble.index.tabix - package htsjdk.tribble.index.tabix
htsjdk.tribble.IntervalList - package htsjdk.tribble.IntervalList
htsjdk.tribble.readers - package htsjdk.tribble.readers
htsjdk.tribble.util - package htsjdk.tribble.util
htsjdk.tribble.util.popgen - package htsjdk.tribble.util.popgen
htsjdk.utils - package htsjdk.utils
htsjdk.variant.bcf2 - package htsjdk.variant.bcf2
htsjdk.variant.example - package htsjdk.variant.example
htsjdk.variant.utils - package htsjdk.variant.utils
htsjdk.variant.variantcontext - package htsjdk.variant.variantcontext
htsjdk.variant.variantcontext.filter - package htsjdk.variant.variantcontext.filter
htsjdk.variant.variantcontext.writer - package htsjdk.variant.variantcontext.writer
htsjdk.variant.vcf - package htsjdk.variant.vcf
HtsjdkException - Exception Class in htsjdk.beta.exception
  Exception type for all exceptions caused at runtime by HTSJDK.
HtsjdkException(String) - Constructor for exception class htsjdk.beta.exception.HtsjdkException
  Constructs an HtsjdkException.
HtsjdkException(String, Throwable) - Constructor for exception class htsjdk.beta.exception.HtsjdkException
  Construct an HtsjdkException with a specified cause.
HtsjdkException(Throwable) - Constructor for exception class htsjdk.beta.exception.HtsjdkException
  Construct an HtsjdkException with a message constructed from the cause.
HtsjdkIOException - Exception Class in htsjdk.beta.exception
  A RuntimeException-derived class for propagating IOExceptions caught and rethrown by the plugin framework.
HtsjdkIOException(String) - Constructor for exception class htsjdk.beta.exception.HtsjdkIOException
  Construct an HtsjdkIOException.
HtsjdkIOException(String, Throwable) - Constructor for exception class htsjdk.beta.exception.HtsjdkIOException
  Construct an HtsjdkIOException exception with a specified cause.
HtsjdkIOException(Throwable) - Constructor for exception class htsjdk.beta.exception.HtsjdkIOException
  Constructs an HtsjdkIOException exception with a message constructed from the cause.
HtsjdkPluginException - Exception Class in htsjdk.beta.exception
  Base class for unexpected conditions caused by codec plugins.
HtsjdkPluginException(String) - Constructor for exception class htsjdk.beta.exception.HtsjdkPluginException
  Construct an HtsjdkPluginException.
HtsjdkUnsupportedOperationException - Exception Class in htsjdk.beta.exception
  Exception thrown when a requested operation is not supported by a plugin codec.
HtsjdkUnsupportedOperationException(String) - Constructor for exception class htsjdk.beta.exception.HtsjdkUnsupportedOperationException
HtsPath - Class in htsjdk.io
  Default implementation for IOPath.
HtsPath(HtsPath) - Constructor for class htsjdk.io.HtsPath
  Create an HtsPath from an existing HtsPath.
HtsPath(String) - Constructor for class htsjdk.io.HtsPath
  Create an HtsPath from a raw input path string.
HtsQuery<RECORD> - Interface in htsjdk.beta.plugin.interval
  Common query interface for `HtsDecoder`s
HtsQueryInterval - Class in htsjdk.beta.plugin.interval
  An concrete query interval implementation of `HtsInterval` used for random access queries on file formats represented by `HtsDecoder`s that support random access.
HtsQueryInterval(QueryInterval, SAMSequenceDictionary) - Constructor for class htsjdk.beta.plugin.interval.HtsQueryInterval
  Convenience method for creating a query interval from an old-style `QueryInterval`.
HtsQueryInterval(String, long, long) - Constructor for class htsjdk.beta.plugin.interval.HtsQueryInterval
  Create an HtsQueryInterval from query components
HtsQueryRule - Enum Class in htsjdk.beta.plugin.interval
  Query rule values used to determine signal whether a query should match overlapping or contained records.
HtsRecord - Interface in htsjdk.beta.plugin
  Tagging interface used as a type-bound for codec/encoder/decoder record type params.
HtsVersion - Class in htsjdk.beta.plugin
  A class for representing 3-part versions with major, minor and patch segments.
HtsVersion(int, int, int) - Constructor for class htsjdk.beta.plugin.HtsVersion
  Construct a 3 part version number.
HtsVersion(String) - Constructor for class htsjdk.beta.plugin.HtsVersion
  Construct a 3 part version number from a string withe the format `major.minor.patch`, where each of major/minor/patch is an integer.
HTTPHelper - Class in htsjdk.tribble.util
  Simple implementation of URLHelper based on the JDK URL and HttpURLConnection classes.
HTTPHelper(URL) - Constructor for class htsjdk.tribble.util.HTTPHelper
HttpUtils - Class in htsjdk.samtools.util
  User: jrobinso Date: Sep 23, 2009
HttpUtils() - Constructor for class htsjdk.samtools.util.HttpUtils
HUFFMAN - Enum constant in enum class htsjdk.samtools.cram.structure.EncodingID
  http://en.wikipedia.org/wiki/Huffman_coding
HuffmanBitCode<T> - Class in htsjdk.samtools.cram.encoding.core.huffmanUtils
  Huffman bit code word consisting of a symbol, the corresponding codeword and codeword bit length.
HuffmanBitCode(T, int, int) - Constructor for class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanBitCode
HuffmanCanoncialCodeGenerator<T> - Class in htsjdk.samtools.cram.encoding.core.huffmanUtils
  Given a set of `HuffmanParams`, creates the set of canonical codes that are be used to read/write symbols from/to an output/input stream.
HuffmanCanoncialCodeGenerator(HuffmanParams) - Constructor for class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanCanoncialCodeGenerator
HuffmanParams<T> - Class in htsjdk.samtools.cram.encoding.core.huffmanUtils
  A class for carrying around encoding parameters for a canonical Huffman encoder.
HuffmanParams(List, List) - Constructor for class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParams
HuffmanParamsCalculator<T> - Class in htsjdk.samtools.cram.encoding.core.huffmanUtils
  A utility class that calculates Huffman encoding parameters based on the frequencies of the symbols to be encoded.
HuffmanParamsCalculator() - Constructor for class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParamsCalculator
humanReadableByteCount(long) - Static method in class htsjdk.samtools.util.StringUtil
  Takes a long value representing the number of bytes and produces a human readable byte count.
hwCalculate(int, int, int) - Static method in class htsjdk.tribble.util.popgen.HardyWeinbergCalculation
  Calculates exact two-sided hardy-weinberg p-value.

## I

I - Enum constant in enum class htsjdk.samtools.CigarOperator
  Insertion vs.
id() - Method in class htsjdk.samtools.cram.encoding.CRAMEncoding
id(String) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells us that the resulting VariantContext should have ID
ID - Enum constant in enum class htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
ID_ATTRIBUTE - Static variable in class htsjdk.variant.vcf.VCFSimpleHeaderLine
ID_ATTRIBUTE_KEY - Static variable in class htsjdk.tribble.gff.Gff3Constants
ID_FIELD_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
ID_TO_ENUM - Static variable in class htsjdk.variant.bcf2.BCF2Utils
IGFGenotypesWriter(VCFHeader, BCF2FieldEncoder, IntGenotypeFieldAccessors.Accessor) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IGFGenotypesWriter
IH - Enum constant in enum class htsjdk.samtools.SAMTag
IH - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
Illumina - Enum constant in enum class htsjdk.samtools.util.FastqQualityFormat
  Recent Solexa/Illumina (pipeline 1.3+) style scores which encode PHRED qualities using an ASCII offset of 64
ILLUMINA - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Illumina
ILLUMINA_TO_PHRED_SUBTRAHEND - Static variable in class htsjdk.samtools.util.SolexaQualityConverter
  This value is removed from an Illumina 1.8 quality score to make it a Phred score
immutable() - Method in class htsjdk.variant.variantcontext.GenotypesContext
IN_Insertion - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
INCLUDE_SOURCE_IN_RECORDS - Enum constant in enum class htsjdk.samtools.SamReaderFactory.Option
  The factory's `SamReader`s will produce populated (non-null) values when calling `SAMRecord.getFileSource()`.
includeIndels - Variable in class htsjdk.samtools.util.AbstractLocusIterator
  If true, include indels in the LocusInfo
INCORRECT_HEADER_SIZE_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
increment(K) - Method in class htsjdk.samtools.util.Histogram
  Increments the value in the designated bin by 1.
increment(K, double) - Method in class htsjdk.samtools.util.Histogram
  Increments the value in the designated bin by the supplied increment.
incrementFeatureCount() - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
incrementValue(int) - Method in class htsjdk.samtools.cram.common.MutableInt
  Increment the current value by `initialValue`.
INDEL - Enum constant in enum class htsjdk.variant.variantcontext.VariantContext.Type
index(SeekableStream) - Method in class htsjdk.samtools.SamInputResource
  Updates the index to point at the provided resource, then returns itself.
index(File) - Method in class htsjdk.samtools.SamInputResource
  Updates the index to point at the provided resource, then returns itself.
index(InputStream) - Method in class htsjdk.samtools.SamInputResource
  Updates the index to point at the provided resource, then returns itself.
index(URL) - Method in class htsjdk.samtools.SamInputResource
  Updates the index to point at the provided resource, then returns itself.
index(Path) - Method in class htsjdk.samtools.SamInputResource
  Updates the index to point at the provided resource, then returns itself.
index(Path, Function) - Method in class htsjdk.samtools.SamInputResource
  Updates the index to point at the provided resource, with the provided wrapper, then returns itself.
Index - Interface in htsjdk.tribble.index
  Interface for all index implementations.
INDEX_ON_THE_FLY - Enum constant in enum class htsjdk.variant.variantcontext.writer.Options
INDEX_TYPE - Static variable in class htsjdk.tribble.index.interval.IntervalTreeIndex
INDEX_TYPE - Static variable in class htsjdk.tribble.index.linear.LinearIndex
IndexCreator - Interface in htsjdk.tribble.index
  An interface for creating indexes
IndexedFastaSequenceFile - Class in htsjdk.samtools.reference
  A fasta file driven by an index for fast, concurrent lookups.
IndexedFastaSequenceFile(IOPath, IOPath, FastaSequenceIndex) - Constructor for class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Open the given indexed fasta sequence file.
IndexedFastaSequenceFile(File) - Constructor for class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Open the given indexed fasta sequence file.
IndexedFastaSequenceFile(File, FastaSequenceIndex) - Constructor for class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Open the given indexed fasta sequence file.
IndexedFastaSequenceFile(String, SeekableStream, FastaSequenceIndex, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Initialise the given indexed fasta sequence file stream.
IndexedFastaSequenceFile(Path) - Constructor for class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Open the given indexed fasta sequence file.
IndexedFastaSequenceFile(Path, FastaSequenceIndex) - Constructor for class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Open the given indexed fasta sequence file.
indexedFileMD5 - Variable in class htsjdk.tribble.index.AbstractIndex
indexedFileSize - Variable in class htsjdk.tribble.index.AbstractIndex
indexedFileTS - Variable in class htsjdk.tribble.index.AbstractIndex
indexedPath - Variable in class htsjdk.tribble.index.AbstractIndex
indexExtension() - Method in class htsjdk.samtools.SamReader.Type
  The recommended file extension for SAM indexes of this type, without a period, or null if this type is not associated with indexes.
IndexFactory - Class in htsjdk.tribble.index
  Factory class for creating indexes.
IndexFactory() - Constructor for class htsjdk.tribble.index.IndexFactory
IndexFactory.IndexBalanceApproach - Enum Class in htsjdk.tribble.index
  We can optimize index-file-creation for different factors.
IndexFactory.IndexType - Enum Class in htsjdk.tribble.index
  an enum that contains all of the information about the index types, and how to create them
indexFile(File) - Static method in class htsjdk.tribble.Tribble
  Return the File of the index file for the provided `file` Does not actually create an index
indexFile(String) - Static method in class htsjdk.tribble.Tribble
  Return the name of the index file for the provided `filename` Does not actually create an index
indexing() - Method in interface htsjdk.samtools.SamReader
  Exposes the `SamReader.Indexing` facet of this `SamReader`.
indexing() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
IndexMerger<T> - Class in htsjdk.samtools
  Merges index files for (headerless) parts of a partitioned main file into a single index file.
IndexMerger(OutputStream, long) - Constructor for class htsjdk.samtools.IndexMerger
  Create an index merger.
indexOf(Object) - Method in class htsjdk.variant.variantcontext.GenotypesContext
indexPath(Path) - Static method in class htsjdk.tribble.Tribble
  Return the name of the index file for the provided `path` Does not actually create an index
IndexToTable - Class in htsjdk.tribble.example
IndexToTable() - Constructor for class htsjdk.tribble.example.IndexToTable
IndicesAreEqual - Class in htsjdk.tribble.example
  Check with two index files are equal
IndicesAreEqual() - Constructor for class htsjdk.tribble.example.IndicesAreEqual
inflaterFactory(InflaterFactory) - Method in class htsjdk.samtools.SamReaderFactory
  Set this factory's `InflaterFactory` to the provided one, then returns itself.
InflaterFactory - Class in htsjdk.samtools.util.zip
  Factory for `Inflater` objects used by `BlockGunzipper`.
InflaterFactory() - Constructor for class htsjdk.samtools.util.zip.InflaterFactory
info(Object...) - Method in class htsjdk.samtools.util.Log
  Logs one or more message parts at level info.
info(Throwable, Object...) - Method in class htsjdk.samtools.util.Log
  Logs a Throwable and optional message parts at level info.
info(Supplier) - Method in class htsjdk.samtools.util.Log
  Logs a message part at level info.
INFO - Enum constant in enum class htsjdk.samtools.util.Log.LogLevel
INFO - Enum constant in enum class htsjdk.variant.vcf.VCFCompoundHeaderLine.SupportedHeaderLineType
INFO - Enum constant in enum class htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
INFO_FIELD_ARRAY_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
INFO_FIELD_ARRAY_SEPARATOR_CHAR - Static variable in class htsjdk.variant.vcf.VCFConstants
INFO_FIELD_SEPARATOR - Static variable in class htsjdk.variant.vcf.VCFConstants
INFO_FIELD_SEPARATOR_CHAR - Static variable in class htsjdk.variant.vcf.VCFConstants
INFO_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
initialize(String, Map) - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
initializeAnyploidPLIndexToAlleleIndices(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  Deprecated.
  as of sept 2020, this method is no longer necessary
initializeCigar(Cigar) - Method in class htsjdk.samtools.SAMRecord
  For setting the Cigar string when BAMRecord has decoded it.
initializeMatchExps(String[], String[]) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Method for creating JexlVCMatchExp from input walker arguments names and exps.
initializeMatchExps(List, List) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Method for creating JexlVCMatchExp from input walker arguments names and exps.
initializeMatchExps(Map) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Method for creating JexlVCMatchExp from input walker arguments mapping from names to exps.
initParameters() - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Initialization method used for simplifying the constructor hierarchy.
initParameters() - Method in class htsjdk.samtools.CSIIndex
inputBundle - Variable in class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
inputReader - Variable in class htsjdk.samtools.cram.encoding.external.ExternalByteArrayCodec
InputStreamResource - Class in htsjdk.beta.io.bundle
  A `BundleResource` backed by an `InputStream`.
InputStreamResource(InputStream, String, String) - Constructor for class htsjdk.beta.io.bundle.InputStreamResource
  Create a `BundleResource` backed by an InputStream.
InputStreamResource(InputStream, String, String, String) - Constructor for class htsjdk.beta.io.bundle.InputStreamResource
  Create a `BundleResource` backed by an InputStream, specifying a display name, content type, and format.
InputStreamUtils - Class in htsjdk.samtools.cram.io
  Convenience methods to read from `InputStream`.
InputStreamUtils() - Constructor for class htsjdk.samtools.cram.io.InputStreamUtils
INS - Enum constant in enum class htsjdk.variant.variantcontext.StructuralVariantType
  Insertion of novel sequence relative to the reference
insert(SAMBinaryTagAndValue) - Method in class htsjdk.samtools.SAMBinaryTagAndValue
  Inserts an item into the ordered list of attributes and returns the head of the list/sub-list
insert(Interval) - Method in class htsjdk.tribble.index.interval.IntervalTree
insert(Interval) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
insert(String, Interval) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex
  Add a new interval to this index
InsertBase - Class in htsjdk.samtools.cram.encoding.readfeatures
  A read feature representing a single insert base.
InsertBase(int, byte) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
Insertion - Class in htsjdk.samtools.cram.encoding.readfeatures
  A read feature representing a multi-base insertion.
Insertion - Enum constant in enum class htsjdk.samtools.util.AbstractRecordAndOffset.AlignmentType
Insertion(int, byte[]) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Insertion
INSERTION - Static variable in enum class htsjdk.samtools.CigarOperator
INSERTION_ALLELE_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
InsertSizeFilter - Class in htsjdk.samtools.filter
  Filter things that fall outside a specified range of insert sizes.
InsertSizeFilter(int, int) - Constructor for class htsjdk.samtools.filter.InsertSizeFilter
INT - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeriesType
  A signed integer ~4 billions of them.
INT16 - Enum constant in enum class htsjdk.variant.bcf2.BCF2Type
INT32 - Enum constant in enum class htsjdk.variant.bcf2.BCF2Type
INT8 - Enum constant in enum class htsjdk.variant.bcf2.BCF2Type
IntArray(VCFCompoundHeaderLine, Map) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.IntArray
Integer - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderLineType
INTEGER - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderLineCount
INTEGER_TYPES_BY_SIZE - Static variable in class htsjdk.variant.bcf2.BCF2Utils
IntegerTypeGenotypesWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IntegerTypeGenotypesWriter
InternalAPI - Annotation Interface in htsjdk.annotations
  Annotation indicating that a package, class, method, or type is release level "internal", even if the access modifier is "public".
InternalCodecException(String) - Constructor for exception class htsjdk.tribble.TribbleException.InternalCodecException
intersect(CRAIEntry, CRAIEntry) - Static method in class htsjdk.samtools.cram.CRAIEntry
intersect(Interval) - Method in class htsjdk.samtools.util.Interval
  Returns a new Interval that represents the intersection between the two intervals.
intersection(IntervalList, IntervalList) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for generating the intersection of two IntervalLists, checks for equal dictionaries.
intersection(Collection) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for intersecting a list of IntervalLists, checks for equal dictionaries.
intersects(Interval) - Method in class htsjdk.samtools.util.Interval
  Returns true if this interval overlaps the other interval, otherwise false.
interval - Variable in class htsjdk.samtools.util.htsget.HtsgetRequest
Interval - Class in htsjdk.samtools.util
  Represents a simple interval on a sequence.
Interval - Class in htsjdk.tribble.index.interval
  Quick and dirty interval class Describes a genomic interval and where in a file information for that interval can be obtained
Interval(int, int) - Constructor for class htsjdk.tribble.index.interval.Interval
Interval(int, int, Block) - Constructor for class htsjdk.tribble.index.interval.Interval
Interval(Locatable) - Constructor for class htsjdk.samtools.util.Interval
  Constructs an interval with the supplied `Locatable`.
Interval(String, int, int) - Constructor for class htsjdk.samtools.util.Interval
  Constructs an interval with the supplied sequence and start and end.
Interval(String, int, int, boolean, String) - Constructor for class htsjdk.samtools.util.Interval
  Constructs an interval with the supplied sequence and start, end, strand and name.
INTERVAL_LIST - Static variable in class htsjdk.samtools.util.FileExtensions
INTERVAL_LIST_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IntervalList
  Deprecated.
  since June 2019 Use `FileExtensions.INTERVAL_LIST` instead.
INTERVAL_LIST_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  since June 2019 Use `FileExtensions.INTERVAL_LIST` instead.
INTERVAL_MERGING_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
INTERVAL_PADDING_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
INTERVAL_SET_RULE_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
INTERVAL_TREE - Enum constant in enum class htsjdk.tribble.index.AbstractIndex.IndexType
INTERVAL_TREE - Enum constant in enum class htsjdk.tribble.index.IndexFactory.IndexType
IntervalCodec - Class in htsjdk.samtools.util
IntervalCodec(SAMSequenceDictionary) - Constructor for class htsjdk.samtools.util.IntervalCodec
  Creates a new binary codec to read or write.
IntervalCombiner() - Constructor for class htsjdk.samtools.util.IntervalUtil.IntervalCombiner
IntervalCoordinateComparator - Class in htsjdk.samtools.util
  Comparator that orders intervals based on their sequence index, by coordinate then by strand and finally by name.
IntervalCoordinateComparator(SAMFileHeader) - Constructor for class htsjdk.samtools.util.IntervalCoordinateComparator
  Constructs a comparator using the supplied sequence header.
IntervalFilter - Class in htsjdk.samtools.filter
  Filter SAMRecords so that only those that overlap the given list of intervals.
IntervalFilter(List, SAMFileHeader) - Constructor for class htsjdk.samtools.filter.IntervalFilter
  Prepare to filter out SAMRecords that do not overlap the given list of intervals
IntervalIndexCreator - Class in htsjdk.tribble.index.interval
  Creates interval indexes from a stream of features
IntervalIndexCreator(File) - Constructor for class htsjdk.tribble.index.interval.IntervalIndexCreator
IntervalIndexCreator(File, int) - Constructor for class htsjdk.tribble.index.interval.IntervalIndexCreator
IntervalIndexCreator(Path) - Constructor for class htsjdk.tribble.index.interval.IntervalIndexCreator
IntervalIndexCreator(Path, int) - Constructor for class htsjdk.tribble.index.interval.IntervalIndexCreator
IntervalKeepPairFilter - Class in htsjdk.samtools.filter
  Filter out SAMRecords where neither record of a pair overlaps a given set of intervals.
IntervalKeepPairFilter(List) - Constructor for class htsjdk.samtools.filter.IntervalKeepPairFilter
  Prepare to filter out SAMRecords that do not overlap the given list of intervals
IntervalList - Class in htsjdk.samtools.util
  Represents a list of intervals against a reference sequence that can be written to and read from a file.
IntervalList(SAMFileHeader) - Constructor for class htsjdk.samtools.util.IntervalList
  Constructs a new interval list using the supplied header information.
IntervalList(SAMSequenceDictionary) - Constructor for class htsjdk.samtools.util.IntervalList
  Constructs a new interval list using the supplied header information.
IntervalList.IntervalMergerIterator - Class in htsjdk.samtools.util
  An iterator that feeds on an `Iterator<Interval>` and combines consecutive intervals that need merging.
IntervalListCodec - Class in htsjdk.tribble.IntervalList
  A tribble codec for IntervalLists.
IntervalListCodec() - Constructor for class htsjdk.tribble.IntervalList.IntervalListCodec
IntervalListCodec(SAMSequenceDictionary) - Constructor for class htsjdk.tribble.IntervalList.IntervalListCodec
IntervalListReferenceSequenceMask - Class in htsjdk.samtools.util
  Serve up loci of interest based on an interval list.
IntervalListReferenceSequenceMask(IntervalList) - Constructor for class htsjdk.samtools.util.IntervalListReferenceSequenceMask
IntervalListWriter - Class in htsjdk.samtools.util
  Writes out the list of intervals to the supplied file.
IntervalListWriter(Path) - Constructor for class htsjdk.samtools.util.IntervalListWriter
  Creates a new writer, writing a header to the file.
IntervalListWriter(Path, SAMFileHeader) - Constructor for class htsjdk.samtools.util.IntervalListWriter
  Creates a new writer, writing a header to the file.
IntervalMergerIterator(Iterator, boolean, boolean, boolean) - Constructor for class htsjdk.samtools.util.IntervalList.IntervalMergerIterator
INTERVALS_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
IntervalTree<V> - Class in htsjdk.samtools.util
  A Red-Black tree with intervals for keys.
IntervalTree - Class in htsjdk.tribble.index.interval
  An implementation of an interval tree, following the explanation.
IntervalTree() - Constructor for class htsjdk.samtools.util.IntervalTree
IntervalTree() - Constructor for class htsjdk.tribble.index.interval.IntervalTree
IntervalTree.FwdIterator - Class in htsjdk.samtools.util
IntervalTree.Node<V1> - Class in htsjdk.samtools.util
IntervalTree.OverlapIterator - Class in htsjdk.samtools.util
IntervalTree.RevIterator - Class in htsjdk.samtools.util
IntervalTree.ValuesIterator<V1> - Class in htsjdk.samtools.util
IntervalTreeIndex - Class in htsjdk.tribble.index.interval
  Index based on an interval tree
IntervalTreeIndex(InputStream) - Constructor for class htsjdk.tribble.index.interval.IntervalTreeIndex
  Load from file.
IntervalTreeIndex(String) - Constructor for class htsjdk.tribble.index.interval.IntervalTreeIndex
  Prepare to build an index.
IntervalTreeIndex(Path) - Constructor for class htsjdk.tribble.index.interval.IntervalTreeIndex
  Prepare to build an index.
IntervalTreeIndex.ChrIndex - Class in htsjdk.tribble.index.interval
IntervalTreeMap<T> - Class in htsjdk.samtools.util
  Utility class that implements an interval map.
IntervalTreeMap() - Constructor for class htsjdk.samtools.util.IntervalTreeMap
IntervalTreeMap(Map) - Constructor for class htsjdk.samtools.util.IntervalTreeMap
IntervalUtil - Class in htsjdk.samtools.util
IntervalUtil() - Constructor for class htsjdk.samtools.util.IntervalUtil
IntervalUtil.IntervalCombiner - Class in htsjdk.samtools.util
IntGenotypeFieldAccessors - Class in htsjdk.variant.variantcontext.writer
  A convenient way to provide a single view on the many int and int[] field values we work with, for writing out the values.
IntGenotypeFieldAccessors() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors
IntGenotypeFieldAccessors.Accessor - Class in htsjdk.variant.variantcontext.writer
IntGenotypeFieldAccessors.ADAccessor - Class in htsjdk.variant.variantcontext.writer
IntGenotypeFieldAccessors.DPAccessor - Class in htsjdk.variant.variantcontext.writer
IntGenotypeFieldAccessors.GQAccessor - Class in htsjdk.variant.variantcontext.writer
IntGenotypeFieldAccessors.PLAccessor - Class in htsjdk.variant.variantcontext.writer
intToNameType(int, boolean) - Static method in class htsjdk.samtools.cram.structure.ReadTag
  Unpack a 3-byte tag ID int into a String.
intToNameType3Bytes(int) - Static method in class htsjdk.samtools.cram.structure.ReadTag
  Shorthand for `intToNameType(value, false)`.
intToNameType4Bytes(int) - Static method in class htsjdk.samtools.cram.structure.ReadTag
  Shorthand for `intToNameType(value, true)`.
intValue() - Method in enum class htsjdk.samtools.SAMFlag
intValuesToString(int[]) - Static method in class htsjdk.samtools.util.StringUtil
intValuesToString(short[]) - Static method in class htsjdk.samtools.util.StringUtil
INV - Enum constant in enum class htsjdk.variant.variantcontext.StructuralVariantType
  Inversion of reference sequence
INVALID_ALIGNMENT_START - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  alignment start is can not be correct
INVALID_CIGAR - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  CIGAR string is empty for mapped read or not empty of unmapped read, or other CIGAR badness.
INVALID_DATE_STRING - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Date string is not ISO-8601
INVALID_FILE_PTR_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
INVALID_FLAG_FIRST_OF_PAIR - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  first of pair flag set for unpaired read
INVALID_FLAG_MATE_NEG_STRAND - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  mate negative strand flag set for unpaired read
INVALID_FLAG_MATE_UNMAPPED - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  mate unmapped flag set when mate is mapped or not set when mate is not mapped
INVALID_FLAG_NOT_PRIM_ALIGNMENT - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  not primary alignment flag set for unmapped read
INVALID_FLAG_PROPER_PAIR - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  proper pair flag set for unpaired read
INVALID_FLAG_READ_UNMAPPED - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  mapped read flag not set for mapped read
INVALID_FLAG_SECOND_OF_PAIR - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  second of pair flag set for unpaired read
INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  supplementary alignment flag set for unmapped read
INVALID_INDEX_FILE_POINTER - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Invalid virtualFilePointer in index
INVALID_INDEXING_BIN - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Indexing bin set on SAMRecord does not agree with computed value.
INVALID_INSERT_SIZE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  inferred insert size is out of range
INVALID_MAPPING_QUALITY - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  mapping quality set for unmapped read or is >= 256
INVALID_MATE_REF_INDEX - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  mate reference index (MRNM) set for unpaired read
INVALID_PLATFORM_VALUE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  The read group has an invalid value set for its PL field
INVALID_PREDICTED_MEDIAN_INSERT_SIZE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  PI tag value is not numeric.
INVALID_QUALITY_FORMAT - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  quality encodings out of range; appear to be Solexa or Illumina when Phread expected
INVALID_REFERENCE_INDEX - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  reference index not found in sequence dictionary
INVALID_TAG_NM - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  the NM tag (nucleotide differences) is incorrect
INVALID_UNALIGNED_MATE_START - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  The unaligned mate read start position should be 0
INVALID_UNPAIRED_MATE_REFERENCE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  The mate reference of the unpaired read should be "*"
INVALID_VERSION_NUMBER - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
invalidateSampleNameMap() - Method in class htsjdk.variant.variantcontext.GenotypesContext
invalidateSampleNameMap() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
invalidateSampleOrdering() - Method in class htsjdk.variant.variantcontext.GenotypesContext
invalidateSampleOrdering() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
InvalidDateException() - Constructor for exception class htsjdk.samtools.util.DateParser.InvalidDateException
InvalidDateException(String) - Constructor for exception class htsjdk.samtools.util.DateParser.InvalidDateException
InvalidDateException(String, Throwable) - Constructor for exception class htsjdk.samtools.util.DateParser.InvalidDateException
InvalidDateException(Throwable) - Constructor for exception class htsjdk.samtools.util.DateParser.InvalidDateException
InvalidDecodeLine(String, int) - Constructor for exception class htsjdk.tribble.TribbleException.InvalidDecodeLine
InvalidDecodeLine(String, String) - Constructor for exception class htsjdk.tribble.TribbleException.InvalidDecodeLine
InvalidHeader(String) - Constructor for exception class htsjdk.tribble.TribbleException.InvalidHeader
invert(IntervalList) - Static method in class htsjdk.samtools.util.IntervalList
  inverts an IntervalList and returns one that has exactly all the bases in the dictionary that the original one does not.
InvertFilter - Class in htsjdk.samtools.filter
  Wraps an existing filter and inverts it.
InvertFilter(SamRecordFilter) - Constructor for class htsjdk.samtools.filter.InvertFilter
  Constructor
IONTORRENT - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Iontorrent
IOPath - Interface in htsjdk.io
  Interface for htsjdk input/output paths/URIs.
IOPathResource - Class in htsjdk.beta.io.bundle
  A `BundleResource` backed by an `IOPath`.
IOPathResource(IOPath, String) - Constructor for class htsjdk.beta.io.bundle.IOPathResource
  Create a `BundleResource` backed by an IOPath, specifying a content type.
IOPathResource(IOPath, String, String) - Constructor for class htsjdk.beta.io.bundle.IOPathResource
  Create a `BundleResource` backed by an IOPath, specifying a content type string and format string.
IOPathUtils - Class in htsjdk.beta.io
IOPathUtils() - Constructor for class htsjdk.beta.io.IOPathUtils
IOUtil - Class in htsjdk.samtools.util
  Miscellaneous stateless static IO-oriented methods.
IOUtil() - Constructor for class htsjdk.samtools.util.IOUtil
IOUtils - Class in htsjdk.beta.plugin
  Class for updated IOUtils methods that use either `IOPath` `Path` in public method argument lists.
IOUtils() - Constructor for class htsjdk.beta.plugin.IOUtils
IS_ADJACENT_AND_EMPTY - Static variable in class htsjdk.samtools.util.IntervalTree.Node
IS_LEFT_OVERHANGING_OVERLAPPER - Static variable in class htsjdk.samtools.util.IntervalTree.Node
IS_RIGHT_OVERHANGING_OVERLAPPER - Static variable in class htsjdk.samtools.util.IntervalTree.Node
IS_STRICTLY_GREATER - Static variable in class htsjdk.samtools.util.IntervalTree.Node
IS_STRICTLY_LESS - Static variable in class htsjdk.samtools.util.IntervalTree.Node
IS_SUBSET - Static variable in class htsjdk.samtools.util.IntervalTree.Node
IS_SUPERSET - Static variable in class htsjdk.samtools.util.IntervalTree.Node
isAdjacent(IntervalTree.Node) - Method in class htsjdk.samtools.util.IntervalTree.Node
isAdjacentTo(Chunk) - Method in class htsjdk.samtools.Chunk
  Returns whether two chunks overlap.
isAlignment() - Method in enum class htsjdk.samtools.CigarOperator
  Returns true if the operator is a M, a X or a EQ
isAllowedAttributeValue(Object) - Static method in class htsjdk.samtools.SAMBinaryTagAndValue
isAllowedAttributeValue(Object) - Static method in class htsjdk.samtools.SAMRecord
  Deprecated.
  The attribute type and value checks have been moved directly into `SAMBinaryTagAndValue`.
isAllowFieldsMissingFromHeader() - Method in class htsjdk.beta.plugin.variants.VariantsEncoderOptions
  Determine if writing fields that are missing from the header is allowed.
isAPDelta() - Method in class htsjdk.samtools.cram.structure.CompressionHeader
  Return true if the header has APDelta set.
isAsyncIO() - Method in class htsjdk.beta.codecs.reads.bam.BAMDecoderOptions
  Determine if async IO is enabled for these options.
isAsyncIO() - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Determine if async IO is enabled for these options.
isAsyncIO() - Method in class htsjdk.beta.plugin.variants.VariantsEncoderOptions
  Determine if async IO is enabled for these options.
isAtLeastAsRecentAs(VCFHeaderVersion) - Method in enum class htsjdk.variant.vcf.VCFHeaderVersion
  Determines whether this version is at least as recent as a given version
isAvailable() - Method in class htsjdk.variant.variantcontext.Genotype
isBam() - Method in interface htsjdk.io.IOPath
  Returns true if the file's extension is ".bam"".
isBamFile(File) - Static method in class htsjdk.samtools.BamFileIoUtils
isBAMFile(InputStream) - Static method in class htsjdk.samtools.SamStreams
isBamReadBase(byte) - Static method in class htsjdk.samtools.util.SequenceUtil
  Check if the given base belongs to BAM read base set '=ABCDGHKMNRSTVWY'
isBCF(File) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Returns true if the given file appears to be a BCF file.
isBCF(Path) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Returns true if the given path appears to be a BCF file.
isBeingHandledByLegacyUrlSupport(String) - Static method in class htsjdk.samtools.seekablestream.SeekableStreamFactory
  is this path being handled by one of the legacy SeekableStream types (http(s) / ftp)
isBiallelic() - Method in class htsjdk.variant.variantcontext.VariantContext
isBisulfiteConverted(byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil
isBisulfiteConverted(byte, byte, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
  Checks for bisulfite conversion, C->T on the positive strand and G->A on the negative strand.
isBisulfiteSequenced() - Method in class htsjdk.samtools.SamFileValidator
isBlank(String) - Static method in class htsjdk.samtools.util.StringUtil
  Checks if a String is whitespace, empty ("") or null.
isBlockCompressed(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Checks if the provided path is block-compressed (including extension).
isBlockCompressed(Path, boolean) - Static method in class htsjdk.samtools.util.IOUtil
  Checks if the provided path is block-compressed.
isBreakpoint() - Method in interface htsjdk.variant.variantcontext.Allele
isBreakpoint() - Method in class htsjdk.variant.variantcontext.SimpleAllele
isCalled() - Method in interface htsjdk.variant.variantcontext.Allele
isCalled() - Method in class htsjdk.variant.variantcontext.Genotype
isCalled() - Method in class htsjdk.variant.variantcontext.SimpleAllele
isCAT() - Method in class htsjdk.samtools.cram.compression.range.RangeParams
isCAT() - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
isCircular() - Method in class htsjdk.tribble.gff.SequenceRegion
isClipped() - Method in class htsjdk.samtools.Cigar
  returns true if the cigar is clipped
isClipping() - Method in enum class htsjdk.samtools.CigarOperator
  Returns true if the operator is a clipped (hard or soft) operator
isCollapsedString(String) - Static method in class htsjdk.variant.bcf2.BCF2Utils
isCombineAbutting() - Method in class htsjdk.samtools.util.IntervalUtil.IntervalCombiner
isCompatible(Collection) - Method in class htsjdk.variant.variantcontext.VariantContextComparator
  Returns true if the given header lines are from a file sorted according to this VariantContextComparator.
isComplexIndel() - Method in class htsjdk.variant.variantcontext.VariantContext
isConcatenateNames() - Method in class htsjdk.samtools.util.IntervalUtil.IntervalCombiner
isConcrete(Class) - Static method in class htsjdk.utils.ClassFinder
  Determines whether or not the specified class is concrete (ie., non-abstract and non-interface)
isCram() - Method in interface htsjdk.io.IOPath
  Returns true if the GATKPath's extension is ".cram".
isCRAMFile(InputStream) - Static method in class htsjdk.samtools.SamStreams
isCurrentVersion() - Method in class htsjdk.tribble.index.AbstractIndex
  check the current version against the version we read in
isCurrentVersion() - Method in interface htsjdk.tribble.index.Index
isCurrentVersion() - Method in class htsjdk.tribble.index.linear.LinearIndex
isCurrentVersion() - Method in class htsjdk.tribble.index.tabix.TabixIndex
isDecodeEagerly() - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Get eagerly decoding state used for these options.
isDestructiveIteration() - Method in class htsjdk.samtools.util.SortingCollection
isDetached() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Return true if this record stores mate information explicitly (detached state).
isDetached(int) - Static method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Test the detached bit in the given CRAM flags value.
isDeterminationAmbiguous() - Method in class htsjdk.samtools.util.QualityEncodingDetector
  Tests whether or not the detector can make a determination without guessing (i.e., if all but one quality format can be excluded using established exclusion conventions).
isDoDedup() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
isDoDelta() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
isDone() - Method in interface htsjdk.tribble.readers.Positional
  Is the stream done? Equivalent to ! hasNext() for an iterator?
isDone() - Method in class htsjdk.tribble.readers.PositionalBufferedStream
isDone(LineIterator) - Method in class htsjdk.tribble.AsciiFeatureCodec
isDone(LineIterator) - Method in class htsjdk.tribble.gff.Gff3Codec
isDone(PositionalBufferedStream) - Method in class htsjdk.tribble.BinaryFeatureCodec
isDone(SOURCE) - Method in interface htsjdk.tribble.FeatureCodec
  Adapter method that assesses whether the provided `SOURCE` has more data.
isDoPos() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
isDoQmap() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
isDoQtab() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
isDoSel() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
isDynamicallyTyped() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
  Is the BCF2 type of this field static, or does it have to be determine from the actual field value itself?
ISeekableStreamFactory - Interface in htsjdk.samtools.seekablestream
  Factory for creating `SeekableStream`s based on URLs/paths.
isEmitUncoveredLoci() - Method in class htsjdk.samtools.util.AbstractLocusIterator
isEmpty() - Method in class htsjdk.samtools.BAMFileSpan
  Does this chunk list map to any position within the BAM file?
isEmpty() - Method in class htsjdk.samtools.Cigar
isEmpty() - Method in class htsjdk.samtools.DuplicateSet
isEmpty() - Method in interface htsjdk.samtools.SAMFileSpan
  Does this file span point to any data, or is it completely empty?
isEmpty() - Method in class htsjdk.samtools.SAMSequenceDictionary
isEmpty() - Method in class htsjdk.samtools.util.AbstractLocusInfo
isEmpty() - Method in class htsjdk.samtools.util.DiskBackedQueue
isEmpty() - Method in class htsjdk.samtools.util.Histogram
  Returns true if this histogram has no data in in, false otherwise.
isEmpty() - Method in class htsjdk.samtools.util.IntervalTreeMap
isEmpty() - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo
isEmpty() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer
  Returns true if we are tracking no records, false otherwise
isEmpty() - Method in class htsjdk.variant.variantcontext.GenotypesContext
isEmpty() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
isEnabled(Log.LogLevel) - Static method in class htsjdk.samtools.util.Log
  Returns true if the specified log level is enabled otherwise false.
isEnforceSameStrand() - Method in class htsjdk.samtools.util.IntervalUtil.IntervalCombiner
isEOF() - Method in class htsjdk.samtools.cram.structure.Container
isEOF() - Method in class htsjdk.samtools.cram.structure.ContainerHeader
isExternalCompression() - Method in class htsjdk.samtools.cram.compression.range.RangeParams
isExternalEncoding() - Method in enum class htsjdk.samtools.cram.structure.EncodingID
  Return true if this encoding can be used in an external block.
isFasta() - Method in interface htsjdk.io.IOPath
isFileBasedIndexCached() - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Get the file based index cache setting used for these options.
isFilePath(String) - Static method in class htsjdk.samtools.seekablestream.SeekableStreamFactory
  Deprecated.
  this method is simplistic and no longer particularly useful since IOPath allows similar access to various non-file data sources, internal use has been replaced with `SeekableStreamFactory.isBeingHandledByLegacyUrlSupport(String)`
isFiltered() - Method in class htsjdk.variant.variantcontext.CommonInfo
isFiltered() - Method in class htsjdk.variant.variantcontext.Genotype
  Is this genotype filtered or not?
isFiltered() - Method in class htsjdk.variant.variantcontext.VariantContext
isFirstSegment() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Return true if this record is the first segment in the template.
isFixedCount() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
isForbiddenKey(String) - Static method in class htsjdk.variant.variantcontext.Genotype
isForcePreserveQualityScores() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Return true if quality scores are preserved as a full array for this record.
isForcePreserveQualityScores(int) - Static method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Test the quality-scores-preserved-as-array bit in the given CRAM flags value.
isFormatString(String) - Static method in enum class htsjdk.variant.vcf.VCFHeaderVersion
  are we a valid format string for some type
isFullyDecoded() - Method in class htsjdk.variant.variantcontext.VariantContext
  See VariantContext document about fully decoded
isFullyDecoded() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
isGZIPInputStream(InputStream) - Static method in class htsjdk.samtools.util.IOUtil
  Test whether a input stream looks like a GZIP input.
isGzippedSAMFile(InputStream) - Static method in class htsjdk.samtools.SamStreams
  Deprecated.
  use `IOUtil.isGZIPInputStream(InputStream)` instead
isHasMateDownStream() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Return true if this record's CRAM flags indicate a downstream mate in the same slice.
isHasMateDownStream(int) - Static method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Test the has-mate-downstream bit in the given CRAM flags value.
isHeaderLine(String) - Static method in class htsjdk.variant.vcf.VCFHeaderLine
isHet() - Method in class htsjdk.variant.variantcontext.Genotype
isHetNonRef() - Method in class htsjdk.variant.variantcontext.Genotype
isHigherAccuracy() - Method in class htsjdk.samtools.DownsamplingIterator
  Indicates whether or not the strategy implemented by this DownsamplingIterator makes any effort to increase accuracy beyond random sampling (i.e.
isHom() - Method in class htsjdk.variant.variantcontext.Genotype
isHomRef() - Method in class htsjdk.variant.variantcontext.Genotype
isHomVar() - Method in class htsjdk.variant.variantcontext.Genotype
isIncludeIndels() - Method in class htsjdk.samtools.util.AbstractLocusIterator
isIncludeNonPfReads() - Method in class htsjdk.samtools.util.AbstractLocusIterator
isIndel() - Method in enum class htsjdk.samtools.CigarOperator
  Returns true if the operator is a Insertion or Deletion operator
isIndel() - Method in class htsjdk.variant.variantcontext.VariantContext
  convenience method for indels
isIndelOrSkippedRegion() - Method in enum class htsjdk.samtools.CigarOperator
  Returns true if the operator is a Skipped Region Insertion or Deletion operator
isIndexed() - Method in class htsjdk.samtools.reference.FastaSequenceFile
  default implementation -- override if index is supported
isIndexed() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
isIndexed() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
isIndexed() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
isInitialized() - Method in class htsjdk.samtools.util.Lazy
isIntegerType() - Method in enum class htsjdk.variant.bcf2.BCF2Type
isIterating() - Method in class htsjdk.samtools.util.AbstractIterator
isIUPAC(byte) - Static method in class htsjdk.samtools.util.SequenceUtil
  Checks if the given base is a IUPAC code
isLastSegment() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Return true if this record is the last segment in the template.
isLazyWithData() - Method in class htsjdk.variant.variantcontext.GenotypesContext
isLeftClipped() - Method in class htsjdk.samtools.Cigar
  returns true if the cigar string starts With a clipping operator
isMappedSingleRef() - Method in class htsjdk.samtools.cram.ref.ReferenceContext
  Determine if this ReferenceContext represents a single reference.
isMemoryMapIndexes() - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Get whether mapping indexes is enabled.
isMissingType() - Method in enum class htsjdk.variant.bcf2.BCF2Type
isMixed() - Method in class htsjdk.variant.variantcontext.Genotype
isMixed() - Method in class htsjdk.variant.variantcontext.VariantContext
  convenience method for indels
isMNP() - Method in class htsjdk.variant.variantcontext.VariantContext
isMonomorphicInSamples() - Method in class htsjdk.variant.variantcontext.VariantContext
  Genotype-specific functions -- are the genotypes monomorphic w.r.t.
isMultiParam() - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZGlobalFlags
isMultiRef() - Method in class htsjdk.samtools.cram.ref.ReferenceContext
  Determine if this ReferenceContext represents: - reads placed on multiple references - or a combination of placed and unplaced reads?
isMutable() - Method in class htsjdk.variant.variantcontext.GenotypesContext
isNegativeStrand() - Method in class htsjdk.samtools.util.Interval
  Returns true if the interval is on the negative strand, otherwise false.
isNoCall() - Method in interface htsjdk.variant.variantcontext.Allele
isNoCall() - Method in class htsjdk.variant.variantcontext.Genotype
isNoCall() - Method in class htsjdk.variant.variantcontext.SimpleAllele
isNoCall(byte) - Static method in class htsjdk.samtools.util.SequenceUtil
  returns true if the value of base represents a no call
isNonEmpty(Collection) - Static method in class htsjdk.utils.ValidationUtils
  Checks that a `Collection` is not `null` and that it is not empty.
isNonInformative() - Method in class htsjdk.variant.variantcontext.Genotype
  Are all likelihoods for this sample non-informative? Returns true if all PLs are 0 => 0,0,0 => true 0,0,0,0,0,0 => true 0,10,100 => false
isNonRefAllele() - Method in interface htsjdk.variant.variantcontext.Allele
isNonRefAllele() - Method in class htsjdk.variant.variantcontext.SimpleAllele
isNonReference() - Method in interface htsjdk.variant.variantcontext.Allele
isNonReference() - Method in class htsjdk.variant.variantcontext.SimpleAllele
isNormalized() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  When a CRAM record is read from a CRAM stream, it is "raw" in that the record's read bases, quality scores, and mate graph are not stored directly as part of the record.
isNosz() - Method in class htsjdk.samtools.cram.compression.range.RangeParams
isNosz() - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
isNotFiltered() - Method in class htsjdk.variant.variantcontext.CommonInfo
isNotFiltered() - Method in class htsjdk.variant.variantcontext.VariantContext
Iso8601Date - Class in htsjdk.samtools.util
  Use this type rather than java.util.Date in command-line options in order to get ISO 8601 parsing.
Iso8601Date(String) - Constructor for class htsjdk.samtools.util.Iso8601Date
Iso8601Date(Date) - Constructor for class htsjdk.samtools.util.Iso8601Date
isOpen() - Method in class htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel
isPack() - Method in class htsjdk.samtools.cram.compression.range.RangeParams
isPack() - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
isPadding() - Method in enum class htsjdk.samtools.CigarOperator
  Returns true if the operator is a Padding operator
isPath() - Method in class htsjdk.io.HtsPath
isPath() - Method in interface htsjdk.io.IOPath
  Return true if this {code IOPath} can be resolved to an `java.nio` Path.
isPhased() - Method in class htsjdk.variant.variantcontext.FastGenotype
isPhased() - Method in class htsjdk.variant.variantcontext.Genotype
  Are the alleles phased w.r.t.
isPlaced() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Determine is read is "placed".
isPointEvent() - Method in class htsjdk.variant.variantcontext.VariantContext
  convenience method for point events
isPolymorphicInSamples() - Method in class htsjdk.variant.variantcontext.VariantContext
  Genotype-specific functions -- are the genotypes polymorphic w.r.t.
isPositiveCompletion() - Method in class htsjdk.samtools.util.ftp.FTPReply
  Determine if a reply code is a positive completion response.
isPositiveIntermediate() - Method in class htsjdk.samtools.util.ftp.FTPReply
  Determine if a reply code is a positive intermediate response.
isPositiveStrand() - Method in class htsjdk.samtools.util.Interval
  Returns true if the interval is on the positive strand, otherwise false.
isPrefixOf(Allele) - Method in interface htsjdk.variant.variantcontext.Allele
isPrefixOf(Allele) - Method in class htsjdk.variant.variantcontext.SimpleAllele
isPreserveReadNames() - Method in class htsjdk.samtools.cram.structure.CompressionHeader
isPreSorted() - Method in class htsjdk.beta.plugin.reads.ReadsEncoderOptions
  Get the preSorted setting for these options.
isProperPair(SAMRecord, SAMRecord, List) - Static method in class htsjdk.samtools.SamPairUtil
isQueryable() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
isQueryable() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
isQueryable() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
isQueryable() - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
isQueryable() - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0
isQueryable() - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
isQueryable() - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Gte true if the underlying resource is queryable.
isQueryable() - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Note that this source is queryable by interval despite NOT having an index
isQueryable() - Method in interface htsjdk.samtools.SamReader
isQueryable() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
isQueryable() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
isQueryable() - Method in class htsjdk.tribble.AbstractFeatureReader
isQueryable() - Method in interface htsjdk.tribble.FeatureReader
isQueryable() - Method in class htsjdk.tribble.TribbleIndexedFeatureReader
isQueryable() - Method in class htsjdk.variant.vcf.VCFFileReader
  A method to check if the reader is query-able, i.e.
isQueryable() - Method in interface htsjdk.variant.vcf.VCFReader
  A method to check if the reader is query-able, i.e.
isReadPaired() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Return true if this record has the read-paired BAM flag set.
isReference() - Method in interface htsjdk.variant.variantcontext.Allele
isReference() - Method in class htsjdk.variant.variantcontext.SimpleAllele
isReferenceBlock() - Method in class htsjdk.variant.variantcontext.VariantContext
isReferenceRequired() - Method in class htsjdk.samtools.cram.structure.CompressionHeader
isReferenceSequenceCompatibleWithBAI(SAMSequenceRecord) - Static method in class htsjdk.samtools.SAMUtils
  Deprecated.
  because the method does the exact opposite of what it says. Use the correctly named isReferenceSequenceIncompatibleWithBAI() instead.
isReferenceSequenceIncompatibleWithBAI(SAMSequenceRecord) - Static method in class htsjdk.samtools.SAMUtils
  Checks if reference sequence is compatible with BAI indexing format.
isRegularPath(File) - Static method in class htsjdk.samtools.util.IOUtil
isRegularPath(Path) - Static method in class htsjdk.samtools.util.IOUtil
isRightClipped() - Method in class htsjdk.samtools.Cigar
  returns true if the cigar string ends With a clipping operator
isRLE() - Method in class htsjdk.samtools.cram.compression.range.RangeParams
isRLE() - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
isSam() - Method in interface htsjdk.io.IOPath
  Returns true if the file's extension is ".sam"".
isSameDictionary(SAMSequenceDictionary) - Method in class htsjdk.samtools.SAMSequenceDictionary
  Non-comprehensive `SAMSequenceDictionary.equals(Object)`-validation: instead of calling `SAMSequenceRecord.equals(Object)` on constituent `SAMSequenceRecord`s in this dictionary against its pair in the target dictionary, in order, call `SAMSequenceRecord.isSameSequence(SAMSequenceRecord)`.
isSameSequence(SAMSequenceRecord) - Method in class htsjdk.samtools.SAMSequenceRecord
  Looser comparison than equals().
isSecondaryAlignment() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Return true if this record has the secondary alignment BAM flag set.
isSecondaryAlignment() - Method in class htsjdk.samtools.SAMRecord
isSecondaryOrSupplementary() - Method in class htsjdk.samtools.SAMRecord
  Tests if this record is either a secondary and/or supplementary alignment; equivalent to `(getNotPrimaryAlignmentFlag() || getSupplementaryAlignmentFlag())`.
isSegmentUnmapped() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Does this record have the mapped flag set? This is independent of placement/alignment status.
isSegmentUnmapped(int) - Static method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Test the segment-unmapped bit in the given BAM flags value.
isSet(int) - Method in enum class htsjdk.samtools.SAMFlag
isSimpleDeletion() - Method in class htsjdk.variant.variantcontext.VariantContext
isSimpleIndel() - Method in class htsjdk.variant.variantcontext.VariantContext
isSimpleInsertion() - Method in class htsjdk.variant.variantcontext.VariantContext
isSingleBreakend() - Method in interface htsjdk.variant.variantcontext.Allele
isSingleBreakend() - Method in class htsjdk.variant.variantcontext.SimpleAllele
isSnappyAvailable() - Method in class htsjdk.samtools.util.SnappyLoader
  Returns true if Snappy is available, false otherwise.
isSNP() - Method in class htsjdk.variant.variantcontext.VariantContext
  convenience method for SNPs
isSorted(SAMRecord) - Method in class htsjdk.samtools.SAMSortOrderChecker
  Check if given SAMRecord violates sort order relative to previous SAMRecord.
isSorted(Iterable) - Static method in class htsjdk.tribble.util.ParsingUtils
isStaticallyTyped() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
  Is the BCF2 type of this field static, or does it have to be determine from the actual field value itself?
isStripe() - Method in class htsjdk.samtools.cram.compression.range.RangeParams
isStripe() - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
isStructuralIndel() - Method in class htsjdk.variant.variantcontext.VariantContext
isSuccess() - Method in class htsjdk.samtools.util.ftp.FTPReply
isSupportedVersion(CRAMVersion) - Static method in class htsjdk.samtools.cram.common.CramVersions
  Return true if `candidateVersion` is a supported CRAM version.
isSymbolic() - Method in interface htsjdk.variant.variantcontext.Allele
isSymbolic() - Method in class htsjdk.variant.variantcontext.SimpleAllele
isSymbolic() - Method in class htsjdk.variant.variantcontext.VariantContext
isSymbolicOrSV() - Method in class htsjdk.variant.variantcontext.VariantContext
isTabix(String, String) - Method in class htsjdk.tribble.AbstractFeatureReader.ComponentMethods
isTabix(String, String) - Static method in class htsjdk.tribble.AbstractFeatureReader
isTopLevelFeature() - Method in interface htsjdk.tribble.gff.Gff3Feature
isTopLevelFeature() - Method in class htsjdk.tribble.gff.Gff3FeatureImpl
isTransition(VariantContext) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Answers if the provided variant is transitional (otherwise, it's transversional).
isUnknownBases() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Return true if the original sequence was unknown (SEQ="*").
isUnknownBases(int) - Static method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Test the unknown-bases bit in the given CRAM flags value.
isUnmappedUnplaced() - Method in class htsjdk.samtools.cram.ref.ReferenceContext
  Determine if this ReferenceContext represents unmapped-unplaced ?
isUnset(int) - Method in enum class htsjdk.samtools.SAMFlag
isUnsignedArray - Variable in class htsjdk.samtools.TagValueAndUnsignedArrayFlag
isUnsignedArray() - Method in class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue
isUnsignedArray() - Method in class htsjdk.samtools.SAMBinaryTagAndValue
isUnsignedArrayAttribute(String) - Method in class htsjdk.samtools.SAMRecord
isUpperACGTN(byte) - Static method in class htsjdk.samtools.util.SequenceUtil
  Check if the given base is one of upper case ACGTN
isUrl(String) - Static method in class htsjdk.samtools.util.IOUtil
  Returns true iff the string is a url.
isUsingPOST() - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Can be used to determine whether the specified source supports the POST api
isValid() - Method in class htsjdk.samtools.SAMRecord
  Perform various validations of SAMRecord.
isValid() - Method in class htsjdk.tribble.index.interval.IntervalTree
  Test code: make sure that the tree has all the properties defined by Red Black trees and interval trees
isValid() - Method in class htsjdk.variant.bcf2.BCF2Codec.SitesInfoForDecoding
isValid(boolean) - Method in class htsjdk.samtools.SAMRecord
  Perform various validations of SAMRecord.
isValid(String, long) - Method in class htsjdk.samtools.Cigar
  Exhaustive validation of CIGAR.
isValidateCRCChecksums() - Method in class htsjdk.beta.codecs.reads.bam.BAMDecoderOptions
  Determine whether validation of CRC checksums is enabled for these options.
isValidBase(byte) - Static method in class htsjdk.samtools.util.SequenceUtil
  Returns true if the byte is in [acgtACGT].
isValidFile(InputStream) - Static method in class htsjdk.samtools.util.BlockCompressedInputStream
isValidUnsignedIntegerAttribute(long) - Static method in class htsjdk.samtools.SAMUtils
  Checks if a long attribute value is within the allowed range of a 32-bit unsigned integer.
isVariant() - Method in class htsjdk.variant.variantcontext.VariantContext
  convenience method for variants
isVersionString(String) - Static method in enum class htsjdk.variant.vcf.VCFHeaderVersion
  are we a valid version string of some type
isWithinHammingDistance(String, String, int) - Static method in class htsjdk.samtools.util.StringUtil
  Determines if two strings s1 and s2 are within maxHammingDistance of each other using the Hamming distance metric.
isWriteCommandLine() - Method in class htsjdk.variant.vcf.VCFHeader
  If true, and isWriteEngineHeaders also returns true, the command line will be written to the VCF.
isWriteEngineHeaders() - Method in class htsjdk.variant.vcf.VCFHeader
  If true additional engine headers will be written to the VCF, otherwise only the walker headers will be output.
isWriteFullFormatField() - Method in class htsjdk.beta.plugin.variants.VariantsEncoderOptions
  True if only full format fields should always be written (suppress trimming of trailing missing values).
isWriteSitesOnly() - Method in class htsjdk.beta.plugin.variants.VariantsEncoderOptions
  Determine if sites-only writing is enabled (suppresses writing of genotypes).
isWriting() - Method in class htsjdk.samtools.util.BinaryCodec
IterableAdapter<T> - Class in htsjdk.samtools.util
  Provides an adapter to wrap an Iterator with an Iterable, allowing it to be run through a foreach loop.
IterableAdapter(Iterator) - Constructor for class htsjdk.samtools.util.IterableAdapter
IterableOnceIterator<T> - Class in htsjdk.samtools.util
  Abstract implementation of an iterator that also implements Iterable (to return itself) so that it can be used if for() loops.
IterableOnceIterator() - Constructor for class htsjdk.samtools.util.IterableOnceIterator
Iterables - Class in htsjdk.samtools.util
iterateInSampleNameOrder() - Method in class htsjdk.variant.variantcontext.GenotypesContext
  Iterate over the Genotypes in this context in their sample name order (A, B, C) regardless of the underlying order in the vector of genotypes
iterateInSampleNameOrder(Iterable) - Method in class htsjdk.variant.variantcontext.GenotypesContext
  Iterate over the Genotypes in this context in the order specified by sampleNamesInOrder
iterator() - Method in class htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
iterator() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
iterator() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
iterator() - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
iterator() - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0
iterator() - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
iterator() - Method in class htsjdk.beta.io.bundle.Bundle
  Get an iterator of BundleResources for this bundle.
iterator() - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator of all records in the underlying resource.
iterator() - Method in class htsjdk.samtools.BinList
  Gets an iterator over all selected bins.
iterator() - Method in class htsjdk.samtools.BinningIndexContent.BinList
iterator() - Method in class htsjdk.samtools.Cigar
  shortcut to `getCigarElements().iterator()`
iterator() - Method in class htsjdk.samtools.CoordinateSortedPairInfoMap
  Creates an iterator over all elements in map, in arbitrary order.
iterator() - Method in class htsjdk.samtools.fastq.FastqReader
  WARNING: Despite the fact that this class implements Iterable, calling iterator() method does not start iteration from the beginning of the file.
iterator() - Method in class htsjdk.samtools.reference.FastaSequenceIndex
  Creates an iterator which can iterate through all entries in a fasta index.
iterator() - Method in interface htsjdk.samtools.SamReader
  Iterate through file in order.
iterator() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
iterator() - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Returns a CloseableIterator over the collection of SAMRecords.
iterator() - Method in class htsjdk.samtools.util.AbstractLocusIterator
iterator() - Method in class htsjdk.samtools.util.DiskBackedQueue
  Not supported at this time
iterator() - Method in class htsjdk.samtools.util.IntervalList
  Returns an iterator over the intervals.
iterator() - Method in class htsjdk.samtools.util.IntervalTree
  Return an iterator over the entire tree.
iterator() - Method in class htsjdk.samtools.util.IterableAdapter
iterator() - Method in class htsjdk.samtools.util.IterableOnceIterator
  On the first call returns this object which is also an iterator.
iterator() - Method in class htsjdk.samtools.util.SortingCollection
  Prepare to iterate through the records in order.
iterator() - Method in interface htsjdk.tribble.FeatureReader
  Provides access to all the features in the reader
iterator() - Method in class htsjdk.tribble.TabixFeatureReader
iterator() - Method in class htsjdk.tribble.TribbleIndexedFeatureReader
iterator() - Method in class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator
  function to satisfy the Iterable interface
iterator() - Method in class htsjdk.variant.variantcontext.GenotypesContext
iterator() - Method in class htsjdk.variant.vcf.VCFFileReader
  Returns an iterator over all records in this VCF/BCF file.
iterator() - Method in interface htsjdk.variant.vcf.VCFReader
iterator(int, int) - Method in class htsjdk.samtools.util.IntervalTree
  Return an iterator over all intervals greater than or equal to the specified interval.
iterator(SAMFileSpan) - Method in class htsjdk.samtools.CRAMFileReader
iterator(SAMFileSpan) - Method in interface htsjdk.samtools.SamReader.Indexing
  Iterate through the given chunks in the file.
iterator(SAMFileSpan) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
ITF8 - Class in htsjdk.samtools.cram.io
  Methods to read and write int values as per ITF8 specification in CRAM.
ITF8() - Constructor for class htsjdk.samtools.cram.io.ITF8

## J

JavascriptSamRecordFilter - Class in htsjdk.samtools.filter
  JavaScript-based `SamRecordFilter`.
JavascriptSamRecordFilter(File, SAMFileHeader) - Constructor for class htsjdk.samtools.filter.JavascriptSamRecordFilter
  constructor using a javascript File
JavascriptSamRecordFilter(Reader, SAMFileHeader) - Constructor for class htsjdk.samtools.filter.JavascriptSamRecordFilter
  constructor using a java.io.Reader
JavascriptSamRecordFilter(String, SAMFileHeader) - Constructor for class htsjdk.samtools.filter.JavascriptSamRecordFilter
  constructor using a javascript expression
JavascriptVariantFilter - Class in htsjdk.variant.variantcontext.filter
  JavaScript-based `VariantContextFilter`.
JavascriptVariantFilter(File, VCFHeader) - Constructor for class htsjdk.variant.variantcontext.filter.JavascriptVariantFilter
  constructor using a javascript File
JavascriptVariantFilter(Reader, VCFHeader) - Constructor for class htsjdk.variant.variantcontext.filter.JavascriptVariantFilter
  constructor using a Reader
JavascriptVariantFilter(String, VCFHeader) - Constructor for class htsjdk.variant.variantcontext.filter.JavascriptVariantFilter
  constructor using a javascript expression
JexlMissingValueTreatment - Enum Class in htsjdk.variant.variantcontext
  How to treat values that appear in a jexl expression but are missing in the context it's applied to
JexlVCMatchExp(String, Expression) - Constructor for class htsjdk.variant.variantcontext.VariantContextUtils.JexlVCMatchExp
  Create a new matcher expression with name and JEXL expression exp
join(String, String[]) - Static method in class htsjdk.tribble.util.ParsingUtils
  join an array of strings given a seperator
join(String, String[], int, int) - Static method in class htsjdk.tribble.util.ParsingUtils
  join a set of strings, using the separator provided, from index start to index stop
join(String, Collection) - Static method in class htsjdk.samtools.util.StringUtil
join(String, Collection) - Static method in class htsjdk.tribble.util.ParsingUtils
join(String, Collection) - Static method in class htsjdk.variant.utils.GeneralUtils
  Returns a string of the form elt1.toString() [sep elt2.toString() ...
join(String, T...) - Static method in class htsjdk.samtools.util.StringUtil
join(Collection, String) - Static method in class htsjdk.samtools.util.CollectionUtil
  Construct a string by toString()ing each item in the collection with inBetween between each item.
JSON_PROPERTY_FORMAT - Static variable in class htsjdk.beta.io.bundle.BundleJSON
JSON_PROPERTY_PATH - Static variable in class htsjdk.beta.io.bundle.BundleJSON
JSON_PROPERTY_PRIMARY - Static variable in class htsjdk.beta.io.bundle.BundleJSON
JSON_PROPERTY_SCHEMA - Static variable in class htsjdk.beta.io.bundle.BundleJSON
JSON_PROPERTY_SCHEMA_NAME - Static variable in class htsjdk.beta.io.bundle.BundleJSON
JSON_PROPERTY_SCHEMA_VERSION - Static variable in class htsjdk.beta.io.bundle.BundleJSON
JSON_SCHEMA_NAME - Static variable in class htsjdk.beta.io.bundle.BundleJSON
JSON_SCHEMA_VERSION - Static variable in class htsjdk.beta.io.bundle.BundleJSON

## K

key - Variable in class htsjdk.samtools.cram.structure.TagKeyCache.TagKeyInfo
  Two-character tag name, e.g.
KEY_SEQUENCE_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
KEY_VALUE_SEPARATOR - Static variable in class htsjdk.tribble.gff.Gff3Constants
keySet() - Method in class htsjdk.samtools.util.Histogram
  Returns the set of keys for this histogram.
keyType3Bytes - Variable in class htsjdk.samtools.cram.structure.ReadTag
keyType3Bytes - Variable in class htsjdk.samtools.cram.structure.TagKeyCache.TagKeyInfo
  Three-character tag name + type, e.g.
keyType3BytesAsInt - Variable in class htsjdk.samtools.cram.structure.ReadTag
keyType3BytesAsInt - Variable in class htsjdk.samtools.cram.structure.TagKeyCache.TagKeyInfo
  The 3-byte tag ID packed as an int (name high bytes, type low byte).
knownAtEof() - Method in class htsjdk.samtools.util.BinaryCodec

## L

l - Variable in class htsjdk.tribble.util.TabixUtils.TIndex
lastIndexOf(Object) - Method in class htsjdk.variant.variantcontext.GenotypesContext
Lazy<T> - Class in htsjdk.samtools.util
  Simple utility for building an on-demand (lazy) object-initializer.
Lazy(Supplier) - Constructor for class htsjdk.samtools.util.Lazy
LAZY_NOW_LABEL - Static variable in class htsjdk.samtools.util.RelativeIso8601Date
Lazy.LazyInitializer<T> - Interface in htsjdk.samtools.util
  Deprecated.
  since 1/2017 use a `Supplier` instead
LazyData(VCFHeader, int, byte[]) - Constructor for class htsjdk.variant.bcf2.BCF2Codec.LazyData
LazyData(ArrayList, List, Map) - Constructor for class htsjdk.variant.variantcontext.LazyGenotypesContext.LazyData
LazyGenotypesContext - Class in htsjdk.variant.variantcontext
  Lazy-loading GenotypesContext.
LazyGenotypesContext(LazyGenotypesContext.LazyParser, Object, int) - Constructor for class htsjdk.variant.variantcontext.LazyGenotypesContext
  Creates a new lazy loading genotypes context using the LazyParser to create genotypes data on demand.
LazyGenotypesContext.LazyData - Class in htsjdk.variant.variantcontext
  Returns the data used in the full GenotypesContext constructor `GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List)`
LazyGenotypesContext.LazyParser - Interface in htsjdk.variant.variantcontext
  Simple lazy parser interface.
LB - Enum constant in enum class htsjdk.samtools.SAMTag
LB - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
length() - Method in class htsjdk.samtools.fastq.FastqRecord
  Deprecated.
  since 02/2017. Use `FastqRecord.getReadLength()` instead
length() - Method in class htsjdk.samtools.reference.ReferenceSequence
  Gets the length of this reference sequence in bases.
length() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
length() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
length() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
length() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
length() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
length() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
length() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
length() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
length() - Method in class htsjdk.samtools.seekablestream.SeekableStream
length() - Method in class htsjdk.samtools.util.Interval
  Gets the length of this interval.
length() - Method in interface htsjdk.variant.variantcontext.Allele
length() - Method in class htsjdk.variant.variantcontext.SimpleAllele
LENIENT - Enum constant in enum class htsjdk.samtools.ValidationStringency
  Emit warnings but keep going if possible.
LESS_EXHAUSTIVE - Enum constant in enum class htsjdk.samtools.BamIndexValidator.IndexValidationStringency
less64(long, long) - Static method in class htsjdk.tribble.util.TabixUtils
lessExhaustivelyTestIndex(SamReader) - Static method in class htsjdk.samtools.BamIndexValidator
  A less time-consuming index validation that only looks at the first and last references in the index and the first and last chunks in each of those
LEVEL_STARTS - Static variable in class htsjdk.samtools.GenomicIndexUtil
  What is the starting bin for each level?
levelToSize(int) - Static method in class htsjdk.samtools.GenomicIndexUtil
  Return the binning index bin size for bins in the given bin.
levenshteinDistance(String, String, int, int, int, int) - Static method in class htsjdk.samtools.util.StringUtil
LIBRARY_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
liftOver(Interval) - Method in class htsjdk.samtools.liftover.LiftOver
  Lift over the given interval to the new genome build using the liftOverMinMatch set for this LiftOver object.
liftOver(Interval, double) - Method in class htsjdk.samtools.liftover.LiftOver
  Lift over the given interval to the new genome build.
LiftOver - Class in htsjdk.samtools.liftover
  Java port of UCSC liftOver.
LiftOver(File) - Constructor for class htsjdk.samtools.liftover.LiftOver
  Load UCSC chain file in order to lift over Intervals.
LiftOver(InputStream, String) - Constructor for class htsjdk.samtools.liftover.LiftOver
  Load UCSC chain file in order to lift over Intervals.
LiftOver.PartialLiftover - Class in htsjdk.samtools.liftover
  Represents a portion of a liftover operation, for use in diagnosing liftover failures.
LINEAR - Enum constant in enum class htsjdk.tribble.index.AbstractIndex.IndexType
LINEAR - Enum constant in enum class htsjdk.tribble.index.IndexFactory.IndexType
LinearIndex - Class in htsjdk.samtools
  The linear index associated with a given reference in a BAM index.
LinearIndex - Class in htsjdk.tribble.index.linear
  Index defined by dividing the genome by chromosome, then each chromosome into bins of fixed width (in genomic coordinates).
LinearIndex(int, int, long[]) - Constructor for class htsjdk.samtools.LinearIndex
LinearIndex(InputStream) - Constructor for class htsjdk.tribble.index.linear.LinearIndex
  Load from file.
LinearIndex(String) - Constructor for class htsjdk.tribble.index.linear.LinearIndex
  Initialize with default parameters
LinearIndex(Path) - Constructor for class htsjdk.tribble.index.linear.LinearIndex
  Initialize with default parameters
LinearIndex(List, File) - Constructor for class htsjdk.tribble.index.linear.LinearIndex
  Initialize using the specified `indices`
LinearIndex(List, Path) - Constructor for class htsjdk.tribble.index.linear.LinearIndex
  Initialize using the specified `indices`
LinearIndex.ChrIndex - Class in htsjdk.tribble.index.linear
  Blocks are organized as a simple flat list:
LinearIndexCreator - Class in htsjdk.tribble.index.linear
  For creating a LinearIndex from a stream of features.
LinearIndexCreator(File) - Constructor for class htsjdk.tribble.index.linear.LinearIndexCreator
LinearIndexCreator(File, int) - Constructor for class htsjdk.tribble.index.linear.LinearIndexCreator
LinearIndexCreator(Path) - Constructor for class htsjdk.tribble.index.linear.LinearIndexCreator
LinearIndexCreator(Path, int) - Constructor for class htsjdk.tribble.index.linear.LinearIndexCreator
LineIterator - Interface in htsjdk.tribble.readers
  A very simple descriptor for line-iterables.
LineIteratorImpl - Class in htsjdk.tribble.readers
  A simple iterator over the elements in LineReader.
LineIteratorImpl(LineReader) - Constructor for class htsjdk.tribble.readers.LineIteratorImpl
lineNo - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
LineReader - Interface in htsjdk.samtools.util
  Interface allows for implementations that read lines from a String, an ASCII file, or somewhere else.
LineReader - Interface in htsjdk.tribble.readers
  Interface for line-oriented readers.
listIterator() - Method in class htsjdk.variant.variantcontext.GenotypesContext
listIterator(int) - Method in class htsjdk.variant.variantcontext.GenotypesContext
ListMap<K,V> - Class in htsjdk.samtools.util
  A Map class that holds a list of entries under each key instead of a single entry, and provides utility methods for adding an entry under a key.
ListMap() - Constructor for class htsjdk.samtools.util.ListMap
LittleEndianInputStream - Class in htsjdk.tribble.util
  Input stream with methods to convert byte arrays to numeric values using "little endian" order.
LittleEndianInputStream(InputStream) - Constructor for class htsjdk.tribble.util.LittleEndianInputStream
LittleEndianOutputStream - Class in htsjdk.tribble.util
LittleEndianOutputStream(OutputStream) - Constructor for class htsjdk.tribble.util.LittleEndianOutputStream
load(InputStream) - Static method in class htsjdk.samtools.SBIIndex
  Load an SBI into memory from a stream.
load(Path) - Static method in class htsjdk.samtools.SBIIndex
  Load an SBI into memory from a path.
loadDictionary(InputStream) - Static method in class htsjdk.samtools.reference.ReferenceSequenceFileFactory
  Loads the sequence dictionary from a FASTA file input stream.
loadIndex(File, FeatureCodec) - Static method in class htsjdk.tribble.example.CountRecords
loadIndex(String) - Static method in class htsjdk.tribble.example.IndicesAreEqual
loadIndex(String) - Static method in class htsjdk.tribble.index.IndexFactory
  Load in index from the specified file.
loadIndex(String, InputStream) - Static method in class htsjdk.samtools.util.GZIIndex
  Loads the index from the provided input stream.
loadIndex(String, InputStream) - Static method in class htsjdk.tribble.index.IndexFactory
  Load in index from the specified stream.
loadIndex(String, ReadableByteChannel) - Static method in class htsjdk.samtools.util.GZIIndex
  Loads the index from the provided channel.
loadIndex(String, Function) - Static method in class htsjdk.tribble.index.IndexFactory
  Load in index from the specified file.
loadIndex(Path) - Static method in class htsjdk.samtools.util.GZIIndex
  Loads the index from the provided file.
loadSequenceDictionary(IOPath) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Attempt to load a sequence dictionary given a file path.
loadSequenceDictionary(IOPath) - Static method in class htsjdk.samtools.reference.FastaSequenceFile
  Attempt to load a sequence dictionary given a file path.
loadSequenceDictionary(IOPath) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Attempt to load a sequence dictionary given a file path.
loc(String, long, long) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells us that the resulting VariantContext should have the specified location
Locatable - Interface in htsjdk.samtools.util
  Any class that has a single logical mapping onto the genome should implement Locatable positions should be reported as 1-based and closed at both ends
LocationAware - Interface in htsjdk.samtools.util
  Describes API for getting current position in a stream, writer, or underlying file.
locParts - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
Locus - Interface in htsjdk.samtools.util
  Location info about a locus.
LocusComparator<T> - Class in htsjdk.samtools.util
  compares first by sequence index then by position
LocusComparator() - Constructor for class htsjdk.samtools.util.LocusComparator
LocusImpl - Class in htsjdk.samtools.util
  Simple implementation of Locus interface for ease of passing as an arg and comparing with other Locus implementations.
LocusImpl(int, int) - Constructor for class htsjdk.samtools.util.LocusImpl
LocusInfo(SAMSequenceRecord, int) - Constructor for class htsjdk.samtools.util.SamLocusIterator.LocusInfo
log() - Method in class htsjdk.samtools.util.AbstractProgressLogger
  Logs the last last record if it wasn't previously logged.
log(String...) - Method in class htsjdk.samtools.util.AbstractProgressLogger
  Log a message to whatever logger is being used
log(String...) - Method in class htsjdk.samtools.util.ProgressLogger
Log - Class in htsjdk.samtools.util
  A wafer thin wrapper around System.err that uses var-args to make it much more efficient to call the logging methods in without having to surround every call site with calls to Log.isXXXEnabled().
Log.LogLevel - Enum Class in htsjdk.samtools.util
  Enumeration for setting log levels.
LOG10_P_OF_ZERO - Static variable in class htsjdk.variant.utils.GeneralUtils
  The smallest log10 value we'll emit from normalizeFromLog10 and other functions where the real-space value is 0.0.
log10PError(double) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Set the GQ with a log10PError value
log10PError(double) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells us that the resulting VariantContext should have log10PError
logger - Variable in class htsjdk.tribble.index.AbstractIndex
login(String, String) - Method in class htsjdk.samtools.util.ftp.FTPClient
  Wrapper for the commands `user [username]` and `pass [password]`.
LONG - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeriesType
  A signed long value, 64 bits, too many to count.
LongLineBufferedReader - Class in htsjdk.tribble.readers
  A variant of `BufferedReader` with improved performance reading files with long lines.
LongLineBufferedReader(Reader) - Constructor for class htsjdk.tribble.readers.LongLineBufferedReader
  Creates a buffering character-input stream that uses a default-sized input buffer.
LongLineBufferedReader(Reader, int) - Constructor for class htsjdk.tribble.readers.LongLineBufferedReader
  Creates a buffering character-input stream that uses an input buffer of the specified size.
LS454 - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  454 Life Sciences
LTF8 - Class in htsjdk.samtools.cram.io
  Methods to read and write LTF8 as per CRAM specs.
LTF8() - Constructor for class htsjdk.samtools.cram.io.LTF8
LZMA - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
LZMAExternalCompressor - Class in htsjdk.samtools.cram.compression
LZMAExternalCompressor() - Constructor for class htsjdk.samtools.cram.compression.LZMAExternalCompressor

## M

M - Enum constant in enum class htsjdk.samtools.CigarOperator
  Match or mismatch
magic - Variable in enum class htsjdk.samtools.SamIndexes
MAGIC - Static variable in class htsjdk.samtools.cram.structure.CramHeader
MAGIC_HEADER_START - Static variable in class htsjdk.variant.bcf2.BCFVersion
  BCF2 begins with the MAGIC info BCF_M_m where M is the major version (currently 2) and m is the minor version, currently 1
MAGIC_NUMBER - Static variable in class htsjdk.tribble.index.AbstractIndex
MAGIC_NUMBER - Static variable in class htsjdk.tribble.index.tabix.TabixIndex
main(String[]) - Static method in class htsjdk.samtools.apps.TimeChannel
  Deprecated.
main(String[]) - Static method in class htsjdk.samtools.apps.TimeRandomAccessFile
  Deprecated.
main(String[]) - Static method in class htsjdk.samtools.BamConverter
  Entry point.
main(String[]) - Static method in class htsjdk.samtools.cram.CramComparison
main(String[]) - Static method in class htsjdk.samtools.cram.CramConverter
  Entry point.
main(String[]) - Static method in class htsjdk.samtools.cram.CramStats
  Entry point.
main(String[]) - Static method in class htsjdk.samtools.example.PrintReadsExample
main(String[]) - Static method in class htsjdk.samtools.seekablestream.SeekableFTPStream
main(String[]) - Static method in class htsjdk.samtools.util.HttpUtils
main(String[]) - Static method in class htsjdk.tribble.example.CountRecords
  The main method of this class: 1) checks to see that the feature file exists 2) loads an index from disk, if one doesn't exist, it creates it and writes it to disk 3) creates a FeatureSource 4) iterates over the records, emitting a final tally for the number of features seen
main(String[]) - Static method in class htsjdk.tribble.example.IndexToTable
  this class: 1) checks to see that the feature file exists 2) loads an index from disk, if one doesn't exist, it creates it and writes it to disk 3) Converts the index to a human readable table
main(String[]) - Static method in class htsjdk.tribble.example.IndicesAreEqual
main(String[]) - Static method in class htsjdk.tribble.example.ProfileIndexReading
  This class times the loading of an index file a number of times, and prints the result of each trial
main(String[]) - Static method in class htsjdk.tribble.readers.PositionalBufferedStream
main(String[]) - Static method in class htsjdk.variant.example.PrintVariantsExample
MAJOR_HEADER_PREFIX - Static variable in class htsjdk.samtools.metrics.MetricsFile
make() - Static method in class htsjdk.samtools.SamReaderFactory
  Creates an "empty" factory with no enabled `SamReaderFactory.Option`s, `ValidationStringency.DEFAULT_STRINGENCY`, no path wrapper, and `DefaultSAMRecordFactory`.
make() - Method in interface htsjdk.samtools.util.Lazy.LazyInitializer
  Deprecated.
  Returns the desired object instance.
make() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Create a new Genotype object using the values set in this builder.
make() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Takes all of the builder data provided up to this point, and instantiates a freshly allocated VariantContext with all of the builder data.
make(boolean) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
make(SamReader, DownsamplingIteratorFactory.Strategy, double, double, int) - Static method in class htsjdk.samtools.DownsamplingIteratorFactory
  Convenience method that constructs a downsampling iterator for all the reads available from a SamReader.
make(File, DownsamplingIteratorFactory.Strategy, double, double, int) - Static method in class htsjdk.samtools.DownsamplingIteratorFactory
  Convenience method that constructs a downsampling iterator for all the reads in a SAM file.
make(Iterator, DownsamplingIteratorFactory.Strategy, double, double, int) - Static method in class htsjdk.samtools.DownsamplingIteratorFactory
  Creates a new DownsamplingIterator using the supplied Strategy that attempts to read from the provided iterator and return approximately proportion of the records read.
make(K) - Method in interface htsjdk.samtools.util.CollectionUtil.DefaultingMap.Factory
makeBAMWriter(SAMFileHeader, boolean, File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a BAMFileWriter that is ready to receive SAMRecords.
makeBAMWriter(SAMFileHeader, boolean, File, int) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a BAMFileWriter that is ready to receive SAMRecords.
makeBAMWriter(SAMFileHeader, boolean, OutputStream) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a BAMFileWriter for writing to a stream that is ready to receive SAMRecords.
makeBAMWriter(SAMFileHeader, boolean, Path) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a BAMFileWriter that is ready to receive SAMRecords.
makeBAMWriter(SAMFileHeader, boolean, Path, int) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a BAMFileWriter that is ready to receive SAMRecords.
makeBinaryTag(String) - Static method in enum class htsjdk.samtools.SAMTag
  Convert from String representation of tag name to short representation.
makeBinaryTag(String) - Method in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `instead`
makeCigarStringWithIndelPossibleClipping(int, int, int, int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
  Create a cigar string for a gapped alignment, which may have soft clipping at either end
makeCigarStringWithPossibleClipping(int, int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
  Create a simple ungapped cigar string, which might have soft clipping at either end
makeCollection(Iterator) - Static method in class htsjdk.samtools.util.CollectionUtil
makeContigHeaderLines(SAMSequenceDictionary, File) - Static method in class htsjdk.variant.vcf.VCFUtils
  Create VCFHeaderLines for each refDict entry, and optionally the assembly if referenceFile != null
makeCRAMWriter(SAMFileHeader, boolean, File, File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a CRAMFileWriter on an output file.
makeCRAMWriter(SAMFileHeader, boolean, Path, File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Deprecated.
  since 6/18, prefer `SAMFileWriterFactory.makeWriter(SAMFileHeader, boolean, Path, Path)` for creating bam/cram writers however `SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader, boolean, Path, Path)` is the direct replacement for this method
makeCRAMWriter(SAMFileHeader, boolean, Path, Path) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a CRAMFileWriter on an output file.
makeCRAMWriter(SAMFileHeader, File, File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a CRAMFileWriter on an output file.
makeCRAMWriter(SAMFileHeader, OutputStream, File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a CRAMFileWriter on an output stream.
makeCRAMWriter(SAMFileHeader, OutputStream, Path) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a CRAMFileWriter on an output stream.
makeCRAMWriter(SAMFileHeader, Path, File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Deprecated.
  since 6/18, prefer `SAMFileWriterFactory.makeWriter(SAMFileHeader, boolean, Path, Path)` for creating bam/cram writers however `SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader, boolean, Path, Path)` is the direct replacement for this method
makeDefault() - Static method in class htsjdk.samtools.SamReaderFactory
  Creates a copy of the default `SamReaderFactory`.
makeDefaultHeader(SAMFileHeader.SortOrder, int, boolean) - Static method in class htsjdk.samtools.SAMRecordSetBuilder
  creates a simple header
makeDeflater(int, boolean) - Method in class htsjdk.samtools.util.zip.DeflaterFactory
  Returns a deflater object that will be used when writing BAM files.
makeDictionary(VCFHeader) - Static method in class htsjdk.variant.bcf2.BCF2Utils
  Create a strings dictionary from the VCF header The dictionary is an ordered list of common VCF identifers (FILTER, INFO, and FORMAT) fields.
makeFileNameSafe(String) - Static method in class htsjdk.samtools.util.IOUtil
  Takes a string and replaces any characters that are not safe for filenames with an underscore
makeFilePointer(long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
makeFilePointer(long, int) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
makeIndexableSourceFromStream(InputStream) - Method in class htsjdk.tribble.AsciiFeatureCodec
makeIndexableSourceFromStream(InputStream) - Method in class htsjdk.tribble.BinaryFeatureCodec
  `PositionalBufferedStream` is already `LocationAware`.
makeIndexableSourceFromStream(InputStream) - Method in interface htsjdk.tribble.FeatureCodec
  Return a `SOURCE` for this `FeatureCodec` that implements `LocationAware`, and is thus suitable for use during indexing.
makeIndexableSourceFromStream(InputStream) - Method in class htsjdk.tribble.gff.Gff3Codec
makeInflater(boolean) - Method in class htsjdk.samtools.util.zip.InflaterFactory
  Returns an inflater object that will be used when reading DEFLATE compressed files.
makeList(T...) - Static method in class htsjdk.samtools.util.CollectionUtil
makePermutations(List, int, boolean) - Static method in class htsjdk.variant.utils.GeneralUtils
  Make all combinations of N size of objects if objects = [A, B, C] if N = 1 => [[A], [B], [C]] if N = 2 => [[A, A], [B, A], [C, A], [A, B], [B, B], [C, B], [A, C], [B, C], [C, C]]
makeReadUnmapped(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  Strip mapping information from a SAMRecord.
makeReadUnmappedWithOriginalTags(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  Strip mapping information from a SAMRecord, but preserve it in the 'O' tags if it isn't already set.
makeReferenceFromAlignment(SAMRecord, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
  Produce reference bases from an aligned SAMRecord with MD string and Cigar.
makeSAMFileHeaderContainer(int) - Static method in class htsjdk.samtools.cram.structure.ContainerHeader
  Create a ContainerHeader for a SAMFileHeader container.
makeSAMOrBAMWriter(SAMFileHeader, boolean, File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create either a SAM or a BAM writer based on examination of the outputFile extension, defaults to BAM writer.
makeSAMOrBAMWriter(SAMFileHeader, boolean, Path) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create either a SAM or a BAM writer based on examination of the outputPath extension.
makeSamRecordIntervalIterator(SamReader, List, boolean) - Method in class htsjdk.samtools.util.SamRecordIntervalIteratorFactory
makeSAMWriter(SAMFileHeader, boolean, File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a SAMTextWriter that is ready to receive SAMRecords.
makeSAMWriter(SAMFileHeader, boolean, OutputStream) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a SAMTextWriter for writing to a stream that is ready to receive SAMRecords.
makeSAMWriter(SAMFileHeader, boolean, Path) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a SAMTextWriter that is ready to receive SAMRecords.
makeSentinelCigar(Cigar) - Static method in class htsjdk.samtools.BAMRecordCodec
  Create a "Sentinel" cigar that will be placed in BAM file when the actual cigar has more than 0xffff operator, which are not supported by the bam format.
makeSet(T...) - Static method in class htsjdk.samtools.util.CollectionUtil
makeSoftClipCigar(int) - Static method in class htsjdk.samtools.util.SequenceUtil
makeSourceFromStream(InputStream) - Method in class htsjdk.tribble.AsciiFeatureCodec
makeSourceFromStream(InputStream) - Method in class htsjdk.tribble.BinaryFeatureCodec
makeSourceFromStream(InputStream) - Method in interface htsjdk.tribble.FeatureCodec
  Generates a reader of type `SOURCE` appropriate for use by this codec from the generic input stream.
makeSourceFromStream(InputStream) - Method in class htsjdk.tribble.gff.Gff3Codec
makeStringTag(short) - Static method in enum class htsjdk.samtools.SAMTag
  Convert from short representation of tag name to String representation.
makeStringTag(short) - Method in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.makeStringTag(short)` instead
makeValue(Key) - Method in interface htsjdk.samtools.util.ResourceLimitedMapFunctor
  Create a new value corresponding to the key
makeWithShallowCopy() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Create a new Genotype object using the values set in this builder, and perform a shallow copy of reference types to allow safer re-use of this builder After creation the values in this builder can be modified and more Genotypes created.
makeWriter(SAMFileHeader, boolean, File, File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a SAM, BAM or CRAM writer based on examination of the outputFile extension.
makeWriter(SAMFileHeader, boolean, Path, File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Deprecated.
  since 6/18, use `SAMFileWriterFactory.makeWriter(SAMFileHeader, boolean, Path, Path)` instead
makeWriter(SAMFileHeader, boolean, Path, Path) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Create a SAM, BAM or CRAM writer based on examination of the outputPath extension.
MalformedFeatureFile(String, String) - Constructor for exception class htsjdk.tribble.TribbleException.MalformedFeatureFile
MalformedFeatureFile(String, String, Exception) - Constructor for exception class htsjdk.tribble.TribbleException.MalformedFeatureFile
MAPPED_SLICE - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockContentType
MAPPING_QUALITY_ZERO_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
MappingQualityFilter - Class in htsjdk.samtools.filter
  Filter things with low mapping quality.
MappingQualityFilter(int) - Constructor for class htsjdk.samtools.filter.MappingQualityFilter
MAPQ - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
mark - Variable in class htsjdk.samtools.seekablestream.SeekableStream
  If the stream is marked with `SeekableStream.mark(int)` this represents the `SeekableStream.position()` where the stream was; otherwise, this is empty.
mark(int) - Method in class htsjdk.samtools.cram.io.CountingInputStream
mark(int) - Method in class htsjdk.samtools.cram.io.CRC32InputStream
mark(int) - Method in class htsjdk.samtools.seekablestream.SeekableStream
  Mark the current position of the stream.
mark(int) - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
mark(int) - Method in class htsjdk.tribble.readers.LongLineBufferedReader
  Marks the present position in the stream.
markRowUsed(int) - Method in class htsjdk.samtools.cram.compression.rans.RANSDecode
  Mark a context row as used.
markSupported() - Method in class htsjdk.samtools.cram.io.CountingInputStream
markSupported() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
markSupported() - Method in class htsjdk.samtools.seekablestream.SeekableStream
  Mark is always supported by any `SeekableStream`.
markSupported() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
markSupported() - Method in class htsjdk.tribble.readers.LongLineBufferedReader
  Tells whether this stream supports the mark() operation, which it does.
match(VariantContext, Genotype, VariantContextUtils.JexlVCMatchExp) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Returns true if `exp` match `vc`, `g`.
match(VariantContext, Genotype, VariantContextUtils.JexlVCMatchExp, JexlMissingValueTreatment) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Returns true if `exp` match `vc`, `g`.
match(VariantContext, Genotype, Collection) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Matches each `VariantContextUtils.JexlVCMatchExp` exp against the data contained in `vc`, `g`, and returns a map from these expressions to `true` (if they matched) or `false` (if they didn't).
match(VariantContext, Genotype, Collection, JexlMissingValueTreatment) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Matches each `VariantContextUtils.JexlVCMatchExp` exp against the data contained in `vc`, `g`, and returns a map from these expressions to `true` (if they matched) or `false` (if they didn't).
match(VariantContext, VariantContextUtils.JexlVCMatchExp) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Returns true if `exp` match `vc`.
match(VariantContext, Collection) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Matches each `VariantContextUtils.JexlVCMatchExp` exp against the data contained in `vc`, and returns a map from these expressions to `true` (if they matched) or `false` (if they didn't).
Match - Enum constant in enum class htsjdk.samtools.util.AbstractRecordAndOffset.AlignmentType
MATCH_OR_MISMATCH - Static variable in enum class htsjdk.samtools.CigarOperator
MATE_CIGAR_STRING_INVALID_PRESENCE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  There is a Cigar String (stored in the MC Tag) for a read whose mate is NOT mapped.
MATE_FIELD_MISMATCH - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  the record's mate fields do not match the corresponding fields of the mate
MATE_NOT_FOUND - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Read is marked as paired, but its pair was not found.
MATE_REVERSE_STRAND - Enum constant in enum class htsjdk.samtools.SAMFlag
MATE_UNMAPPED - Enum constant in enum class htsjdk.samtools.SAMFlag
MATES_ARE_SAME_END - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Both mates are marked as first of pair, or both mates are marked as second of pair.
MathUtils - Class in htsjdk.tribble.util
  a collection of functions and classes for various common calculations
MathUtils() - Constructor for class htsjdk.tribble.util.MathUtils
MathUtils.RunningStat - Class in htsjdk.tribble.util
  a class for calculating moving statistics - this class returns the mean, variance, and std dev after accumulating any number of records.
max() - Method in class htsjdk.samtools.util.IntervalTree
  Find the greatest interval in the tree.
max(int, int) - Method in class htsjdk.samtools.util.IntervalTree
  Find the latest interval in the tree less than or equal to the specified interval.
MAX_ALLELE_SIZE_BEFORE_WARNING - Static variable in class htsjdk.variant.vcf.AbstractVCFCodec
MAX_ALLELES_IN_GENOTYPES - Static variable in class htsjdk.variant.bcf2.BCF2Utils
MAX_BINS - Static variable in class htsjdk.samtools.GenomicIndexUtil
  Reports the maximum number of bins that can appear in a binning index.
MAX_BLOCK_ADDRESS - Static variable in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
MAX_BYTES - Static variable in class htsjdk.samtools.cram.io.ITF8
MAX_CIGAR_ELEMENT_LENGTH - Static variable in class htsjdk.samtools.BAMRecord
MAX_CIGAR_OPERATORS - Static variable in class htsjdk.samtools.BAMRecord
  Maximal number of cigar operators that can be represented normally in the cigar part of the bam record.
MAX_COMPRESSED_BLOCK_SIZE - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED - Static variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  The maximum number of diploid alternate alleles that we can represent as genotype likelihoods
MAX_FEATURES_PER_BIN - Static variable in class htsjdk.tribble.index.linear.LinearIndex
MAX_FREQ - Static variable in class htsjdk.samtools.cram.compression.range.Constants
MAX_GENOTYPE_QUAL - Static variable in class htsjdk.variant.vcf.VCFConstants
MAX_INLINE_ELEMENTS - Static variable in class htsjdk.variant.bcf2.BCF2Utils
MAX_INSERT_SIZE - Static variable in class htsjdk.samtools.SAMRecord
  `abs(insertSize) <=` this
MAX_ITEMS_IN_RAM - Static variable in class htsjdk.samtools.util.SortingLongCollection
MAX_LINEAR_INDEX_SIZE - Static variable in class htsjdk.samtools.GenomicIndexUtil
MAX_LINEAR_INDEX_SIZE - Static variable in class htsjdk.samtools.LinearIndex
MAX_OFFSET - Static variable in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
MAX_PHRED_SCORE - Static variable in class htsjdk.samtools.SAMUtils
MAX_PL - Static variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods
MAX_QUALITY - Static variable in class htsjdk.samtools.SQTagUtil
  Deprecated.
MAX_QUALITY_NOT_STORED_ERRORS - Static variable in class htsjdk.samtools.SamFileValidator
MAX_RANGE - Static variable in class htsjdk.samtools.cram.compression.range.Constants
MAX_UBYTE - Static variable in class htsjdk.samtools.util.BinaryCodec
MAX_UINT - Static variable in class htsjdk.samtools.util.BinaryCodec
MAX_USHORT - Static variable in class htsjdk.samtools.util.BinaryCodec
maxAttributes(int) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Tell's this builder that we have at most these number of attributes
maxBinNumber - Variable in class htsjdk.samtools.BinningIndexContent.BinList
maxElementIndex(double[]) - Static method in class htsjdk.variant.utils.GeneralUtils
maxElementIndex(double[], int) - Static method in class htsjdk.variant.utils.GeneralUtils
maxIntegerType(BCF2Type, BCF2Type) - Static method in class htsjdk.variant.bcf2.BCF2Utils
  Returns the maximum BCF2 integer size of t1 and t2 For example, if t1 == INT8 and t2 == INT16 returns INT16
maxSymbol - Variable in class htsjdk.samtools.cram.compression.range.ByteModel
maybeBgzfWrapOutputStream(File, OutputStream) - Static method in class htsjdk.samtools.util.BlockCompressedOutputStream
maybeBufferedSeekableStream(SeekableStream) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferedSeekableStream(SeekableStream, int) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferedSeekableStream(File) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferedSeekableStream(URL) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferInputStream(InputStream) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferInputStream(InputStream, int) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferOutputStream(OutputStream) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferOutputStream(OutputStream, int) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferReader(Reader) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferReader(Reader, int) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferWriter(Writer) - Static method in class htsjdk.samtools.util.IOUtil
maybeBufferWriter(Writer, int) - Static method in class htsjdk.samtools.util.IOUtil
maybeOpen(URL) - Method in class htsjdk.samtools.CustomReaderFactory
  Check if the url is supposed to be handled by the custom factory and if so attempt to create reader via an instance of this custom factory.
MC - Enum constant in enum class htsjdk.samtools.SAMTag
MC - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
MD - Enum constant in enum class htsjdk.samtools.SAMTag
MD - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
md5() - Method in class htsjdk.samtools.SAMSequenceDictionary
  return a MD5 sum for ths dictionary, the checksum is re-computed each time this method is called.
md5() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
md5() - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
MD5 - Static variable in class htsjdk.samtools.util.FileExtensions
MD5_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
Md5CalculatingInputStream - Class in htsjdk.samtools.util
  Class to generate an MD5 string for a file as it is being read
Md5CalculatingInputStream(InputStream, File) - Constructor for class htsjdk.samtools.util.Md5CalculatingInputStream
  Constructor that takes in the InputStream that we are wrapping and creates the MD5 MessageDigest
Md5CalculatingOutputStream - Class in htsjdk.samtools.util
  Class to generate an MD5 string for a file as it is being read
Md5CalculatingOutputStream(OutputStream, File) - Constructor for class htsjdk.samtools.util.Md5CalculatingOutputStream
Md5CalculatingOutputStream(OutputStream, Path) - Constructor for class htsjdk.samtools.util.Md5CalculatingOutputStream
  Constructor that takes in the OutputStream that we are wrapping and creates the MD5 MessageDigest
md5DigestToString(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
  Convets the result of an md5Digest to a string
mdString - Variable in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures.DecodeResult
mean() - Method in class htsjdk.tribble.util.MathUtils.RunningStat
merge(int, int, V, BiFunction) - Method in class htsjdk.samtools.util.IntervalTree
  If the specified start and end positions are not already associated with a value or are associated with the sentinel ( see `IntervalTree.getSentinel()`, associates it with the given (non-sentinel) value.
merge(BAMFileSpan[]) - Static method in class htsjdk.samtools.BAMFileSpan
mergeBins(List, long[]) - Static method in class htsjdk.samtools.BAMIndexMerger
  Merge bins for (headerless) BAM file parts.
mergeDictionaries(SAMSequenceDictionary, SAMSequenceDictionary, List) - Static method in class htsjdk.samtools.SAMSequenceDictionary
  Will merge dictionaryTags from two dictionaries into one focusing on merging the tags rather than the sequences.
mergeLinearIndexes(int, List, long[]) - Static method in class htsjdk.samtools.BAMIndexMerger
  Merge linear indexes for (headerless) BAM file parts.
MergingIterator<T> - Class in htsjdk.samtools.util
  An iterator over Iterators that return Ts.
MergingIterator(Comparator, Collection) - Constructor for class htsjdk.samtools.util.MergingIterator
  Creates a MergingIterator over the given Collection of iterators whose elements will be returned in the order defined by the given Comparator.
MergingSamRecordIterator - Class in htsjdk.samtools
  Provides an iterator interface for merging multiple underlying iterators into a single iterable stream.
MergingSamRecordIterator(SamFileHeaderMerger, boolean) - Constructor for class htsjdk.samtools.MergingSamRecordIterator
  Deprecated.
  replaced by `MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean)`
MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean) - Constructor for class htsjdk.samtools.MergingSamRecordIterator
  Constructs a new merging iterator with the same set of readers and sort order as provided by the header merger parameter.
MergingSamRecordIterator(SamFileHeaderMerger, Map, boolean) - Constructor for class htsjdk.samtools.MergingSamRecordIterator
  Add a set of SAM file iterators to the merging iterator.
META_HEADER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
META_HEADER_OFFSET - Static variable in class htsjdk.variant.vcf.VCFConstants
META_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
metaCharacter - Variable in class htsjdk.tribble.index.tabix.TabixFormat
  Lines in the file being indexed that start with this character are ignored.
METADATA_INDICATOR - Static variable in class htsjdk.variant.vcf.VCFHeader
method() - Method in record class htsjdk.samtools.cram.structure.CompressorDescriptor
  Returns the value of the `method` record component.
METRIC_HEADER - Static variable in class htsjdk.samtools.metrics.MetricsFile
MetricBase - Class in htsjdk.samtools.metrics
  A base class from which all Metric classes should inherit.
MetricBase() - Constructor for class htsjdk.samtools.metrics.MetricBase
MetricsFile<BEAN,HKEY> - Class in htsjdk.samtools.metrics
  Contains a set of metrics that can be written to a file and parsed back again.
MetricsFile() - Constructor for class htsjdk.samtools.metrics.MetricsFile
MF - Enum constant in enum class htsjdk.samtools.SAMTag
  Deprecated.
  for backwards compatibility only
MF - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
MF_MATE_NEG_STRAND - Static variable in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
MF_MATE_UNMAPPED - Static variable in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
MF_MateBitFlags - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
MI - Enum constant in enum class htsjdk.samtools.SAMTag
MI - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
min() - Method in class htsjdk.samtools.util.IntervalTree
  Find the least interval in the tree.
min(int, int) - Method in class htsjdk.samtools.util.IntervalTree
  Find the earliest interval in the tree greater than or equal to the specified interval.
mIndex - Variable in class htsjdk.tribble.readers.TabixReader
MINOR_HEADER_PREFIX - Static variable in class htsjdk.samtools.metrics.MetricsFile
minOverlapper(int, int) - Method in class htsjdk.samtools.util.IntervalTree
  Find the earliest interval in the tree that overlaps the specified interval.
MISMATCH_CIGAR_SEQ_LENGTH - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Mismatch between the number of bases covered by the CIGAR and sequence
MISMATCH_FILE_SEQ_DICT - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Mismatch between file and sequence dictionaries
MISMATCH_FLAG_MATE_NEG_STRAND - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  mate negative strand flag does not match read negative strand flag of mate
MISMATCH_FLAG_MATE_UNMAPPED - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  mate unmapped flag does not match read unmapped flag of mate
MISMATCH_MATE_ALIGNMENT_START - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  mate alignment does not match alignment start of mate
MISMATCH_MATE_CIGAR_STRING - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  The Cigar String in the MC Tag does not match the Cigar String for the mate of this read.
MISMATCH_MATE_REF_INDEX - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  mate reference index (MRNM) does not match reference index of mate
MISMATCH_READ_LENGTH_AND_E2_LENGTH - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Length of E2 (secondary base calls) and U2 (secondary base quals) tag values should match read length
MISMATCH_READ_LENGTH_AND_QUALS_LENGTH - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
MISMATCH_READ_LENGTH_AND_U2_LENGTH - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
MISMATCH_SEQ_QUAL_LENGTH - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Mismatch between the sequence and quality length
MISSING - Enum constant in enum class htsjdk.variant.bcf2.BCF2Type
MISSING_DEPTH_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
MISSING_GENOTYPE_QUALITY_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
MISSING_HAPLOTYPE_QUALITY_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
MISSING_HEADER - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  the sam/bam file is missing the header
MISSING_PLATFORM_VALUE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  The read group is missing its PL (platform unit) field
MISSING_QUALITY_SCORE - Static variable in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
MISSING_QUALITY_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
MISSING_QUALITY_v3_DOUBLE - Static variable in class htsjdk.variant.vcf.VCFConstants
MISSING_READ_GROUP - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  the header is missing read group information
MISSING_SEQUENCE_DICTIONARY - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  there is no sequence dictionary in the header
MISSING_TAG_NM - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  the NM tag (nucleotide differences) is missing
MISSING_VALUE_v4 - Static variable in class htsjdk.variant.vcf.VCFConstants
MISSING_VERSION_NUMBER - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
MIXED - Enum constant in enum class htsjdk.variant.variantcontext.GenotypeType
  Some chromosomes are NO_CALL and others are called
MIXED - Enum constant in enum class htsjdk.variant.variantcontext.VariantContext.Type
mMateReferenceIndex - Variable in class htsjdk.samtools.SAMRecord
mNextRecord - Variable in class htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator
  The next record to be returned.
MNP - Enum constant in enum class htsjdk.variant.variantcontext.VariantContext.Type
modelDecode(ByteBuffer, RangeCoder) - Method in class htsjdk.samtools.cram.compression.range.ByteModel
  Decode one symbol from the compressed stream, update the model frequencies, and return the symbol.
modelEncode(RangeCoder, int) - Method in class htsjdk.samtools.cram.compression.range.ByteModel
  Encode one symbol to the compressed stream and update the model frequencies.
modelRenormalize() - Method in class htsjdk.samtools.cram.compression.range.ByteModel
  Halve all frequencies (avoiding zeros) when total frequency exceeds `Constants.MAX_FREQ`.
modifyOption(Options, boolean) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set or unset option depending on the boolean given
mostUpstreamWritableLoc - Variable in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
MQ - Enum constant in enum class htsjdk.samtools.SAMTag
MQ - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
MQ_MappingQualityScore - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
mReferenceIndex - Variable in class htsjdk.samtools.SAMRecord
MULTI_PARAM_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.fqzcomp.FQZGlobalFlags
MultiMap() - Constructor for class htsjdk.samtools.util.CollectionUtil.MultiMap
MULTIPLE_REFERENCE_CONTEXT - Static variable in class htsjdk.samtools.cram.ref.ReferenceContext
MULTIPLE_REFERENCE_CONTEXT - Static variable in class htsjdk.samtools.cram.structure.AlignmentContext
MULTIPLE_REFERENCE_ID - Static variable in class htsjdk.samtools.cram.ref.ReferenceContext
MULTIPLE_REFERENCE_TYPE - Enum constant in enum class htsjdk.samtools.cram.ref.ReferenceContextType
Murmur3 - Class in htsjdk.samtools.util
  Provides an implementation of the Murmur3_32 hash algorithm that has desirable properties in terms of randomness and uniformity of the distribution of output values that make it a useful hashing algorithm for downsampling.
Murmur3(int) - Constructor for class htsjdk.samtools.util.Murmur3
  Constructs a Murmur3 hash with the given seed.
MutableFeature - Class in htsjdk.tribble
  A mutable concrete Feature.
MutableFeature(Feature) - Constructor for class htsjdk.tribble.MutableFeature
MutableFeature(String, int, int) - Constructor for class htsjdk.tribble.MutableFeature
MutableIndex - Interface in htsjdk.tribble.index
  Some Index implementations can be modified in memory.
MutableInt - Class in htsjdk.samtools.cram.common
  Mutable integer class suitable for use with collection classes that take a type parameter.
MutableInt() - Constructor for class htsjdk.samtools.cram.common.MutableInt
  Create a mutable integer with initial value 0.
MutableInt(int) - Constructor for class htsjdk.samtools.cram.common.MutableInt
  Create a mutable integer with initial value `initialValue`.
myIndexSeekableStream() - Static method in class htsjdk.samtools.example.ExampleSamUsage

## N

n - Static variable in class htsjdk.samtools.util.SequenceUtil
  Byte typed variables for all normal bases.
N - Enum constant in enum class htsjdk.samtools.CigarOperator
  Skipped region from the reference.
N - Static variable in class htsjdk.samtools.util.SequenceUtil
  Byte typed variables for all normal bases.
N32_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
name - Variable in class htsjdk.variant.variantcontext.VariantContextUtils.JexlVCMatchExp
name - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
name() - Method in class htsjdk.samtools.SamReader.Type
  A string representation of this type.
name(String) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Set this genotype's name
NAME_ATTRIBUTE_KEY - Static variable in class htsjdk.tribble.gff.Gff3Constants
NAME_SEPARATOR - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.NameTokenisationDecode
NAME_TOKENISER - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
name3BytesToInt(byte[]) - Static method in class htsjdk.samtools.cram.structure.ReadTag
  Pack a 3-byte tag ID (2 bytes name + 1 byte type) into an int.
NameAwareCodec - Interface in htsjdk.tribble
  Created by IntelliJ IDEA.
NamedFeature - Interface in htsjdk.tribble
  An interface for features provided via an interval file, e.g.
NameTokenisationDecode - Class in htsjdk.samtools.cram.compression.nametokenisation
  CRAM 3.1 NameTokenisation decoder, used to compress read names in CRAM files.
NameTokenisationDecode() - Constructor for class htsjdk.samtools.cram.compression.nametokenisation.NameTokenisationDecode
NameTokenisationEncode - Class in htsjdk.samtools.cram.compression.nametokenisation
  Name tokenization encoder that compresses read names by tokenizing them and encoding each token stream independently using rANS or arithmetic coding.
NameTokenisationEncode() - Constructor for class htsjdk.samtools.cram.compression.nametokenisation.NameTokenisationEncode
NameTokeniserExternalCompressor - Class in htsjdk.samtools.cram.compression.nametokenisation
NameTokeniserExternalCompressor(NameTokenisationEncode, NameTokenisationDecode) - Constructor for class htsjdk.samtools.cram.compression.nametokenisation.NameTokeniserExternalCompressor
nameType3BytesToInt(String, char) - Static method in class htsjdk.samtools.cram.structure.ReadTag
  Pack a 2-character tag name and a type character into a 3-byte int.
NEGATIVE - Enum constant in enum class htsjdk.tribble.annotation.Strand
  Represents the negative or reverse strand.
NEW_POSITION_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
NEWEST_VERSION - Static variable in class htsjdk.beta.plugin.HtsVersion
  Sentinel constant used to indicate the newest version available
newInstance(SortingCollection.Codec, int, List) - Static method in class htsjdk.samtools.util.DiskBackedQueue
  Syntactic sugar around the ctor, to save some typing of type parameters
newInstance(Class, SortingCollection.Codec, Comparator, int) - Static method in class htsjdk.samtools.util.SortingCollection
  Syntactic sugar around the ctor, to save some typing of type parameters.
newInstance(Class, SortingCollection.Codec, Comparator, int, boolean) - Static method in class htsjdk.samtools.util.SortingCollection
  Syntactic sugar around the ctor, to save some typing of type parameters.
newInstance(Class, SortingCollection.Codec, Comparator, int, boolean, Path...) - Static method in class htsjdk.samtools.util.SortingCollection
  Syntactic sugar around the ctor, to save some typing of type parameters
newInstance(Class, SortingCollection.Codec, Comparator, int, File...) - Static method in class htsjdk.samtools.util.SortingCollection
  Deprecated.
  since 2017-09. Use `SortingCollection.newInstance(Class, Codec, Comparator, int, Path...)` instead
newInstance(Class, SortingCollection.Codec, Comparator, int, Path...) - Static method in class htsjdk.samtools.util.SortingCollection
  Syntactic sugar around the ctor, to save some typing of type parameters
newInstance(Class, SortingCollection.Codec, Comparator, int, Collection) - Static method in class htsjdk.samtools.util.SortingCollection
  Deprecated.
  since 2017-09. Use `SortingCollection.newInstanceFromPaths(Class, Codec, Comparator, int, Collection)` instead
newInstanceFromPaths(SortingCollection.Codec, int, List) - Static method in class htsjdk.samtools.util.DiskBackedQueue
  Syntactic sugar around the ctor, to save some typing of type parameters
newInstanceFromPaths(Class, SortingCollection.Codec, Comparator, int, Collection) - Static method in class htsjdk.samtools.util.SortingCollection
  Syntactic sugar around the ctor, to save some typing of type parameters
newTempFile(String, String, File[]) - Static method in class htsjdk.samtools.util.IOUtil
  Creates a new tmp file on one of the potential filesystems that has at least 5GB free.
newTempFile(String, String, File[], long) - Static method in class htsjdk.samtools.util.IOUtil
  Creates a new tmp file on one of the available temp filesystems, registers it for deletion on JVM exit and then returns it.
newTempPath(String, String, Path[]) - Static method in class htsjdk.samtools.util.IOUtil
  Creates a new tmp file on one of the potential filesystems that has at least 5GB free.
newTempPath(String, String, Path[], long) - Static method in class htsjdk.samtools.util.IOUtil
  Creates a new tmp path on one of the available temp filesystems, registers it for deletion on JVM exit and then returns it.
newWriter(File) - Method in class htsjdk.samtools.fastq.FastqWriterFactory
next - Variable in class htsjdk.samtools.SAMBinaryTagAndValue
next - Variable in class htsjdk.samtools.util.AbstractIterator
next() - Method in class htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator
  Gets the next record from the given iterator.
next() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
next() - Method in class htsjdk.samtools.cram.build.CramSpanContainerIterator
next() - Method in class htsjdk.samtools.CRAMIterator
next() - Method in class htsjdk.samtools.DuplicateSetIterator
next() - Method in class htsjdk.samtools.fastq.FastqReader
next() - Method in class htsjdk.samtools.filter.FilteringSamIterator
  Returns the next element in the iteration.
next() - Method in class htsjdk.samtools.MergingSamRecordIterator
  Returns the next record from the top most iterator during merging.
next() - Method in class htsjdk.samtools.reference.SamLocusAndReferenceIterator
next() - Method in class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
next() - Method in class htsjdk.samtools.SamReader.AssertingIterator
next() - Method in class htsjdk.samtools.util.AbstractIterator
next() - Method in class htsjdk.samtools.util.AbstractLocusIterator
  hasNext() has been fixed so that if it returns true, next() is now guaranteed not to return null.
next() - Method in class htsjdk.samtools.util.AsyncBufferedIterator
next() - Method in class htsjdk.samtools.util.DelegatingIterator
next() - Method in class htsjdk.samtools.util.IntervalList.IntervalMergerIterator
next() - Method in class htsjdk.samtools.util.IntervalTree.FwdIterator
next() - Method in class htsjdk.samtools.util.IntervalTree.OverlapIterator
next() - Method in class htsjdk.samtools.util.IntervalTree.RevIterator
next() - Method in class htsjdk.samtools.util.IntervalTree.ValuesIterator
next() - Method in class htsjdk.samtools.util.MergingIterator
next() - Method in class htsjdk.samtools.util.PeekableIterator
  Returns the next object and advances the iterator.
next() - Method in class htsjdk.samtools.util.PeekIterator
next() - Method in class htsjdk.samtools.util.SAMRecordPrefetchingIterator
next() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer
  Returns the next element in the iteration.
next() - Method in class htsjdk.samtools.util.SortingLongCollection
  Call only if hasNext() == true.
next() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
next() - Method in interface htsjdk.tribble.readers.TabixReader.Iterator
  return null when there is no more data to read
next() - Method in class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator
  Returns the next element in the iteration.
nextBlock(byte[]) - Method in class htsjdk.samtools.util.AsyncBlockCompressedInputStream
nextBlock(byte[]) - Method in class htsjdk.samtools.util.BlockCompressedInputStream
  Reads and decompresses the next block
nextPosition(int, int) - Method in class htsjdk.samtools.util.IntervalListReferenceSequenceMask
  It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
nextPosition(int, int) - Method in interface htsjdk.samtools.util.ReferenceSequenceMask
  It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
nextPosition(int, int) - Method in class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
nextSequence() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Gets the next sequence if available, or null if not present.
nextSequence() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Gets the next sequence if available, or null if not present.
nextSequence() - Method in class htsjdk.samtools.reference.FastaSequenceFile
nextSequence() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
  Retrieves the next whole sequences from the file.
NF_RecordsToNextFragment - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
nGenotypeFields - Variable in class htsjdk.variant.bcf2.BCF2Codec.LazyData
NH - Enum constant in enum class htsjdk.samtools.SAMTag
NH - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
NM - Enum constant in enum class htsjdk.samtools.SAMTag
NM - Static variable in class htsjdk.samtools.ReservedTagConstants
  Number of nucleotide differences (Specified in the SAM spec doc)
NM - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
nmCount - Variable in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures.DecodeResult
NO_ALIGNMENT_CIGAR - Static variable in class htsjdk.samtools.SAMRecord
  Cigar string for an unaligned read.
NO_ALIGNMENT_END - Static variable in class htsjdk.samtools.cram.structure.AlignmentContext
NO_ALIGNMENT_REFERENCE_INDEX - Static variable in class htsjdk.samtools.SAMRecord
  If a read has this reference index, it is unaligned, but not all unaligned reads have this reference index (see above).
NO_ALIGNMENT_REFERENCE_NAME - Static variable in class htsjdk.samtools.SAMRecord
  If a read has this reference name, it is unaligned, but not all unaligned reads have this reference name (see above).
NO_ALIGNMENT_SPAN - Static variable in class htsjdk.samtools.cram.structure.AlignmentContext
NO_ALIGNMENT_START - Static variable in class htsjdk.samtools.cram.structure.AlignmentContext
NO_ALIGNMENT_START - Static variable in class htsjdk.samtools.SAMRecord
  If a read has reference name "*", it will have this value for position.
NO_CALL - Enum constant in enum class htsjdk.variant.variantcontext.GenotypeType
  The sample is no-called (all alleles are NO_CALL
NO_CALL - Static variable in interface htsjdk.variant.variantcontext.Allele
NO_CALL_ALLELE - Static variable in class htsjdk.variant.vcf.VCFConstants
NO_CALL_STRING - Static variable in interface htsjdk.variant.variantcontext.Allele
  A generic static NO_CALL allele for use
NO_CALL alleles - Section in class htsjdk.variant.variantcontext.VariantContext
NO_CODE - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
NO_COMPRESSION_ARG - Static variable in class htsjdk.samtools.cram.compression.ExternalCompressor
NO_COMPRESSION_OVERHEAD - Static variable in class htsjdk.samtools.util.BlockCompressedStreamConstants
NO_CONTENT_ID - Static variable in class htsjdk.samtools.cram.structure.block.Block
  Only external blocks have meaningful Content IDs Other blocks are required to have a Content ID of 0
NO_GENOTYPES - Static variable in class htsjdk.variant.variantcontext.GenotypesContext
  static constant value for an empty GenotypesContext.
NO_GENOTYPES - Static variable in class htsjdk.variant.variantcontext.VariantContext
NO_HEADER_END - Static variable in class htsjdk.tribble.FeatureCodecHeader
  The value of the headerEnd field when there's no header
NO_LOG10_PERROR - Static variable in class htsjdk.variant.variantcontext.CommonInfo
NO_LOG10_PERROR - Static variable in class htsjdk.variant.variantcontext.VariantContext
NO_MAPPING_QUALITY - Static variable in class htsjdk.samtools.SAMRecord
  Alignment score for an unaligned read.
NO_OPTIONS - Static variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
NO_READGROUP_ID - Static variable in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
NO_VARIATION - Enum constant in enum class htsjdk.variant.variantcontext.VariantContext.Type
noAD() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype has no AD value
noAttributes() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Tells this builder to remove all extended attributes
noDP() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype has no DP value
noGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells this builder that the resulting VariantContext should not contain any GenotypeContext
noGQ() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype has no GQ value
noID() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells us that the resulting VariantContext should not have an ID
NON_REF_ALLELE - Static variable in interface htsjdk.variant.variantcontext.Allele
NON_REF_STRING - Static variable in interface htsjdk.variant.variantcontext.Allele
NON_ZERO_BUFFER_SIZE - Static variable in class htsjdk.samtools.Defaults
  Even if BUFFER_SIZE is 0, this is guaranteed to be non-zero.
none - Enum constant in enum class htsjdk.samtools.SAMFileHeader.GroupOrder
NONE - Enum constant in enum class htsjdk.samtools.BamIndexValidator.IndexValidationStringency
NONE - Enum constant in enum class htsjdk.samtools.SamFlagField
NONE - Enum constant in enum class htsjdk.tribble.annotation.Strand
  Denotes that a strand designation is not applicable or is unknown.
nonEmpty(String) - Static method in class htsjdk.utils.ValidationUtils
  Checks that a `String` is not `null` and that it is not empty.
nonEmpty(String, String) - Static method in class htsjdk.utils.ValidationUtils
  Checks that a `String` is not `null` and that it is not empty.
nonEmpty(T) - Static method in class htsjdk.utils.ValidationUtils
  Checks that a `Collection` is not `null` and that it is not empty.
nonEmpty(T, String) - Static method in class htsjdk.utils.ValidationUtils
  Checks that a `Collection` is not `null` and that it is not empty.
nonNull(T) - Static method in class htsjdk.utils.ValidationUtils
  Checks that an Object `object` is not null and returns the same object or throws an `IllegalArgumentException`
nonNull(T, String) - Static method in class htsjdk.utils.ValidationUtils
  Checks that an `Object` is not `null` and returns the same object or throws an `IllegalArgumentException`
nonNull(T, Supplier) - Static method in class htsjdk.utils.ValidationUtils
  Checks that an `Object` is not `null` and returns the same object or throws an `IllegalArgumentException`
noPL() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype has no PL value
NORMAL - Enum constant in enum class htsjdk.samtools.cram.structure.CRAMCompressionProfile
  Balanced profile (default).
normaliseFrequenciesOrder0(int[], int) - Static method in class htsjdk.samtools.cram.compression.rans.Utils
  Normalize symbol frequencies so they sum to `1 << bits`.
normaliseFrequenciesOrder0Shift(int[], int) - Static method in class htsjdk.samtools.cram.compression.rans.Utils
  Shift-based frequency normalization: scale frequencies by a power of 2 so they sum to `1 << bits`.
normaliseFrequenciesOrder1(int[][], int) - Static method in class htsjdk.samtools.cram.compression.rans.Utils
  Normalize Order-1 frequency tables: for each context symbol with non-zero frequency, compute the minimum bit size and normalize that context's frequency table.
normaliseFrequenciesOrder1Shift(int[][], int) - Static method in class htsjdk.samtools.cram.compression.rans.Utils
  Shift-based normalization for all Order-1 context rows.
normalizeBase(byte) - Static method in class htsjdk.samtools.cram.build.Utils
  CRAM operates with upper case bases, so both read and ref bases should be upper-cased and vocab controlled.
normalizeCRAMRecords(List, CRAMReferenceRegion) - Method in class htsjdk.samtools.cram.structure.Slice
  Normalize a list of CRAMCompressionRecord that have been read in from a CRAM stream.
normalizeFromLog10(double[]) - Static method in class htsjdk.variant.utils.GeneralUtils
  normalizes the log10-based array.
normalizeFromLog10(double[], boolean) - Static method in class htsjdk.variant.utils.GeneralUtils
  normalizes the log10-based array.
normalizeFromLog10(double[], boolean, boolean) - Static method in class htsjdk.variant.utils.GeneralUtils
  See #normalizeFromLog10 but with the additional option to use an approximation that keeps the calculation always in log-space
NOSZ_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.range.RangeParams
NOSZ_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
NOT_PRIMARY_ALIGNMENT - Enum constant in enum class htsjdk.samtools.SAMFlag
  Deprecated.
  use `SAMFlag.SECONDARY_ALIGNMENT` instead.
notags - Variable in class htsjdk.samtools.util.htsget.HtsgetRequest
Not currently supported: - Section in enum class htsjdk.variant.variantcontext.VariantContext.Type
noteCurrentRecord(VariantContext) - Method in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
Notes on Headerless SAMRecords - Section in class htsjdk.samtools.SAMRecord
NotPrimaryAlignmentFilter - Class in htsjdk.samtools.filter
  Deprecated.
  use `SecondaryAlignmentFilter` instead.
NotPrimaryAlignmentFilter() - Constructor for class htsjdk.samtools.filter.NotPrimaryAlignmentFilter
  Deprecated.
NotPrimarySkippingIterator - Class in htsjdk.samtools
  Deprecated.
  use `SecondaryAlignmentSkippingIterator` instead.
NotPrimarySkippingIterator(CloseableIterator) - Constructor for class htsjdk.samtools.NotPrimarySkippingIterator
  Deprecated.
notToBeDirectlyAccessedGenotypes - Variable in class htsjdk.variant.variantcontext.GenotypesContext
  An ArrayList of genotypes contained in this context WARNING: TO ENABLE THE LAZY VERSION OF THIS CLASS, NO METHODS SHOULD DIRECTLY ACCESS THIS VARIABLE.
NP_NextFragmentAlignmentStart - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
NS_NextFragmentReferenceSequenceID - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
NULL - Enum constant in enum class htsjdk.samtools.cram.structure.EncodingID
  "Do nothing" encoding.
NULL_ALLELE - Static variable in class htsjdk.variant.vcf.VCFConstants
NULL_QUALS - Static variable in class htsjdk.samtools.SAMRecord
  This should rarely be used, since all reads should have quality scores.
NULL_QUALS_STRING - Static variable in class htsjdk.samtools.SAMRecord
NULL_SEQUENCE - Static variable in class htsjdk.samtools.SAMRecord
  This should rarely be used, since a read with no sequence doesn't make much sense.
NULL_SEQUENCE_STRING - Static variable in class htsjdk.samtools.SAMRecord
NUM_STANDARD_FIELDS - Static variable in class htsjdk.variant.vcf.AbstractVCFCodec
NUMBER_OF_SYMBOLS - Static variable in class htsjdk.samtools.cram.compression.range.Constants
NUMBER_OF_SYMBOLS - Static variable in class htsjdk.samtools.cram.compression.rans.Constants
numberOfNonNullBins - Variable in class htsjdk.samtools.BinningIndexContent.BinList
numCigarElements() - Method in class htsjdk.samtools.Cigar
numDataValues() - Method in class htsjdk.tribble.util.MathUtils.RunningStat
numDuplicates() - Method in class htsjdk.samtools.DuplicateSet
  Returns the number of duplicates in this set, including the representative record.
numElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Flag
numElements() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
numElements(VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
numElements(VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.FTGenotypesWriter
numElements(VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenotypesWriter
numElements(VariantContext, Genotype) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IGFGenotypesWriter
numElements(VariantContext, Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
  A convenience access for the number of elements.
numElements(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
numElementsFromValue(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.IntArray
numElementsFromValue(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
  Given a value, return the number of elements we will encode for it.
numElementsFromValue(Object) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
numHeaderLinesToSkip - Variable in class htsjdk.tribble.index.tabix.TabixFormat
  TODO: This is written, and part of the index header, but does not appear to be used.
numLikelihoods(int, int) - Static method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
  Compute how many likelihood elements are associated with the given number of alleles Equivalent to asking in how many ways N non-negative integers can add up to P is S(N,P) where P = ploidy (number of chromosomes) and N = total # of alleles.

## O

OA - Enum constant in enum class htsjdk.samtools.SAMTag
OBJECT_TOSTRING_COMPARATOR - Static variable in class htsjdk.samtools.util.CollectionUtil
  Simple case-insensitive lexical comparator of objects using their `Object.toString()` value.
obtainAssertedMate(Iterator, SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil
  Obtain the secondOfPair mate belonging to the firstOfPair SAMRecord (assumed to be in the next element of the specified samRecordIterator)
OC - Enum constant in enum class htsjdk.samtools.SAMTag
OC - Static variable in class htsjdk.samtools.ReservedTagConstants
  The original cigar before indel cleaning, or 454 cafie and homopolymer correction
OC - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
OCTAL - Enum constant in enum class htsjdk.samtools.SamFlagField
of(SeekableStream) - Static method in class htsjdk.samtools.SamInputResource
  Creates a `SamInputResource` reading from the provided resource, with no index.
of(File) - Static method in class htsjdk.samtools.SamInputResource
  Creates a `SamInputResource` reading from the provided resource, with no index.
of(InputStream) - Static method in class htsjdk.samtools.SamInputResource
  Creates a `SamInputResource` reading from the provided resource, with no index.
of(String) - Static method in enum class htsjdk.samtools.SamFlagField
  Returns the type of flag field for this string.
of(String) - Static method in class htsjdk.samtools.SamInputResource
  Creates a `SamInputResource` from a string specifying *either* a url or a file path
of(URI) - Static method in class htsjdk.samtools.SamInputResource
  Creates a `SamInputResource` from a URI which may represent an htsget path, or some other resource such as a filesystem path or a URL, with no index.
of(URI, Function) - Static method in class htsjdk.samtools.SamInputResource
  Creates a `SamInputResource` with no index from a URI which may represent an htsget path, or some other resource such as a filesystem path or a URL, with no index, and with a wrapper to apply to the SeekableByteChannel for custom prefetching/buffering.
of(URL) - Static method in class htsjdk.samtools.SamInputResource
  Creates a `SamInputResource` reading from the provided resource, with no index.
of(Path) - Static method in class htsjdk.samtools.SamInputResource
  Creates a `SamInputResource` reading from the provided resource, with no index.
of(Path, Function) - Static method in class htsjdk.samtools.SamInputResource
  Creates a `SamInputResource` reading from the provided resource, with no index, and with a wrapper to apply to the SeekableByteChannel for custom prefetching/buffering.
OF - Enum constant in enum class htsjdk.samtools.SAMTag
OF - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
offer(E) - Method in class htsjdk.samtools.util.DiskBackedQueue
offset - Variable in class htsjdk.samtools.util.AbstractRecordAndOffset
  Zero-based offset in the read corresponding to the current position in AbstractLocusInfo
OLD_DEPTH_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
ONE - Enum constant in enum class htsjdk.samtools.cram.compression.range.RangeParams.ORDER
ONE - Enum constant in enum class htsjdk.samtools.cram.compression.rans.RANSParams.ORDER
ONE - Enum constant in enum class htsjdk.tribble.bed.BEDCodec.StartOffset
ONE_GB - Static variable in class htsjdk.samtools.util.IOUtil
oneAllele(String, List) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec
  create a an allele from an index and an array of alleles
oneIsPrefixOfOther(Allele, Allele) - Static method in interface htsjdk.variant.variantcontext.Allele
ONT - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Oxford Nanopore
OP - Enum constant in enum class htsjdk.samtools.SAMTag
OP - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
open(SamInputResource) - Method in class htsjdk.samtools.SamReaderFactory
open(File) - Method in class htsjdk.samtools.SamReaderFactory
open(File) - Method in class htsjdk.variant.vcf.VCFIteratorBuilder
  creates a VCF iterator from a File
open(InputStream) - Method in class htsjdk.variant.vcf.VCFIteratorBuilder
  creates a VCF iterator from an input stream It detects if the stream is a BCF stream or a GZipped stream.
open(String) - Method in class htsjdk.variant.vcf.VCFIteratorBuilder
  creates a VCF iterator from a URI It detects if the stream is a BCF stream or a GZipped stream.
open(String, Function) - Method in class htsjdk.variant.vcf.VCFIteratorBuilder
  creates a VCF iterator from a URI It detects if the stream is a BCF stream or a GZipped stream.
open(URL) - Method in interface htsjdk.samtools.CustomReaderFactory.ICustomReaderFactory
open(Path) - Method in class htsjdk.samtools.SamReaderFactory
  Open the specified path (without using any wrappers).
open(Path) - Method in class htsjdk.variant.vcf.VCFIteratorBuilder
  creates a VCF iterator from a Path
open(Path, Function) - Method in class htsjdk.variant.vcf.VCFIteratorBuilder
  creates a VCF iterator from a Path
open(Path, Function, Function) - Method in class htsjdk.samtools.SamReaderFactory
  Open the specified path, using the specified wrappers for prefetching/caching.
openCraiFileAsBaiStream(File, SAMSequenceDictionary) - Static method in class htsjdk.samtools.cram.CRAIIndex
openCraiFileAsBaiStream(InputStream, SAMSequenceDictionary) - Static method in class htsjdk.samtools.cram.CRAIIndex
openFileForBufferedReading(File) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that a file exists and is readable, and then returns a buffered reader for it.
openFileForBufferedReading(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Checks that a path exists and is readable, and then returns a buffered reader for it.
openFileForBufferedUtf8Reading(File) - Static method in class htsjdk.samtools.util.IOUtil
  Opens a file for reading, decompressing it if necessary
openFileForBufferedUtf8Writing(File) - Static method in class htsjdk.samtools.util.IOUtil
  Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
openFileForBufferedUtf8Writing(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
openFileForBufferedWriting(File) - Static method in class htsjdk.samtools.util.IOUtil
  Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
openFileForBufferedWriting(File, boolean) - Static method in class htsjdk.samtools.util.IOUtil
  Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
openFileForBufferedWriting(Path, OpenOption...) - Static method in class htsjdk.samtools.util.IOUtil
  Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
openFileForMd5CalculatingWriting(File) - Static method in class htsjdk.samtools.util.IOUtil
openFileForMd5CalculatingWriting(Path) - Static method in class htsjdk.samtools.util.IOUtil
openFileForReading(File) - Static method in class htsjdk.samtools.util.IOUtil
  Opens a file for reading, decompressing it if necessary
openFileForReading(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Opens a file for reading, decompressing it if necessary
openFileForWriting(File) - Static method in class htsjdk.samtools.util.IOUtil
  Opens a file for writing, overwriting the file if it already exists
openFileForWriting(File, boolean) - Static method in class htsjdk.samtools.util.IOUtil
  Opens a file for writing, gzip it if it ends with ".gz" or "bfq"
openFileForWriting(Path, OpenOption...) - Static method in class htsjdk.samtools.util.IOUtil
  Opens a file for writing, gzip it if it ends with ".gz" or "bfq"
openGzipFileForReading(File) - Static method in class htsjdk.samtools.util.IOUtil
  Opens a GZIP-encoded file for reading, decompressing it if necessary
openGzipFileForReading(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Opens a GZIP-encoded file for reading, decompressing it if necessary
openGzipFileForWriting(File, boolean) - Static method in class htsjdk.samtools.util.IOUtil
  Opens a GZIP encoded file for writing
openGzipFileForWriting(Path, OpenOption...) - Static method in class htsjdk.samtools.util.IOUtil
  Opens a GZIP encoded file for writing
openIndex(SeekableStream, SAMSequenceDictionary) - Static method in class htsjdk.samtools.BAMIndexMerger
openIndexFileAsBaiOrNull(File, SAMSequenceDictionary) - Static method in enum class htsjdk.samtools.SamIndexes
openIndexUrlAsBaiOrNull(URL, SAMSequenceDictionary) - Static method in enum class htsjdk.samtools.SamIndexes
openInputStream() - Method in class htsjdk.tribble.util.FTPHelper
openInputStream() - Method in class htsjdk.tribble.util.HTTPHelper
openInputStream() - Method in class htsjdk.tribble.util.RemoteURLHelper
openInputStream() - Method in interface htsjdk.tribble.util.URLHelper
  Open an InputStream to stream the contents of the resource
openInputStream(String) - Static method in class htsjdk.tribble.util.ParsingUtils
openInputStream(String, Function) - Static method in class htsjdk.tribble.util.ParsingUtils
  open an input stream from the given path and wrap the raw byte stream with a wrapper if given the wrapper will only be applied to paths that are 1.
openInputStreamForRange(long, long) - Method in class htsjdk.tribble.util.FTPHelper
openInputStreamForRange(long, long) - Method in class htsjdk.tribble.util.HTTPHelper
  Open an InputStream to stream a slice (range) of the resource.
openInputStreamForRange(long, long) - Method in class htsjdk.tribble.util.RemoteURLHelper
openInputStreamForRange(long, long) - Method in interface htsjdk.tribble.util.URLHelper
  Open an InputStream to stream a slice (range) of the resource.
openSamExamples() - Method in class htsjdk.samtools.example.ExampleSamUsage
  Example usages of `SamReaderFactory`
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Bases
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Padding
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Scores
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
operator - Static variable in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
OPTIMISTIC_VCF_4_4 - Static variable in class htsjdk.samtools.Defaults
OPTIMISTIC_VCF_4_4_PROPERTY - Static variable in class htsjdk.samtools.Defaults
optimize() - Method in class htsjdk.tribble.index.linear.LinearIndex
optimize(double) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
optimize(double) - Method in class htsjdk.tribble.index.linear.LinearIndex
  Adapative optimization of the linear index
optimizeChunkList(List, long) - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Deprecated.
  Invoke `Chunk.optimizeChunkList(List, long)` directly.
optimizeChunkList(List, long) - Static method in class htsjdk.samtools.Chunk
optimizeIntervals(QueryInterval[]) - Static method in class htsjdk.samtools.QueryInterval
options - Variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
Options - Enum Class in htsjdk.variant.variantcontext.writer
  Available writer options for VariantContextWriters
OQ - Enum constant in enum class htsjdk.samtools.SAMTag
OQ - Static variable in class htsjdk.samtools.ReservedTagConstants
  The original pred quality scores before modifications such as 454 cafie and homopolymer correction
OQ - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
OR - Enum constant in enum class htsjdk.samtools.SAMTag
OR - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
ORDER_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.range.RangeParams
ORDER_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
OTHER - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Deprecated.
  OTHER is not an official value. It is recommended to omit PL if it is not in this list or is unknown.
out - Variable in class htsjdk.samtools.IndexMerger
OutputStreamResource - Class in htsjdk.beta.io.bundle
  A `BundleResource` backed by an `OutputStream`.
OutputStreamResource(OutputStream, String, String) - Constructor for class htsjdk.beta.io.bundle.OutputStreamResource
  Create a `BundleResource` backed by an OutputStream, specifying a display name and content type.
OutputStreamResource(OutputStream, String, String, String) - Constructor for class htsjdk.beta.io.bundle.OutputStreamResource
  Create a BundleResource backed by an OutputStream, specifying a display name, content type and format.
outputWriter - Variable in class htsjdk.samtools.cram.encoding.external.ExternalByteArrayCodec
OverclippedReadFilter - Class in htsjdk.samtools.filter
  Filters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e.g.
OverclippedReadFilter(int, boolean) - Constructor for class htsjdk.samtools.filter.OverclippedReadFilter
OVERFLOW_ELEMENT_MARKER - Static variable in class htsjdk.variant.bcf2.BCF2Utils
OverlapDetector<T> - Class in htsjdk.samtools.util
  Utility class to efficiently do in memory overlap detection between a large set of mapping like objects, and one or more candidate mappings.
OverlapDetector(int, int) - Constructor for class htsjdk.samtools.util.OverlapDetector
  Constructs an overlap detector.
OverlapIterator(int, int) - Constructor for class htsjdk.samtools.util.IntervalTree.OverlapIterator
overlappers(int, int) - Method in class htsjdk.samtools.util.IntervalTree
  Return an iterator over all intervals overlapping the specified range.
OVERLAPPING - Enum constant in enum class htsjdk.beta.plugin.interval.HtsQueryRule
  Get all records that overlap the query interval.
overlaps(int, int, int, int) - Static method in class htsjdk.samtools.util.CoordMath
  Checks to see if the two sets of coordinates have any overlap.
overlaps(Chunk) - Method in class htsjdk.samtools.Chunk
  Returns whether two chunks overlap.
overlaps(QueryInterval) - Method in class htsjdk.samtools.QueryInterval
overlaps(IntervalList, IntervalList) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for finding the intervals in the first list that have at least 1bp overlap with any interval in the second list.
overlaps(Locatable) - Method in interface htsjdk.samtools.util.Locatable
  Determines whether this interval overlaps the provided locatable.
overlaps(Interval) - Method in class htsjdk.tribble.index.interval.Interval
overlaps(Collection, Collection) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for finding the intervals in the first list that have at least 1bp overlap with any interval in the second list.
overlapsAny(Locatable) - Method in class htsjdk.samtools.util.OverlapDetector
  Returns true iff the given locatable overlaps any locatable in this detector.
ownsURI(IOPath) - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec
ownsURI(IOPath) - Method in class htsjdk.beta.codecs.reads.sam.SAMCodec
ownsURI(IOPath) - Method in interface htsjdk.beta.plugin.HtsCodec
  Determine if this codec "owns" the URI contained in `ioPath` see (`IOPath.getURI()`).
OX - Enum constant in enum class htsjdk.samtools.SAMTag
OX - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.

## P

P - Enum constant in enum class htsjdk.samtools.CigarOperator
  Padding.
PACBIO - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Pacific Biotechnology
PACK_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.range.RangeParams
PACK_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
pad(int, int) - Method in class htsjdk.samtools.util.Interval
  Returns a new interval that is padded by the amount of bases specified on either side.
padded(int) - Method in class htsjdk.samtools.util.IntervalList
  Returns a new IntervalList where each interval is padded by 'padding' bases on each side.
padded(int, int) - Method in class htsjdk.samtools.util.IntervalList
  Returns a new IntervalList where each interval is padded by the specified amount of bases.
Padding - Class in htsjdk.samtools.cram.encoding.readfeatures
  A read feature representing padding, similar to `CigarOperator.P`.
Padding(int, int) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Padding
PADDING - Static variable in enum class htsjdk.samtools.CigarOperator
PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  pair flag set but not marked as first or second of pair
PARENT_ATTRIBUTE_KEY - Static variable in class htsjdk.tribble.gff.Gff3Constants
parse(Object) - Method in class htsjdk.variant.bcf2.BCF2LazyGenotypesDecoder
parse(Object) - Method in interface htsjdk.variant.variantcontext.LazyGenotypesContext.LazyParser
parse(String) - Method in interface htsjdk.samtools.metrics.Header
  Parses the data contained in the String version of the header.
parse(String) - Method in class htsjdk.samtools.metrics.StringHeader
parse(String) - Method in class htsjdk.samtools.metrics.VersionHeader
parse(String) - Method in enum class htsjdk.samtools.SamFlagField
  Parses the flag.
parse(String) - Static method in class htsjdk.samtools.util.DateParser
  Parse the given string in ISO 8601 format and build a Date object.
parse(String) - Static method in class htsjdk.samtools.util.htsget.HtsgetErrorResponse
parse(String) - Static method in class htsjdk.samtools.util.htsget.HtsgetResponse
  Parses HtsgetResponse object from json string
parse(JSONObject) - Static method in class htsjdk.samtools.util.htsget.HtsgetResponse.Block
  Parse a single data block from a json value
parseAlleles(String, String, int) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec
  parse out the alleles
parseBoolean(String) - Method in class htsjdk.samtools.util.FormatUtil
  Parses a String into a boolean, as per the above convention that true = Y and false = N.
parseChar(String) - Method in class htsjdk.samtools.util.FormatUtil
  Parses a String into a char.
parseColor(String) - Static method in class htsjdk.tribble.util.ParsingUtils
  Convert an rgb string, hex, or symbol to a color.
parseDate(String) - Method in class htsjdk.samtools.util.FormatUtil
  Parses a String into a date.
parseDefault(String) - Static method in enum class htsjdk.samtools.SamFlagField
  Infers the format from the flag string and parses the flag.
parseDouble(String) - Method in class htsjdk.samtools.util.FormatUtil
  Parses a String into a double.
parseEnum(String, Class) - Method in class htsjdk.samtools.util.FormatUtil
  Parses a String into an Enum of the given type.
parseFilters(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  parse the filter string, first checking to see if we already have parsed it in a previous attempt
parseFilters(String) - Method in class htsjdk.variant.vcf.VCF3Codec
  parse the filter string, first checking to see if we already have parsed it in a previous attempt
parseFilters(String) - Method in class htsjdk.variant.vcf.VCFCodec
  parse the filter string, first checking to see if we already have parsed it in a previous attempt
parseFloat(String) - Method in class htsjdk.samtools.util.FormatUtil
  Parses a String into a float.
parseGenotypeAlleles(String, List, Map) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec
  parse genotype alleles from the genotype string
parseHeaderFromLines(List, VCFHeaderVersion) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  create a VCF header from a set of header record lines
parseInt(String) - Method in class htsjdk.samtools.util.FormatUtil
  Parses a String into an int.
parseIso8601Date(String) - Method in class htsjdk.samtools.util.FormatUtil
  Parse a String into an Iso8601 Date
parseLine(VCFHeaderVersion, String, List) - Static method in class htsjdk.variant.vcf.VCFHeaderLineTranslator
parseLine(VCFHeaderVersion, String, List, List) - Static method in class htsjdk.variant.vcf.VCFHeaderLineTranslator
parseLine(String) - Method in class htsjdk.samtools.SAMLineParser
  Parse a SAM line.
parseLine(String, int) - Method in class htsjdk.samtools.SAMLineParser
  Parse a SAM line.
parseLong(String) - Method in class htsjdk.samtools.util.FormatUtil
  Parses a String into a long.
parseObject(String, Class) - Method in class htsjdk.samtools.util.FormatUtil
  Attempts to determine the correct parse method to call based on the desired return type and then parses the String and returns the value.
parseQual(String) - Static method in class htsjdk.variant.vcf.AbstractVCFCodec
  parse out the qual value
parseReg(String) - Method in class htsjdk.tribble.readers.TabixReader
  Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"
parseShort(String) - Method in class htsjdk.samtools.util.FormatUtil
  Parses a String into a short.
parseVcfDouble(String) - Static method in class htsjdk.variant.vcf.VCFUtils
  Parses a String as a Double, being tolerant for case-insensitive NaN and Inf/Infinity.
parseWithoutValidation(String) - Method in enum class htsjdk.samtools.SamFlagField
  Performs the actual parsing based on the radix.
ParsingUtils - Class in htsjdk.tribble.util
ParsingUtils() - Constructor for class htsjdk.tribble.util.ParsingUtils
partition(Collection, CollectionUtil.Partitioner) - Static method in class htsjdk.samtools.util.CollectionUtil
  Deprecated.
  use java8 .stream().collect(Collectors.groupingBy(()-> function)) instead
partition(Collection, Function) - Static method in class htsjdk.samtools.util.CollectionUtil
  Partitions a collection into groups based on a characteristics of that group.
Partitioner() - Constructor for class htsjdk.samtools.util.CollectionUtil.Partitioner
  Deprecated.
partLengths - Variable in class htsjdk.samtools.IndexMerger
parts - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
PASSES_FILTERS - Static variable in class htsjdk.variant.variantcontext.VariantContext
PASSES_FILTERS_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
PASSES_FILTERS_v4 - Static variable in class htsjdk.variant.vcf.VCFConstants
passFilters() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells this builder that the resulting VariantContext should have PASS filters
PassingVariantFilter - Class in htsjdk.variant.variantcontext.filter
  A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).
PassingVariantFilter() - Constructor for class htsjdk.variant.variantcontext.filter.PassingVariantFilter
pasv() - Method in class htsjdk.samtools.util.ftp.FTPClient
PD_padding - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
PEDIGREE_HEADER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
PEDIGREE_HEADER_OFFSET - Static variable in class htsjdk.variant.vcf.VCFConstants
PEDIGREE_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
peek() - Method in class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
peek() - Method in class htsjdk.samtools.util.AbstractIterator
  Returns the next element in the iterator, if one exists.
peek() - Method in class htsjdk.samtools.util.BufferedLineReader
  Non-destructive one-character look-ahead.
peek() - Method in class htsjdk.samtools.util.DiskBackedQueue
peek() - Method in interface htsjdk.samtools.util.LineReader
  Non-destructive one-character look-ahead.
peek() - Method in class htsjdk.samtools.util.PeekableIterator
  Returns the next object but does not advance the iterator.
peek() - Method in class htsjdk.samtools.util.PeekIterator
peek() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
peek() - Method in interface htsjdk.tribble.readers.LineIterator
  Peeks at the next line, without expending any elements in the underlying iterator.
peek() - Method in interface htsjdk.tribble.readers.Positional
  Return the next byte in the first, without actually reading it from the stream.
peek() - Method in class htsjdk.tribble.readers.PositionalBufferedStream
peek() - Method in interface htsjdk.variant.vcf.VCFIterator
  Returns the next object but does not advance the iterator.
PeekableIterator<Object> - Class in htsjdk.samtools.util
  Generic Closable Iterator that allows you to peek at the next value before calling next
PeekableIterator(Iterator) - Constructor for class htsjdk.samtools.util.PeekableIterator
  Constructs a new iterator that wraps the supplied iterator.
peekByte() - Method in class htsjdk.samtools.util.FastLineReader
PeekIterator<T> - Class in htsjdk.samtools.util
  Wrapper around an iterator that enables non-destructive peeking at the next element that would be returned by next()
PeekIterator(Iterator) - Constructor for class htsjdk.samtools.util.PeekIterator
PER_ALLELE_COUNT - Static variable in class htsjdk.variant.vcf.VCFConstants
PER_ALTERNATE_COUNT - Static variable in class htsjdk.variant.vcf.VCFConstants
PER_GENOTYPE_COUNT - Static variable in class htsjdk.variant.vcf.VCFConstants
PG - Enum constant in enum class htsjdk.samtools.SAMTag
PG - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
PgIdGenerator(SAMFileHeader) - Constructor for class htsjdk.samtools.SAMFileHeader.PgIdGenerator
PHASE_QUALITY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
PHASE_SET_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
phased(boolean) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Is this genotype phased?
PHASED - Static variable in class htsjdk.variant.vcf.VCFConstants
PHASED_ALLELE_SEPARATOR - Static variable in class htsjdk.variant.variantcontext.Genotype
PHASED_SWITCH_PROB_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
PHASING_TOKENS - Static variable in class htsjdk.variant.vcf.VCFConstants
PHRED_ADDEND - Static variable in class htsjdk.samtools.util.SolexaQualityConverter
  This value is added to a Phred scord to make it printable ASCII
phredToFastq(byte[]) - Static method in class htsjdk.samtools.SAMUtils
  Convert an array of bytes, in which each byte is a binary phred quality score, to printable ASCII representation of the quality scores, ala FASTQ format.
phredToFastq(byte[], int, int) - Static method in class htsjdk.samtools.SAMUtils
  Convert an array of bytes, in which each byte is a binary phred quality score, to printable ASCII representation of the quality scores, ala FASTQ format.
phredToFastq(int) - Static method in class htsjdk.samtools.SAMUtils
  Convert a single binary phred score to printable ASCII representation, ala FASTQ format.
PL(double[]) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype has this PL value, converted from double[].
PL(int[]) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype has this PL value, as int[].
PLAccessor() - Constructor for class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.PLAccessor
PLATFORM_MODEL_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
PLATFORM_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
PLATFORM_UNIT_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
PLindexConversion - Static variable in class htsjdk.variant.variantcontext.GenotypeLikelihoods
PNEXT - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
poll() - Method in class htsjdk.samtools.util.DiskBackedQueue
pool(Writer, BlockingQueue, int) - Method in class htsjdk.io.AsyncWriterPool
  Exchange a class implementing `Writer` for a `AsyncWriterPool.PooledWriter`.
POORLY_FORMATTED_HEADER_TAG - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Header tag does not have colon
populateFromRecords(List) - Method in class htsjdk.samtools.cram.structure.CRAMCodecModelContext
  Populate this context from the records in a slice.
POS - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
POS - Enum constant in enum class htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
position() - Method in class htsjdk.samtools.AbstractBAMFileIndex
position() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
position() - Method in class htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel
position() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
position() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
position() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
position() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
position() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
position() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
position() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
position() - Method in class htsjdk.samtools.seekablestream.SeekableStream
position(long) - Method in class htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel
Positional - Interface in htsjdk.tribble.readers
  Minimal interface for an object at support getting the current position in the stream / writer / file, as well as a handful of other reader-like features.
PositionalBufferedStream - Class in htsjdk.tribble.readers
  A wrapper around an `InputStream` which performs it's own buffering, and keeps track of the position.
PositionalBufferedStream(InputStream) - Constructor for class htsjdk.tribble.readers.PositionalBufferedStream
PositionalBufferedStream(InputStream, int) - Constructor for class htsjdk.tribble.readers.PositionalBufferedStream
PositionalOutputStream - Class in htsjdk.samtools.util
  Wraps output stream in a manner which keeps track of the position within the file and allowing writes at arbitrary points
PositionalOutputStream(OutputStream) - Constructor for class htsjdk.samtools.util.PositionalOutputStream
POSITIVE - Enum constant in enum class htsjdk.tribble.annotation.Strand
  Represents the positive or forward strand.
positiveFourDigitBase36Str(int) - Static method in class htsjdk.samtools.SamFileHeaderMerger
  Convert an integer to base36, protected solely for testing
PQ - Enum constant in enum class htsjdk.samtools.SAMTag
PQ - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
PREDICTED_MEDIAN_INSERT_SIZE_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
prefillBins(K...) - Method in class htsjdk.samtools.util.Histogram
  Prefill the histogram with the supplied set of bins.
PREMATURE_END_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
prepareForSeek() - Method in class htsjdk.samtools.util.AsyncBlockCompressedInputStream
prepareForSeek() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
  Performs cleanup required before seek is called on the underlying stream
PREVIOUS_PROGRAM_GROUP_ID_TAG - Static variable in class htsjdk.samtools.SAMProgramRecord
PRIMARY_KEYS - Static variable in class htsjdk.variant.variantcontext.Genotype
  A list of genotype field keys corresponding to values we manage inline in the Genotype object.
PrimitiveSamReaderToSamReaderAdapter(SamReader.PrimitiveSamReader, SamInputResource) - Constructor for class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
printHeaderFields(URL) - Static method in class htsjdk.samtools.util.HttpUtils
printIndexInfo() - Method in class htsjdk.tribble.index.AbstractIndex
printIndexStats(File) - Static method in class htsjdk.samtools.BAMIndexMetaData
  Prints meta-data statistics from BAM index (.bai or .csi) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate
printNode() - Method in class htsjdk.samtools.util.IntervalTree.Node
PrintReadsExample - Class in htsjdk.samtools.example
  This is a example program showing how to use SAM readers and (optionally) writers.
printTree() - Method in class htsjdk.samtools.util.IntervalTree
  This method draws a nested picture of the tree on System.out.
printTree() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
printTree() - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex
printUsage() - Static method in class htsjdk.tribble.example.CountRecords
  print usage information
printUsage() - Static method in class htsjdk.tribble.example.IndexToTable
  print usage information
printUsage() - Static method in class htsjdk.tribble.example.IndicesAreEqual
  print usage information
printUsage() - Static method in class htsjdk.tribble.example.ProfileIndexReading
  print usage information
PrintVariantsExample - Class in htsjdk.variant.example
  This is a example program showing how to use Feature readers and (optionally) writers.
processAlignment(SAMRecord) - Method in class htsjdk.samtools.BAMIndexer
  Record any index information for a given BAM record.
processBAIEntry(BAIEntry) - Method in class htsjdk.samtools.CRAMBAIIndexer
processContainer(Container) - Method in class htsjdk.samtools.cram.CRAIIndex
  Create index entries for a single container.
processContainer(Container) - Method in class htsjdk.samtools.CRAMCRAIIndexer
  Create index entries for a single container.
processContainer(Container, ValidationStringency) - Method in class htsjdk.samtools.CRAMBAIIndexer
  Index a container, any of mapped, unmapped and multiple references are allowed.
processContainer(Container, ValidationStringency) - Method in class htsjdk.samtools.CRAMCRAIIndexer
processContainer(Container, ValidationStringency) - Method in interface htsjdk.samtools.CRAMIndexer
  Create index entries for a single container.
ProcessExecutor - Class in htsjdk.samtools.util
  Utility class that will execute sub processes via Runtime.getRuntime().exec(...) and read off the output from stderr and stdout of the sub process.
ProcessExecutor() - Constructor for class htsjdk.samtools.util.ProcessExecutor
ProcessExecutor.ExitStatusAndOutput - Class in htsjdk.samtools.util
processFeature(BinningIndexBuilder.FeatureToBeIndexed) - Method in class htsjdk.samtools.BinningIndexBuilder
processIndex(AbstractBAMFileIndex, long) - Method in class htsjdk.samtools.BAMIndexMerger
processIndex(CRAIIndex, long) - Method in class htsjdk.samtools.cram.CRAIIndexMerger
processIndex(SBIIndex, long) - Method in class htsjdk.samtools.SBIIndexMerger
  Add an index for a part of the data file to the merged index.
processIndex(TabixIndex, long) - Method in class htsjdk.tribble.index.tabix.TabixIndexMerger
processIndex(T, long) - Method in class htsjdk.samtools.IndexMerger
  Process the next index and add to the merged index.
processNextBlock(byte[]) - Method in class htsjdk.samtools.util.BlockCompressedInputStream
  Decompress the next block from the input stream.
processRecord(long) - Method in class htsjdk.samtools.SBIIndexWriter
  Process a record for the index: the offset of every nth record will be written to the index.
processValidationError(SAMValidationError, ValidationStringency) - Static method in class htsjdk.samtools.SAMUtils
processValidationErrors(List, long, ValidationStringency) - Static method in class htsjdk.samtools.SAMUtils
  Handle a list of validation errors according to the validation stringency.
ProfileIndexReading - Class in htsjdk.tribble.example
ProfileIndexReading() - Constructor for class htsjdk.tribble.example.ProfileIndexReading
PROGRAM_GROUP_ID - Static variable in class htsjdk.samtools.ReservedTagConstants
PROGRAM_GROUP_ID_TAG - Static variable in class htsjdk.samtools.SAMProgramRecord
PROGRAM_GROUP_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
PROGRAM_NAME_TAG - Static variable in class htsjdk.samtools.SAMProgramRecord
PROGRAM_VERSION_TAG - Static variable in class htsjdk.samtools.SAMProgramRecord
ProgressLogger - Class in htsjdk.samtools.util
  Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records.
ProgressLogger(Log) - Constructor for class htsjdk.samtools.util.ProgressLogger
  Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.
ProgressLogger(Log, int) - Constructor for class htsjdk.samtools.util.ProgressLogger
  Construct a progress logger with the desired log and frequency and the verb "Processed".
ProgressLogger(Log, int, String) - Constructor for class htsjdk.samtools.util.ProgressLogger
  Construct a progress logger.
ProgressLogger(Log, int, String, String) - Constructor for class htsjdk.samtools.util.ProgressLogger
  Construct a progress logger.
ProgressLoggerInterface - Interface in htsjdk.samtools.util
  An interface defining the record() methods of the Picard-public ProgressLogger implementation.
PROPER_PAIR - Enum constant in enum class htsjdk.samtools.SAMFlag
properties - Variable in class htsjdk.tribble.index.TribbleIndexCreator
PROTOCOL_VERSION - Static variable in class htsjdk.samtools.util.htsget.HtsgetRequest
PSLTBL - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
PT - Enum constant in enum class htsjdk.samtools.SAMTag
PT - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
PU - Enum constant in enum class htsjdk.samtools.SAMTag
PU - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
push(double) - Method in class htsjdk.tribble.util.MathUtils.RunningStat
put(int, int, V) - Method in class htsjdk.samtools.util.IntervalTree
  Put a new interval into the tree (or update the value associated with an existing interval).
put(int, KEY, REC) - Method in class htsjdk.samtools.CoordinateSortedPairInfoMap
  Store the record with the given sequence index and key.
put(Interval, T) - Method in class htsjdk.samtools.util.IntervalTreeMap
putAttribute(String, Object) - Method in class htsjdk.variant.variantcontext.CommonInfo
putAttribute(String, Object, boolean) - Method in class htsjdk.variant.variantcontext.CommonInfo
putAttributes(Map) - Method in class htsjdk.variant.variantcontext.CommonInfo
putAttributes(Map) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells this builder to put this map of attributes into the resulting `VariantContext`.
putExternalEncoding(DataSeries, EncodingDescriptor, ExternalCompressor) - Method in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  Add an external encoding and its corresponding compressor to the encoding map.
putSymbol4x8(long, byte[], int[]) - Method in class htsjdk.samtools.cram.compression.rans.RANSEncodingSymbol
  byte[] variant for 4x8 encoding — writes backwards, decrementing posHolder[0].
putSymbolNx16(long, byte[], int[]) - Method in class htsjdk.samtools.cram.compression.rans.RANSEncodingSymbol
  byte[] variant for Nx16 encoding — writes backwards (decrementing posHolder[0]).
putTagBlockCompression(int, ExternalCompressor) - Method in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  Add an external compressor for a tag block

## Q

Q2 - Enum constant in enum class htsjdk.samtools.SAMTag
Q2 - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
QNAME - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
QQ_scores - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
QS_QualityScore - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
QT - Enum constant in enum class htsjdk.samtools.SAMTag
QT - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
QUAL - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
QUAL - Enum constant in enum class htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
QUALITY_HEADER - Static variable in class htsjdk.samtools.fastq.FastqConstants
QUALITY_HEADER_PARSE_SAM_TAGS - Static variable in class htsjdk.samtools.fastq.FastqEncoder
QUALITY_HEADER_TO_COMMENT_TAG - Static variable in class htsjdk.samtools.fastq.FastqEncoder
  Encodes the quality header into the comment tag (use in `FastqEncoder.asSAMRecord(FastqRecord, SAMFileHeader, BiConsumer)`.
QUALITY_NOT_STORED - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Base quality is not stored for the read.
QualityEncodingDetector - Class in htsjdk.samtools.util
  Utility for determining the type of quality encoding/format (see `FastqQualityFormat`) used in a SAM/BAM or Fastq.
QualityEncodingDetector() - Constructor for class htsjdk.samtools.util.QualityEncodingDetector
QualityEncodingDetector.FileContext - Enum Class in htsjdk.samtools.util
QualityHeader - Enum constant in enum class htsjdk.samtools.fastq.FastqReader.LineType
QualityLine - Enum constant in enum class htsjdk.samtools.fastq.FastqReader.LineType
QualityUtil - Class in htsjdk.samtools.util
  Utility class for working with quality scores and error probabilities.
QualityUtil() - Constructor for class htsjdk.samtools.util.QualityUtil
query - Enum constant in enum class htsjdk.samtools.SAMFileHeader.GroupOrder
query(int, int, int) - Method in class htsjdk.samtools.AbstractBAMFileIndex
query(int, int, int) - Method in class htsjdk.samtools.CSIIndex
query(int, int, int) - Method in class htsjdk.tribble.readers.TabixReader
  Get an iterator for an interval specified by the sequence id and begin and end coordinates
query(HtsInterval, HtsQueryRule) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator over all records from the underlying resource that match the query arguments
query(QueryInterval[], boolean) - Method in class htsjdk.samtools.BAMFileReader
  Prepare to iterate through the SAMRecords that match any of the given intervals.
query(QueryInterval[], boolean) - Method in class htsjdk.samtools.CRAMFileReader
query(QueryInterval[], boolean) - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Prepare to iterate through the SAMRecords that match the given interval.
query(QueryInterval[], boolean) - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
query(QueryInterval[], boolean) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
query(QueryInterval[], boolean) - Method in interface htsjdk.samtools.SamReader
  Iterate over records that match one of the given intervals.
query(Locatable) - Method in interface htsjdk.tribble.FeatureReader
  Query the reader for a particular interval corresponding to a contig and a 1-based closed
query(Locatable) - Method in interface htsjdk.variant.vcf.VCFReader
  Queries for records overlapping the `Locatable` specified.
query(String) - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
query(String) - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
query(String) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator over all records from the underlying resource that match the query string
query(String) - Method in class htsjdk.tribble.readers.TabixReader
query(String, int, int) - Method in interface htsjdk.tribble.FeatureReader
  Query the reader for a particular interval corresponding to a contig and a 1-based closed
query(String, int, int) - Method in class htsjdk.tribble.readers.TabixReader
  Get an iterator for an interval specified by the sequence id and begin and end coordinates
query(String, int, int) - Method in class htsjdk.tribble.TabixFeatureReader
  Return iterator over all features overlapping the given interval
query(String, int, int) - Method in class htsjdk.tribble.TribbleIndexedFeatureReader
  Return an iterator to iterate over features overlapping the specified interval
query(String, int, int) - Method in class htsjdk.variant.vcf.VCFFileReader
  Queries for records overlapping the region specified.
query(String, int, int) - Method in interface htsjdk.variant.vcf.VCFReader
  Queries for records overlapping the region specified.
query(String, int, int, boolean) - Method in class htsjdk.samtools.HtsgetBAMFileReader
query(String, int, int, boolean) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
query(String, int, int, boolean) - Method in interface htsjdk.samtools.SamReader
  Iterate over records that match the given interval.
query(String, long, long, HtsQueryRule) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator over all records from the underlying resource that match the query arguments
query(List, HtsQueryRule) - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
query(List, HtsQueryRule) - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
query(List, HtsQueryRule) - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
query(List, HtsQueryRule) - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
query(List, HtsQueryRule) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator over all records from the underlying resource that match the query arguments.
query(List, boolean) - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Query intervals directly by contig name instead of index relative to reference, to avoid repeated conversion between name and index representations
queryAlignmentStart(String, int) - Method in class htsjdk.samtools.BAMFileReader
  Prepare to iterate through the SAMRecords with the given alignment start.
queryAlignmentStart(String, int) - Method in class htsjdk.samtools.CRAMFileReader
queryAlignmentStart(String, int) - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Prepare to iterate through the SAMRecords with the given alignment start.
queryAlignmentStart(String, int) - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
queryAlignmentStart(String, int) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
queryAlignmentStart(String, int) - Method in interface htsjdk.samtools.SamReader
  Iterate over records that map to the given sequence and start at the given position.
queryBody() - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
queryContained(HtsInterval) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator over all records from the underlying resource that are contained within the query interval
queryContained(QueryInterval[]) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
queryContained(QueryInterval[]) - Method in interface htsjdk.samtools.SamReader
  Iterate over records that are contained in the given interval.
queryContained(String, int, int) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
queryContained(String, int, int) - Method in interface htsjdk.samtools.SamReader
  Iterate over records that are contained in the given interval.
queryContained(String, long, long) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Gte an iterator over all records from the underlying resource that match the query arguments
queryContained(List) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator over all records from the underlying resource that are contained within the query intervals
QueryInterval - Class in htsjdk.samtools
  Interval relative to a reference, for querying a BAM file.
QueryInterval(int, int, int) - Constructor for class htsjdk.samtools.QueryInterval
queryMate(SAMRecord) - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
queryMate(SAMRecord) - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
queryMate(SAMRecord) - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
queryMate(SAMRecord) - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0
queryMate(SAMRecord) - Method in interface htsjdk.beta.plugin.reads.ReadsDecoder
  Fetch the mate for the given read.
queryMate(SAMRecord) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
  Wraps the boilerplate code for querying a record's mate, which is common across many implementations.
queryMate(SAMRecord) - Method in interface htsjdk.samtools.SamReader
  Fetch the mate for the given read.
queryMate(R) - Method in interface htsjdk.beta.plugin.reads.ReadsQuery
  Fetch the mate for the given read.
queryname - Enum constant in enum class htsjdk.samtools.SAMFileHeader.SortOrder
queryOverlapping(HtsInterval) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator over all records from the underlying resource that overlap the query interval
queryOverlapping(QueryInterval[]) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
queryOverlapping(QueryInterval[]) - Method in interface htsjdk.samtools.SamReader
  Iterate over records that overlap any of the given intervals.
queryOverlapping(String, int, int) - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
queryOverlapping(String, int, int) - Method in interface htsjdk.samtools.SamReader
  Iterate over records that overlap the given interval.
queryOverlapping(String, long, long) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator over all records from the underlying resource that match the query arguments
queryOverlapping(List) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator over all records from the underlying resource that overlap the query intervals
queryStart(String, long) - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
queryStart(String, long) - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
queryStart(String, long) - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
queryStart(String, long) - Method in class htsjdk.beta.codecs.variants.vcf.VCFDecoder
queryStart(String, long) - Method in interface htsjdk.beta.plugin.interval.HtsQuery
  Get an iterator over all records from the underlying resource that overlap the start position
queryUnmapped() - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
queryUnmapped() - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoder
queryUnmapped() - Method in class htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
queryUnmapped() - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0
queryUnmapped() - Method in interface htsjdk.beta.plugin.reads.ReadsDecoder
  Get an iterator of unmapped reads.
queryUnmapped() - Method in interface htsjdk.beta.plugin.reads.ReadsQuery
  Get an iterator of unmapped reads.
queryUnmapped() - Method in class htsjdk.samtools.BAMFileReader
  Prepare to iterate through the SAMRecords that are unmapped and do not have a reference name or alignment start.
queryUnmapped() - Method in class htsjdk.samtools.CRAMFileReader
queryUnmapped() - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Prepare to iterate through the SAMRecords that are unmapped and do not have a reference name or alignment start.
queryUnmapped() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
queryUnmapped() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
queryUnmapped() - Method in interface htsjdk.samtools.SamReader
quit() - Method in class htsjdk.samtools.util.ftp.FTPClient
QX - Enum constant in enum class htsjdk.samtools.SAMTag
QX - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.

## R

R - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderLineCount
R2 - Enum constant in enum class htsjdk.samtools.SAMTag
R2 - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
RANDOM - Enum constant in enum class htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy
RANDOM_SEED - Static variable in class htsjdk.samtools.util.TestUtil
RangeCoder - Class in htsjdk.samtools.cram.compression.range
  Arithmetic range coder used by the CRAM 3.1 Range (adaptive arithmetic) codec and FQZComp quality score codec.
RangeCoder() - Constructor for class htsjdk.samtools.cram.compression.range.RangeCoder
rangeDecode(ByteBuffer, int, int) - Method in class htsjdk.samtools.cram.compression.range.RangeCoder
  Update the decoder state after a symbol has been decoded.
RangeDecode - Class in htsjdk.samtools.cram.compression.range
  Decoder for the CRAM 3.1 arithmetic (range) codec.
RangeDecode() - Constructor for class htsjdk.samtools.cram.compression.range.RangeDecode
rangeDecodeStart(ByteBuffer) - Method in class htsjdk.samtools.cram.compression.range.RangeCoder
  Initialize the decoder by reading the first 5 bytes of the compressed stream into the code register.
rangeEncode(int, int, int) - Method in class htsjdk.samtools.cram.compression.range.RangeCoder
  Encode a symbol by narrowing the range interval and emitting output bytes as needed.
RangeEncode - Class in htsjdk.samtools.cram.compression.range
  Encoder for the CRAM 3.1 arithmetic (range) codec.
RangeEncode() - Constructor for class htsjdk.samtools.cram.compression.range.RangeEncode
rangeEncodeEnd() - Method in class htsjdk.samtools.cram.compression.range.RangeCoder
  Flush the encoder state by emitting the final 5 bytes.
RangeExternalCompressor - Class in htsjdk.samtools.cram.compression.range
RangeExternalCompressor(int, RangeEncode, RangeDecode) - Constructor for class htsjdk.samtools.cram.compression.range.RangeExternalCompressor
RangeExternalCompressor(RangeEncode, RangeDecode) - Constructor for class htsjdk.samtools.cram.compression.range.RangeExternalCompressor
rangeGetFrequency(int) - Method in class htsjdk.samtools.cram.compression.range.RangeCoder
  Compute the scaled frequency for symbol lookup during decoding.
RangeParams - Class in htsjdk.samtools.cram.compression.range
RangeParams(int) - Constructor for class htsjdk.samtools.cram.compression.range.RangeParams
RangeParams.ORDER - Enum Class in htsjdk.samtools.cram.compression.range
RANS - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
RANS_4x8_COMPRESSED_BYTE_LENGTH - Static variable in class htsjdk.samtools.cram.compression.rans.Constants
RANS_4x8_LOWER_BOUND - Static variable in class htsjdk.samtools.cram.compression.rans.Constants
RANS_4x8_ORDER_BYTE_LENGTH - Static variable in class htsjdk.samtools.cram.compression.rans.Constants
RANS_4x8_PREFIX_BYTE_LENGTH - Static variable in class htsjdk.samtools.cram.compression.rans.Constants
RANS_4x8_RAW_BYTE_LENGTH - Static variable in class htsjdk.samtools.cram.compression.rans.Constants
RANS_Nx16_LOWER_BOUND - Static variable in class htsjdk.samtools.cram.compression.rans.Constants
RANS4x8Decode - Class in htsjdk.samtools.cram.compression.rans
  Decoder for the CRAM 3.0 rANS 4x8 codec.
RANS4x8Decode() - Constructor for class htsjdk.samtools.cram.compression.rans.RANS4x8Decode
RANS4x8Encode - Class in htsjdk.samtools.cram.compression.rans
  Encoder for the CRAM 3.0 rANS 4x8 codec.
RANS4x8Encode() - Constructor for class htsjdk.samtools.cram.compression.rans.RANS4x8Encode
RANS4x8ExternalCompressor - Class in htsjdk.samtools.cram.compression
  CRAM external compressor that uses the rANS 4x8 entropy coder (CRAM 3.0).
RANS4x8ExternalCompressor(int, RANS4x8Encode, RANS4x8Decode) - Constructor for class htsjdk.samtools.cram.compression.RANS4x8ExternalCompressor
  Create a rANS 4x8 compressor with the specified order (as an integer).
RANS4x8ExternalCompressor(RANS4x8Encode, RANS4x8Decode) - Constructor for class htsjdk.samtools.cram.compression.RANS4x8ExternalCompressor
  We use a shared RANS instance for all compressors.
RANS4x8ExternalCompressor(RANSParams.ORDER, RANS4x8Encode, RANS4x8Decode) - Constructor for class htsjdk.samtools.cram.compression.RANS4x8ExternalCompressor
  Create a rANS 4x8 compressor with the specified order.
RANS4x8Params - Class in htsjdk.samtools.cram.compression.rans
  Parameters for the rANS 4x8 codec: only the encoding order (0 or 1).
RANS4x8Params(RANSParams.ORDER) - Constructor for class htsjdk.samtools.cram.compression.rans.RANS4x8Params
RANSDecode - Class in htsjdk.samtools.cram.compression.rans
  Abstract base class for rANS decoders (both 4x8 and Nx16).
RANSDecode() - Constructor for class htsjdk.samtools.cram.compression.rans.RANSDecode
RANSDecodeRenormalize4x8(long, byte[], int[]) - Static method in class htsjdk.samtools.cram.compression.rans.Utils
  4x8 renormalization: reads 1 byte at a time from buf at posHolder[0] until state reaches lower bound.
RANSDecodeRenormalizeNx16(long, byte[], int[]) - Static method in class htsjdk.samtools.cram.compression.rans.Utils
  Nx16 renormalization: reads 2 LE bytes from buf at posHolder[0] if state is below lower bound.
RANSDecodingSymbol - Class in htsjdk.samtools.cram.compression.rans
  Holds the start and frequency for a single symbol in the rANS decoding table.
RANSDecodingSymbol() - Constructor for class htsjdk.samtools.cram.compression.rans.RANSDecodingSymbol
RANSEncode<T> - Class in htsjdk.samtools.cram.compression.rans
  Abstract base class for rANS encoders (both 4x8 and Nx16).
RANSEncode() - Constructor for class htsjdk.samtools.cram.compression.rans.RANSEncode
RANSEncodingSymbol - Class in htsjdk.samtools.cram.compression.rans
  Encoding state for a single symbol in the rANS codec.
RANSEncodingSymbol() - Constructor for class htsjdk.samtools.cram.compression.rans.RANSEncodingSymbol
RANSGetCumulativeFrequency(long, int) - Static method in class htsjdk.samtools.cram.compression.rans.Utils
  Extract the cumulative frequency from a rANS state by masking off the lower `scaleBits` bits.
RANSNx16 - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
RANSNx16Decode - Class in htsjdk.samtools.cram.compression.rans
  Decoder for the CRAM 3.1 rANSNx16 codec.
RANSNx16Decode() - Constructor for class htsjdk.samtools.cram.compression.rans.RANSNx16Decode
RANSNx16Encode - Class in htsjdk.samtools.cram.compression.rans
  Encoder for the CRAM 3.1 rANSNx16 codec.
RANSNx16Encode() - Constructor for class htsjdk.samtools.cram.compression.rans.RANSNx16Encode
RANSNx16ExternalCompressor - Class in htsjdk.samtools.cram.compression
  CRAM external compressor that uses the rANS Nx16 entropy coder (CRAM 3.1).
RANSNx16ExternalCompressor(int, RANSNx16Encode, RANSNx16Decode) - Constructor for class htsjdk.samtools.cram.compression.RANSNx16ExternalCompressor
  Create a rANS Nx16 compressor with the specified flag combination.
RANSNx16ExternalCompressor(RANSNx16Encode, RANSNx16Decode) - Constructor for class htsjdk.samtools.cram.compression.RANSNx16ExternalCompressor
  We use a shared RANS instance for all compressors.
RANSNx16Params - Class in htsjdk.samtools.cram.compression.rans
  Parameters for the rANS Nx16 codec.
RANSNx16Params(int) - Constructor for class htsjdk.samtools.cram.compression.rans.RANSNx16Params
RANSParams - Interface in htsjdk.samtools.cram.compression.rans
RANSParams.ORDER - Enum Class in htsjdk.samtools.cram.compression.rans
RAW - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
RAWExternalCompressor - Class in htsjdk.samtools.cram.compression
  Raw compressor that does no compression.
RAWExternalCompressor() - Constructor for class htsjdk.samtools.cram.compression.RAWExternalCompressor
read() - Method in class htsjdk.samtools.cram.encoding.core.BetaIntegerCodec
read() - Method in interface htsjdk.samtools.cram.encoding.CRAMCodec
  Read a single object from the stream
read() - Method in class htsjdk.samtools.cram.encoding.external.ExternalByteArrayCodec
read() - Method in class htsjdk.samtools.cram.io.CountingInputStream
read() - Method in class htsjdk.samtools.cram.io.CRAMByteReader
  Read one byte, returning it as an unsigned int (0-255), or -1 if at end of buffer.
read() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
read() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
read() - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
read() - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
read() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
read() - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
read() - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
read() - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
read() - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
read() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
  Reads the next byte of data from the input stream.
read() - Method in class htsjdk.samtools.util.CoordSpanInputSteam
read() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
read() - Method in class htsjdk.tribble.readers.LongLineBufferedReader
  Reads a single character.
read() - Method in class htsjdk.tribble.readers.PositionalBufferedStream
read(byte[]) - Method in class htsjdk.samtools.cram.io.CountingInputStream
read(byte[]) - Method in class htsjdk.samtools.cram.io.CRC32InputStream
read(byte[]) - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
read(byte[]) - Method in class htsjdk.samtools.util.BlockCompressedInputStream
  Reads some number of bytes from the input stream and stores them into the buffer array b.
read(byte[]) - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
read(byte[]) - Method in class htsjdk.tribble.readers.PositionalBufferedStream
read(byte[], int, int) - Method in class htsjdk.samtools.cram.io.CountingInputStream
read(byte[], int, int) - Method in class htsjdk.samtools.cram.io.CRAMByteReader
  Read up to `len` bytes into the destination array.
read(byte[], int, int) - Method in class htsjdk.samtools.cram.io.CRC32InputStream
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
read(byte[], int, int) - Method in class htsjdk.samtools.seekablestream.SeekableStream
read(byte[], int, int) - Method in class htsjdk.samtools.util.BlockCompressedInputStream
  Reads up to len bytes of data from the input stream into an array of bytes.
read(byte[], int, int) - Method in class htsjdk.samtools.util.CoordSpanInputSteam
read(byte[], int, int) - Method in class htsjdk.samtools.util.ftp.FTPStream
read(byte[], int, int) - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
read(byte[], int, int) - Method in class htsjdk.tribble.readers.PositionalBufferedStream
read(char[], int, int) - Method in class htsjdk.tribble.readers.LongLineBufferedReader
  Reads characters into a portion of an array.
read(int) - Method in class htsjdk.samtools.cram.encoding.core.BetaIntegerCodec
read(int) - Method in interface htsjdk.samtools.cram.encoding.CRAMCodec
  Read a array of specified length from the stream
read(int) - Method in class htsjdk.samtools.cram.encoding.external.ExternalByteArrayCodec
read(CRAMVersion, InputStream) - Static method in class htsjdk.samtools.cram.structure.block.Block
  Deserialize the Block from the `InputStream`.
read(BitInputStream) - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanCanoncialCodeGenerator
  Read a single huffman-encoded symbol from a stream
read(LittleEndianInputStream) - Method in class htsjdk.tribble.index.AbstractIndex
read(LittleEndianInputStream) - Method in interface htsjdk.tribble.index.ChrIndex
read(LittleEndianInputStream) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
read(LittleEndianInputStream) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
read(InputStream) - Method in enum class htsjdk.variant.bcf2.BCF2Type
  Read a value from in stream of this BCF2 type as an int [32 bit] collection of bits For intX and char values this is just the int / byte value of the underlying data represented as a 32 bit int For a char the result must be converted to a char by (char)(byte)(0x0F & value) For doubles it's necessary to convert subsequently this value to a double via Double.bitsToDouble()
read(Reader) - Method in class htsjdk.samtools.metrics.MetricsFile
  Reads the Metrics in from the given reader.
read(ByteBuffer) - Method in class htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel
READ_FAILS_VENDOR_QUALITY_CHECK - Enum constant in enum class htsjdk.samtools.SAMFlag
READ_GROUP_ID - Static variable in class htsjdk.samtools.ReservedTagConstants
READ_GROUP_ID_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
READ_GROUP_NOT_FOUND - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  A read group ID on a SAMRecord is not found in the header
READ_GROUP_SAMPLE_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
READ_PAIRED - Enum constant in enum class htsjdk.samtools.SAMFlag
READ_REVERSE_STRAND - Enum constant in enum class htsjdk.samtools.SAMFlag
READ_TIMEOUT - Static variable in class htsjdk.samtools.util.ftp.FTPClient
READ_UNMAPPED - Enum constant in enum class htsjdk.samtools.SAMFlag
ReadableSeekableStreamByteChannel - Class in htsjdk.samtools.seekablestream
  A class to wrap a `SeekableStream` in a read-only `SeekableByteChannel`.
ReadableSeekableStreamByteChannel(SeekableStream) - Constructor for class htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel
readActualHeader(LineIterator) - Method in class htsjdk.tribble.AsciiFeatureCodec
  Read and return the header, or null if there is no header.
readActualHeader(LineIterator) - Method in class htsjdk.tribble.bed.BEDCodec
  The BED codec doesn't retain the actual header, but we need to parse through it and advance to the beginning of the first feature.
readActualHeader(LineIterator) - Method in class htsjdk.tribble.IntervalList.IntervalListCodec
readActualHeader(LineIterator) - Method in class htsjdk.variant.vcf.VCF3Codec
readActualHeader(LineIterator) - Method in class htsjdk.variant.vcf.VCFCodec
  Reads all of the header from the provided iterator, but no reads no further.
readArray(ByteBuffer, int[], int) - Static method in class htsjdk.samtools.cram.compression.fqzcomp.FQZUtils
  Read a table from a two-level run-length encoded stream.
ReadBase - Class in htsjdk.samtools.cram.encoding.readfeatures
  A read feature representing a single base with associated quality score.
ReadBase(int, byte, byte) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
readBaseMatchesRefBaseWithAmbiguity(byte, byte) - Static method in class htsjdk.samtools.util.SequenceUtil
  Efficiently compare two IUPAC base codes, one coming from a read sequence and the other coming from a reference sequence, using the reference code as a 'pattern' that the read base must match.
readBases - Variable in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures.DecodeResult
readBCFVersion(InputStream) - Static method in class htsjdk.variant.bcf2.BCFVersion
  Return a new BCFVersion object describing the major and minor version of the BCF file in stream Note that stream must be at the very start of the file.
readBeans(File) - Static method in class htsjdk.samtools.metrics.MetricsFile
  Convenience method to read all the Metric beans from a metrics file.
readBit() - Method in interface htsjdk.samtools.cram.io.BitInputStream
  Reads a single bit from the stream.
readBit() - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream
readBits(int) - Method in interface htsjdk.samtools.cram.io.BitInputStream
  Read specified number of bits from the stream.
readBits(int) - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream
readBlockSize(InputStream) - Method in class htsjdk.variant.bcf2.BCF2Decoder
  Read the size of the next block from inputStream
readBoolean() - Method in class htsjdk.samtools.util.BinaryCodec
  Reads a boolean off the input stream, represented as a byte with value 1 or 0
readByte() - Method in class htsjdk.samtools.util.BinaryCodec
readByte() - Method in class htsjdk.tribble.util.LittleEndianInputStream
readByte(InputStream) - Static method in class htsjdk.variant.bcf2.BCF2Utils
readBytes(byte[]) - Method in class htsjdk.samtools.AbstractBAMFileIndex
readBytes(byte[]) - Method in class htsjdk.samtools.util.BinaryCodec
  Read a byte array from the input stream.
readBytes(byte[], int, int) - Method in class htsjdk.samtools.util.BinaryCodec
  Read a byte array from the input stream
readBytesOrFewer(byte[], int, int) - Method in class htsjdk.samtools.util.BinaryCodec
  Reads a byte array from the input stream.
readChunks(int, List) - Method in class htsjdk.samtools.AbstractBAMFileIndex
readCramHeader(InputStream) - Static method in class htsjdk.samtools.cram.build.CramIO
  Read CRAM header from the given `InputStream`.
readCRAMRecord(long, int) - Method in class htsjdk.samtools.cram.encoding.reader.CramRecordReader
  Read a CRAMCompressionRecord, using this reader's data series readers.
readDouble() - Method in class htsjdk.samtools.util.BinaryCodec
  Reads a double off the input stream
readDouble() - Method in class htsjdk.tribble.util.LittleEndianInputStream
ReaderImplementation() - Constructor for class htsjdk.samtools.SamReader.ReaderImplementation
ReadFeature - Interface in htsjdk.samtools.cram.encoding.readfeatures
  An interface to capture data in read coordinates.
readFloat() - Method in class htsjdk.samtools.util.BinaryCodec
  Reads a float off the input stream
readFloat() - Method in class htsjdk.tribble.util.LittleEndianInputStream
readFromPosition(ByteBuffer, long) - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
readFromPosition(ByteBuffer, long) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Reads a sequence of bytes from this channel into the given buffer, starting at the given file position.
readFully(byte[]) - Method in class htsjdk.samtools.seekablestream.SeekableStream
  Read enough bytes to fill the input buffer.
readFully(int) - Method in class htsjdk.samtools.cram.io.CRAMByteReader
  Read exactly `len` bytes, returning them as a new array.
readFully(InputStream) - Static method in class htsjdk.samtools.cram.io.InputStreamUtils
  Read the `InputStream` until the end into a new byte array.
readFully(InputStream) - Static method in class htsjdk.samtools.util.IOUtil
  Reads everything from an input stream as characters and returns a single String.
readFully(InputStream, byte[], int, int) - Static method in class htsjdk.samtools.cram.io.InputStreamUtils
  Read the specified number of bytes from the `InputStream` into the byte array starting from the specified position.
readFully(InputStream, int) - Static method in class htsjdk.samtools.cram.io.InputStreamUtils
  Read the specified number of bytes from the `InputStream` into a new byte array.
readHeader(BinaryCodec, ValidationStringency, String) - Static method in class htsjdk.samtools.BAMFileReader
  Reads the header of a BAM file from a stream
readHeader(LineIterator) - Method in class htsjdk.tribble.AsciiFeatureCodec
readHeader(LineIterator) - Method in class htsjdk.tribble.gff.Gff3Codec
readHeader(PositionalBufferedStream) - Method in class htsjdk.tribble.example.ExampleBinaryCodec
readHeader(PositionalBufferedStream) - Method in class htsjdk.variant.bcf2.BCF2Codec
readHeader(SOURCE) - Method in interface htsjdk.tribble.FeatureCodec
  Read and return the header, or null if there is no header.
readHeaderFrom(SeekableStream) - Static method in class htsjdk.variant.utils.VCFHeaderReader
  Read a VCF header from a stream that may be a VCF file (possibly gzip or block compressed) or a BCF file.
readHeaderLine(String) - Method in class htsjdk.tribble.bed.BEDCodec
readHeaders(File) - Static method in class htsjdk.samtools.metrics.MetricsFile
  Method to read the header from a metrics file.
readIndex(InputStream) - Static method in class htsjdk.samtools.CRAMCRAIIndexer
  Read an input stream containing a .crai index and return a CRAIIndex object.
readInt() - Method in class htsjdk.samtools.util.BinaryCodec
  Read an int off the input stream
readInt() - Method in class htsjdk.tribble.util.LittleEndianInputStream
readInt(InputStream) - Static method in class htsjdk.tribble.readers.TabixReader
readInt32(byte[]) - Static method in class htsjdk.samtools.cram.io.CramInt
  Read unsigned little-endian 4 byte integer from an array of bytes.
readInt32(InputStream) - Static method in class htsjdk.samtools.cram.io.CramInt
  Read unsigned little-endian 4 byte integer from an `InputStream`.
readInt32(ByteBuffer) - Static method in class htsjdk.samtools.cram.io.CramInt
  Read unsigned little-endian 4 byte integer from an `ByteBuffer`.
readInteger() - Method in class htsjdk.samtools.AbstractBAMFileIndex
readLengthAndString(boolean) - Method in class htsjdk.samtools.util.BinaryCodec
  Read an int length, and then a String of that length
readLine() - Method in class htsjdk.samtools.util.BlockCompressedInputStream
  Reads a whole line.
readLine() - Method in class htsjdk.samtools.util.BufferedLineReader
  Read a line and remove the line terminator
readLine() - Method in interface htsjdk.samtools.util.LineReader
  Read a line and remove the line terminator
readLine() - Method in class htsjdk.tribble.readers.AsciiLineReader
  Same as `AsciiLineReader.readLine(PositionalBufferedStream)` but uses the stream provided in the constructor
readLine() - Method in interface htsjdk.tribble.readers.LineReader
readLine() - Method in class htsjdk.tribble.readers.LongLineBufferedReader
  Reads a line of text.
readLine() - Method in class htsjdk.tribble.readers.SynchronousLineReader
readLine() - Method in class htsjdk.tribble.readers.TabixIteratorLineReader
readLine() - Method in class htsjdk.tribble.readers.TabixReader
  Read one line from the data file.
readLine(PositionalBufferedStream) - Method in class htsjdk.tribble.readers.AsciiLineReader
  Deprecated.
  8/8/2017 use `AsciiLineReader.from(InputStream)` to create a new AsciiLineReader and `AsciiLineReader.readLine()`
readLine(InputStream) - Static method in class htsjdk.tribble.readers.TabixReader
readLines(File) - Static method in class htsjdk.samtools.util.IOUtil
  Returns an iterator over the lines in a text file.
readLong() - Method in class htsjdk.samtools.AbstractBAMFileIndex
readLong() - Method in class htsjdk.samtools.util.BinaryCodec
  Reads a long off the input stream
readLong() - Method in class htsjdk.tribble.util.LittleEndianInputStream
readLong(InputStream) - Static method in class htsjdk.tribble.readers.TabixReader
readLongBits(int) - Method in interface htsjdk.samtools.cram.io.BitInputStream
  Read specified number of bits from the stream.
readLongBits(int) - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream
ReadNameFilter - Class in htsjdk.samtools.filter
  Filter by a set of specified readnames
ReadNameFilter(File, boolean) - Constructor for class htsjdk.samtools.filter.ReadNameFilter
ReadNameFilter(Set, boolean) - Constructor for class htsjdk.samtools.filter.ReadNameFilter
readNextBlock(int, InputStream) - Method in class htsjdk.variant.bcf2.BCF2Decoder
  Reads the next record from input stream and prepare this decoder to decode values from it
readNullTerminatedString() - Method in class htsjdk.samtools.util.BinaryCodec
  Read ASCII bytes from the input stream until a null byte is read
readNullTerminatedString(BinaryCodec) - Static method in class htsjdk.samtools.util.StringUtil
readSAMFileHeaderContainer(CRAMVersion, InputStream, String) - Static method in class htsjdk.samtools.cram.structure.Container
  Reads the special container that contains the SAMFileHeader from a CRAM stream, and returns just the SAMFileHeader (we don't want to hand out the container since its not a real container in that it has no compression header block, slices, etc).
ReadsBundle<T> - Class in htsjdk.beta.plugin.reads
  A class for creating a `Bundle` for reads and reads-related resources.
ReadsBundle(Collection) - Constructor for class htsjdk.beta.plugin.reads.ReadsBundle
  Create a `ReadsBundle` using the resources in an existing bundle.
ReadsBundle(T) - Constructor for class htsjdk.beta.plugin.reads.ReadsBundle
  Create a `ReadsBundle` containing only a reads resource.
ReadsBundle(T, T) - Constructor for class htsjdk.beta.plugin.reads.ReadsBundle
  Create a `ReadsBundle` containing only reads and an index.
ReadsCodec - Interface in htsjdk.beta.plugin.reads
  Base class for all `HtsContentType.ALIGNED_READS` codecs.
ReadsCodecUtils - Class in htsjdk.beta.codecs.reads
  InternalAPI Utilities for use by reads encoder/decoder implementations.
ReadsCodecUtils() - Constructor for class htsjdk.beta.codecs.reads.ReadsCodecUtils
ReadsDecoder - Interface in htsjdk.beta.plugin.reads
  Base class for all `HtsContentType.ALIGNED_READS` decoders.
ReadsDecoderOptions - Class in htsjdk.beta.plugin.reads
  Reads decoder options (shared/common).
ReadsDecoderOptions() - Constructor for class htsjdk.beta.plugin.reads.ReadsDecoderOptions
readsDecoderOptionsToSamReaderFactory(ReadsDecoderOptions, SamReaderFactory) - Static method in class htsjdk.beta.codecs.reads.ReadsCodecUtils
  InternalAPII Propagate options from a `ReadsDecoderOptions` to a SamReaderFactory.
ReadsEncoder - Interface in htsjdk.beta.plugin.reads
  Base interface for `HtsContentType.ALIGNED_READS` encoders.
ReadsEncoderOptions - Class in htsjdk.beta.plugin.reads
  General reads encoder options.
ReadsEncoderOptions() - Constructor for class htsjdk.beta.plugin.reads.ReadsEncoderOptions
ReadsFormats - Class in htsjdk.beta.plugin.reads
  Class with string constants for known formats supported by reads codecs.
ReadsFormats() - Constructor for class htsjdk.beta.plugin.reads.ReadsFormats
readShort() - Method in class htsjdk.samtools.util.BinaryCodec
readShort() - Method in class htsjdk.tribble.util.LittleEndianInputStream
readSingleValue(byte, ByteBuffer, ValidationStringency) - Static method in class htsjdk.samtools.cram.structure.ReadTag
  Read a single tag value from a ByteBuffer in BAM binary format.
readsInQueue() - Method in class htsjdk.samtools.util.SAMRecordPrefetchingIterator
ReadsQuery<R> - Interface in htsjdk.beta.plugin.reads
  Query methods specific to `ReadsDecoder`s.
ReadsResolver - Class in htsjdk.beta.plugin.registry
  Class with methods for resolving inputs and outputs to reads encoders and decoders.
ReadsResolver() - Constructor for class htsjdk.beta.plugin.registry.ReadsResolver
  Create a ReadsResolver.
readString() - Method in class htsjdk.tribble.util.LittleEndianInputStream
  Read a null terminated byte array and return result as a string
readString(int) - Method in class htsjdk.samtools.util.BinaryCodec
  Read a string off the input stream, as ASCII bytes
ReadTag - Class in htsjdk.samtools.cram.structure
  CRAM counterpart of `SAMTag`.
ReadTag(int, byte[], ValidationStringency) - Constructor for class htsjdk.samtools.cram.structure.ReadTag
  Construct a ReadTag from a 3-byte tag ID and raw value bytes.
ReadTag(TagKeyCache.TagKeyInfo, byte[], ValidationStringency) - Constructor for class htsjdk.samtools.cram.structure.ReadTag
  Construct a ReadTag using pre-cached key metadata to avoid repeated String allocation.
readTags(byte[], int, int, ValidationStringency) - Static method in class htsjdk.samtools.BinaryTagCodec
  Convert tags from little-endian disk representation to in-memory representation.
readToEndOfOutputBufferOrEoln(byte[], int) - Method in class htsjdk.samtools.util.FastLineReader
  Read from input until input is exhausted, EOLN is seen, or output buffer is filled
readTypeDescriptor() - Method in class htsjdk.variant.bcf2.BCF2Decoder
readUByte() - Method in class htsjdk.samtools.util.BinaryCodec
  Reads an 8-bit unsigned byte from the input stream.
readUInt() - Method in class htsjdk.samtools.util.BinaryCodec
  Reads a 32-bit unsigned int from the input stream.
readUint7(byte[], int[]) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Read uint7 from byte[] at posHolder[0], advancing posHolder[0].
readUint7(ByteBuffer) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Read an unsigned integer using 7-bit variable-length encoding (uint7).
readUnsignedITF8(byte[]) - Static method in class htsjdk.samtools.cram.io.ITF8
  Reads an unsigned (32 bit) integer from an array of bytes.
readUnsignedITF8(CRAMByteReader) - Static method in class htsjdk.samtools.cram.io.ITF8
  Reads an unsigned ITF8 integer from a `CRAMByteReader`.
readUnsignedITF8(InputStream) - Static method in class htsjdk.samtools.cram.io.ITF8
  Reads an unsigned (32 bit) integer from an `InputStream`.
readUnsignedITF8(ByteBuffer) - Static method in class htsjdk.samtools.cram.io.ITF8
  Reads an unsigned (32 bit) integer from a `ByteBuffer`.
readUnsignedLTF8(CRAMByteReader) - Static method in class htsjdk.samtools.cram.io.LTF8
  Reads an unsigned LTF8 long from a `CRAMByteReader`.
readUnsignedLTF8(InputStream) - Static method in class htsjdk.samtools.cram.io.LTF8
  Reads an unsigned long value from the input stream.
readUShort() - Method in class htsjdk.samtools.util.BinaryCodec
  Reads a 16-bit unsigned short from the input stream.
ready() - Method in class htsjdk.tribble.readers.LongLineBufferedReader
  Tells whether this stream is ready to be read.
reapplyOptions(SamReader) - Method in class htsjdk.samtools.SamReaderFactory
  Reapplies any changed options to the reader *
record - Variable in class htsjdk.samtools.util.AbstractRecordAndOffset
  A SAMRecord aligned to reference position
record(SAMRecord) - Method in class htsjdk.samtools.util.AbstractProgressLogger
  Records that a given record has been processed and triggers logging if necessary.
record(SAMRecord) - Method in interface htsjdk.samtools.util.ProgressLoggerInterface
record(SAMRecord...) - Method in class htsjdk.samtools.util.AbstractProgressLogger
  Records multiple SAMRecords and triggers logging if necessary.
record(SAMRecord...) - Method in interface htsjdk.samtools.util.ProgressLoggerInterface
record(String, int) - Method in class htsjdk.samtools.util.AbstractProgressLogger
record(String, int) - Method in interface htsjdk.samtools.util.ProgressLoggerInterface
record(String, int, String) - Method in class htsjdk.samtools.util.AbstractProgressLogger
RECORD_MISSING_READ_GROUP - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  A SAMRecord is found with no read group id
RECORD_OUT_OF_ORDER - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  the record is out of order
recordAcceptedRecord() - Method in class htsjdk.samtools.DownsamplingIterator
  Method for subclasses to record a specific record as being accepted.
recordAcceptedRecords(long) - Method in class htsjdk.samtools.DownsamplingIterator
  Record one or more records as having been discarded.
RecordAndOffset(SAMRecord, int) - Constructor for class htsjdk.samtools.util.SamLocusIterator.RecordAndOffset
RecordAndOffset(SAMRecord, int, AbstractRecordAndOffset.AlignmentType) - Constructor for class htsjdk.samtools.util.SamLocusIterator.RecordAndOffset
recordDiscardedRecord() - Method in class htsjdk.samtools.DownsamplingIterator
  Method for subclasses to record a record as being discarded.
recordDiscardRecords(long) - Method in class htsjdk.samtools.DownsamplingIterator
  Record one or more records as having been discarded.
recordMapsEntirelyBeyondEndOfReference(SAMRecord) - Static method in class htsjdk.samtools.SAMUtils
  Tests if the provided record is mapped entirely beyond the end of the reference (i.e., the alignment start is greater than the length of the sequence to which the record is mapped).
recursiveDelete(File) - Static method in class htsjdk.samtools.util.TestUtil
  Deprecated.
  Since 3/19, prefer `IOUtil.recursiveDelete(Path)`
recursiveDelete(Path) - Static method in class htsjdk.samtools.util.IOUtil
  Delete a directory and all files in it.
REF - Enum constant in enum class htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
REF_A - Static variable in interface htsjdk.variant.variantcontext.Allele
REF_C - Static variable in interface htsjdk.variant.variantcontext.Allele
REF_G - Static variable in interface htsjdk.variant.variantcontext.Allele
REF_N - Static variable in interface htsjdk.variant.variantcontext.Allele
REF_SEQ_TOO_LONG_FOR_BAI - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  One or more reference sequences in the dictionary are too long for BAI indexing.
REF_T - Static variable in interface htsjdk.variant.variantcontext.Allele
reference - Enum constant in enum class htsjdk.samtools.SAMFileHeader.GroupOrder
REFERENCE_FASTA - Static variable in class htsjdk.samtools.Defaults
  The reference FASTA file.
REFERENCE_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
referenceBundleFromFastaPath(IOPath, Function) - Static method in class htsjdk.beta.plugin.registry.HaploidReferenceResolver
  Create a reference bundle given only a fasta path, including an index and a dictionary file if they are present and located in the same directory as the fasta.
ReferenceContext - Class in htsjdk.samtools.cram.ref
  ReferenceContext defines how a given Slice or Container relates to a reference sequence.
ReferenceContext(int) - Constructor for class htsjdk.samtools.cram.ref.ReferenceContext
  Create a ReferenceContext from a value that is either a valid sequence ID, or a reference context sentinel value: 0 or greater for single reference -1 for unmapped-unplaced -2 for multiple reference
ReferenceContextType - Enum Class in htsjdk.samtools.cram.ref
  Is this `ReferenceContext` Single Reference, Multiple Reference, or Unmapped? Section 8.5 of the CRAM spec defines the following values for the Slice Header sequence ID field: -2: Multiple Reference Slice -1: Unmapped-Unplaced Slice Any positive integer (including zero): Single Reference Slice
referenceIndex - Variable in class htsjdk.samtools.QueryInterval
  Index of reference sequence, based on the sequence dictionary of the BAM file being queried.
referenceSequence(File) - Method in class htsjdk.samtools.SamReaderFactory
  Sets the specified reference sequence *
referenceSequence(Path) - Method in class htsjdk.samtools.SamReaderFactory
  Sets the specified reference sequence.
ReferenceSequence - Class in htsjdk.samtools.reference
  Wrapper around a reference sequence that has been read from a reference file.
ReferenceSequence(String, int, byte[]) - Constructor for class htsjdk.samtools.reference.ReferenceSequence
  creates a fully formed ReferenceSequence
ReferenceSequenceFile - Interface in htsjdk.samtools.reference
  An interface for working with files of reference sequences regardless of the file format being used.
ReferenceSequenceFileFactory - Class in htsjdk.samtools.reference
  Factory class for creating ReferenceSequenceFile instances for reading reference sequences store in various formats.
ReferenceSequenceFileFactory() - Constructor for class htsjdk.samtools.reference.ReferenceSequenceFileFactory
ReferenceSequenceFileWalker - Class in htsjdk.samtools.reference
  Manages a ReferenceSequenceFile.
ReferenceSequenceFileWalker(ReferenceSequenceFile) - Constructor for class htsjdk.samtools.reference.ReferenceSequenceFileWalker
ReferenceSequenceFileWalker(File) - Constructor for class htsjdk.samtools.reference.ReferenceSequenceFileWalker
ReferenceSequenceFileWalker(Path) - Constructor for class htsjdk.samtools.reference.ReferenceSequenceFileWalker
ReferenceSequenceMask - Interface in htsjdk.samtools.util
  Interface for specifying loci of interest for genotype calling and other operations.
referenceSource() - Method in class htsjdk.samtools.SamReaderFactory
referenceSource(CRAMReferenceSource) - Method in class htsjdk.samtools.SamReaderFactory
  Sets the specified reference sequence *
ReferenceSource - Class in htsjdk.samtools.cram.ref
  Used to represent a CRAM reference, the backing source for which can either be a file or the EBI ENA reference service.
ReferenceSource(ReferenceSequenceFile) - Constructor for class htsjdk.samtools.cram.ref.ReferenceSource
ReferenceSource(File) - Constructor for class htsjdk.samtools.cram.ref.ReferenceSource
ReferenceSource(Path) - Constructor for class htsjdk.samtools.cram.ref.ReferenceSource
RefSkip - Class in htsjdk.samtools.cram.encoding.readfeatures
  A read feature representing a reference skip similar to `CigarOperator.N`.
RefSkip(int, int) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
regexPattern - Variable in enum class htsjdk.tribble.gff.Gff3Codec.Gff3Directive
regionToBin(int, int) - Static method in class htsjdk.samtools.GenomicIndexUtil
  calculate the bin given an alignment in [beg,end) Described in "The Human Genome Browser at UCSC.
regionToBin(int, int, int, int) - Static method in class htsjdk.samtools.GenomicIndexUtil
  calculate the bin given an alignment in [beg,end) Described in "The Human Genome Browser at UCSC.
regionToBins(int, int) - Method in class htsjdk.samtools.AbstractBAMFileIndex
  Deprecated.
  Use `GenomicIndexUtil.regionToBins(int, int)` instead. Get candidate bins for the specified region
regionToBins(int, int) - Static method in class htsjdk.samtools.GenomicIndexUtil
  Get candidate bins for the specified region
regionToBins(int, int, int, int) - Static method in class htsjdk.samtools.GenomicIndexUtil
  Get candidate bins for the specified region
registerCodec(C) - Method in class htsjdk.beta.plugin.registry.HtsCodecResolver
  Register a codec of type `C`.
registerCodec(HtsCodec) - Method in class htsjdk.beta.plugin.registry.HtsCodecRegistry
  Add a codec to the registry.
reheaderBamFile(SAMFileHeader, File, File, boolean, boolean) - Static method in class htsjdk.samtools.BamFileIoUtils
  Support File input types for backward compatibility.
reheaderBamFile(SAMFileHeader, Path, Path) - Static method in class htsjdk.samtools.BamFileIoUtils
reheaderBamFile(SAMFileHeader, Path, Path, boolean, boolean) - Static method in class htsjdk.samtools.BamFileIoUtils
  Copy a BAM file but replacing the header
RelativeIso8601Date - Class in htsjdk.samtools.util
  Like `Iso8601Date`, but also comes in a "lazy now" flavor.
RelativeIso8601Date(String) - Constructor for class htsjdk.samtools.util.RelativeIso8601Date
RelativeIso8601Date(Date) - Constructor for class htsjdk.samtools.util.RelativeIso8601Date
remappedSampleName - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
  If non-null, we will replace the sample name read from the VCF header with this sample name.
RemoteURLHelper - Class in htsjdk.tribble.util
  Implementation of URLHelper designed for remote resources.
RemoteURLHelper(URL) - Constructor for class htsjdk.tribble.util.RemoteURLHelper
remove() - Method in class htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator
remove() - Method in class htsjdk.samtools.cram.build.CramContainerIterator
remove() - Method in class htsjdk.samtools.cram.build.CramSpanContainerIterator
remove() - Method in class htsjdk.samtools.CRAMIterator
remove() - Method in class htsjdk.samtools.DownsamplingIterator
  Not supported.
remove() - Method in class htsjdk.samtools.DuplicateSetIterator
remove() - Method in class htsjdk.samtools.fastq.FastqReader
remove() - Method in class htsjdk.samtools.filter.FilteringSamIterator
  Required method for Iterator API.
remove() - Method in class htsjdk.samtools.MergingSamRecordIterator
  Unsupported operation.
remove() - Method in class htsjdk.samtools.SamReader.AssertingIterator
remove() - Method in class htsjdk.samtools.util.AbstractIterator
remove() - Method in class htsjdk.samtools.util.AbstractLocusIterator
remove() - Method in class htsjdk.samtools.util.DelegatingIterator
remove() - Method in class htsjdk.samtools.util.DiskBackedQueue
remove() - Method in class htsjdk.samtools.util.IntervalTree.FwdIterator
remove() - Method in class htsjdk.samtools.util.IntervalTree.OverlapIterator
remove() - Method in class htsjdk.samtools.util.IntervalTree.RevIterator
remove() - Method in class htsjdk.samtools.util.IntervalTree.ValuesIterator
remove() - Method in class htsjdk.samtools.util.IterableOnceIterator
  Operation not supported.
remove() - Method in class htsjdk.samtools.util.MergingIterator
  Unsupported.
remove() - Method in class htsjdk.samtools.util.PeekableIterator
  Unsupported Operation.
remove() - Method in class htsjdk.samtools.util.PeekIterator
  Unsupported
remove() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer
  Removes the next record from this buffer
remove() - Method in class htsjdk.tribble.readers.AsciiLineReaderIterator
remove() - Method in class htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator
  Required method for Iterator API.
remove(int) - Method in class htsjdk.variant.variantcontext.GenotypesContext
  Note that remove requires us to invalidate our sample -> index cache.
remove(int, int) - Method in class htsjdk.samtools.util.IntervalTree
  Remove an interval from the tree.
remove(int, KEY) - Method in class htsjdk.samtools.CoordinateSortedPairInfoMap
remove(short) - Method in class htsjdk.samtools.SAMBinaryTagAndValue
  Removes a tag from the list and returns the new head of the list/sub-list.
remove(Interval) - Method in class htsjdk.samtools.util.IntervalTreeMap
remove(Object) - Method in class htsjdk.samtools.util.DiskBackedQueue
  Not supported.
remove(Object) - Method in class htsjdk.samtools.util.IntervalTreeMap
remove(Object) - Method in class htsjdk.variant.variantcontext.GenotypesContext
  See for important warning `GenotypesContext.remove(int)`
remove(Key) - Method in class htsjdk.samtools.util.ResourceLimitedMap
removeAll(Collection) - Method in class htsjdk.samtools.util.DiskBackedQueue
  Not supported.
removeAll(Collection) - Method in class htsjdk.variant.variantcontext.GenotypesContext
removeAttribute(String) - Method in class htsjdk.variant.variantcontext.CommonInfo
removeContentsAfter(SAMFileSpan) - Method in class htsjdk.samtools.BAMFileSpan
  Creates a new file span by removing all chunks after the given file span ends.
removeContentsBefore(SAMFileSpan) - Method in class htsjdk.samtools.BAMFileSpan
  Creates a new file span by removing all chunks before the given file span starts.
removeContentsBefore(SAMFileSpan) - Method in interface htsjdk.samtools.SAMFileSpan
  Remove all pointers in this file span before the given file span starts.
removeTransientAttribute(Object) - Method in class htsjdk.samtools.SAMRecord
  Removes a transient attribute if it is stored, and returns the stored value.
rename(FastaSequenceIndexEntry, String) - Method in class htsjdk.samtools.reference.FastaSequenceIndex
  Renames the existing index entry to the new index entry with the specified name.
repairStandardHeaderLines(VCFHeader) - Static method in class htsjdk.variant.vcf.VCFStandardHeaderLines
  Walks over the VCF header and repairs the standard VCF header lines in it, returning a freshly allocated `VCFHeader` with standard VCF header lines repaired as necessary.
repeatCharNTimes(char, int) - Static method in class htsjdk.samtools.util.StringUtil
replace(Genotype) - Method in class htsjdk.variant.variantcontext.GenotypesContext
  Replaces the genotype in this context -- note for efficiency reasons we do not add the genotype if it's not present.
replaceExtension(IOPath, String, Function) - Static method in class htsjdk.beta.io.IOPathUtils
  Takes an IOPath and returns a new IOPath object that keeps the same basename as the original but with a new extension.
RESERVED - Enum constant in enum class htsjdk.samtools.cram.structure.block.BlockContentType
RESERVED_MRNM_SEQUENCE_NAME - Static variable in class htsjdk.samtools.SAMSequenceRecord
  Deprecated.
RESERVED_RNEXT_SEQUENCE_NAME - Static variable in class htsjdk.samtools.SAMSequenceRecord
  This is not a valid sequence name, because it is reserved in the RNEXT field of SAM text format to mean "same reference as RNAME field."
ReservedTagConstants - Class in htsjdk.samtools
  Constants for tags used in our SAM/BAM files
ReservedTagConstants() - Constructor for class htsjdk.samtools.ReservedTagConstants
reset() - Method in class htsjdk.samtools.cram.compression.range.ByteModel
  Reset all frequencies to 1 and restore natural symbol ordering.
reset() - Method in class htsjdk.samtools.cram.compression.rans.RANSEncodingSymbol
  Reset all encoding parameters to zero.
reset() - Method in class htsjdk.samtools.cram.io.CountingInputStream
reset() - Method in class htsjdk.samtools.cram.io.CRAMByteWriter
  Reset the writer to empty, reusing the existing buffer.
reset() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
reset() - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream
reset() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Reset the iterator over the index.
reset() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Reset the iterator over the index.
reset() - Method in class htsjdk.samtools.reference.FastaSequenceFile
reset() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
  Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file.
reset() - Method in class htsjdk.samtools.seekablestream.SeekableStream
  Seeks to the marked position if set; otherwise to the beginning of the stream.
reset() - Method in class htsjdk.samtools.util.AbstractProgressLogger
  Resets the start time to now and the number of records to zero.
reset() - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
reset() - Method in interface htsjdk.samtools.util.ProgressLoggerInterface
reset() - Method in class htsjdk.samtools.util.StopWatch
reset() - Method in class htsjdk.tribble.readers.LongLineBufferedReader
  Resets the stream to the most recent mark.
reset(boolean) - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  Reset all of the builder attributes to their defaults.
resetDecoderState() - Method in class htsjdk.samtools.cram.compression.rans.RANSDecode
  Reset only the decoder rows that were used in the previous decode operation.
resetFailedIntervalsBelowThresholdCounter() - Method in class htsjdk.samtools.liftover.LiftOver
  Resets the internal counter that tracks intervals that failed liftover due to insufficient intersection length
resetStatistics() - Method in class htsjdk.samtools.DownsamplingIterator
  Resets the statistics for records seen/accepted/discarded.
resetToDefaultInstance() - Static method in class htsjdk.samtools.CustomReaderFactory
resolveForDecoding(Bundle) - Method in class htsjdk.beta.plugin.registry.HtsCodecResolver
  Inspect a bundle and find a codec that can decode the primary resource.
resolveForEncoding(Bundle) - Method in class htsjdk.beta.plugin.registry.HtsCodecResolver
  Inspect a bundle and find a codec that can encode to the primary resource.
resolveForEncoding(Bundle, HtsVersion) - Method in class htsjdk.beta.plugin.registry.HtsCodecResolver
  Inspect a bundle and find a codec that can encode to the primary resource using the format version requested.
resolveForFormat(String) - Method in class htsjdk.beta.plugin.registry.HtsCodecResolver
  Get a list of codecs that claim to support file format `format` string
resolveFormatAndVersion(String, HtsVersion) - Method in class htsjdk.beta.plugin.registry.HtsCodecResolver
  Get a list of codecs that claim to support version `formatVersion` of file format `format`.
resolveIndex(IOPath) - Static method in class htsjdk.beta.plugin.reads.ReadsBundle
  Find the companion index for a reads source, and create a new `ReadsBundle` containing the reads and the companion index, if one can be found.
resolveIndex(IOPath) - Static method in class htsjdk.beta.plugin.variants.VariantsBundle
  Find the companion index for a variants source, and create a new `VariantsBundle` containing the variants and the companion index, if one can be found.
resolveIndex(T, Function) - Static method in class htsjdk.beta.plugin.reads.ReadsBundle
  Find the companion index for a reads source, and create a new `ReadsBundle` containing the reads and the companion index, if one can be found.
resolveIndex(T, Function) - Static method in class htsjdk.beta.plugin.variants.VariantsBundle
  Attempts to find the companion index for a variants source based on commonly used file extensions, and create a new `VariantsBundle` containing the variants and the companion index, if one can be found.
resolveIndexFromName(String, SAMFileHeader, boolean) - Static method in class htsjdk.samtools.SAMRecord
  Static method that resolves and returns the reference index corresponding to a given reference name.
resolveIndexNameForBgzipFile(Path) - Static method in class htsjdk.samtools.util.GZIIndex
  Gets the default index path for the bgzip file.
resolveNameFromIndex(int, SAMFileHeader) - Static method in class htsjdk.samtools.SAMRecord
  Static method that resolves and returns the reference name corresponding to a given reference index.
resolveQualityScores() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Resolve the quality scores for this CRAM record based on preserved scores, read features and flags.
resourceAvailable(URL) - Static method in class htsjdk.samtools.util.ftp.FTPUtils
resourceAvailable(URL) - Static method in class htsjdk.samtools.util.HttpUtils
resourceExists(String) - Static method in class htsjdk.tribble.util.ParsingUtils
ResourceLimitedMap<Key,Value> - Class in htsjdk.samtools.util
  LRU collection class for managing objects that place some resource burden such that not too many of them can existing in the VM at one time, but they can be reconstructed ias necessary.
ResourceLimitedMap(int, ResourceLimitedMapFunctor) - Constructor for class htsjdk.samtools.util.ResourceLimitedMap
  Create LRU cache
ResourceLimitedMapFunctor<Key,Value> - Interface in htsjdk.samtools.util
  c.f.
restoreBasesAndTags(List, boolean, int, int, CRAMReferenceRegion, SubstitutionMatrix, boolean) - Static method in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
  Fused single-pass decode: restore read bases from the reference + read features, build the CIGAR, and optionally compute the MD string and NM edit distance, all in a single iteration through the features list.
restoreMateInfo() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Restore mate information by walking the linked list of segments starting from this record, setting mate fields on each segment pair, and computing template length.
restoreReadBases(CRAMReferenceRegion, SubstitutionMatrix) - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Restore the actual read bases for this record.
restoreReadBases(List, boolean, int, int, CRAMReferenceRegion, SubstitutionMatrix) - Static method in class htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
  Get the read bases for a CRAMRecord given a set of read feaures and a reference region.
retainAll(Collection) - Method in class htsjdk.samtools.util.DiskBackedQueue
  Not supported.
retainAll(Collection) - Method in class htsjdk.variant.variantcontext.GenotypesContext
retr(String) - Method in class htsjdk.samtools.util.ftp.FTPClient
reverse(byte[], int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
reverse(List) - Static method in class htsjdk.variant.utils.GeneralUtils
REVERSE - Static variable in enum class htsjdk.tribble.annotation.Strand
  Common alias for the `Strand.NEGATIVE` strand.
reverseComplement() - Method in class htsjdk.samtools.SAMRecord
  Reverse-complement bases and reverse quality scores along with known optional attributes that need the same treatment.
reverseComplement(boolean) - Method in class htsjdk.samtools.SAMRecord
  Reverse-complement bases and reverse quality scores along with known optional attributes that need the same treatment.
reverseComplement(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
  Reverses and complements the bases in place.
reverseComplement(byte[], int, int) - Static method in class htsjdk.samtools.util.SequenceUtil
reverseComplement(String) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculate the reverse complement of the specified sequence (Stolen from Reseq)
reverseComplement(Collection, Collection, boolean) - Method in class htsjdk.samtools.SAMRecord
  Reverse complement bases and reverse quality scores.
reverseComplementSqArray(byte[]) - Static method in class htsjdk.samtools.SQTagUtil
  Deprecated.
  Reverses and complements the sqValues in place.
reverseIterator() - Method in class htsjdk.samtools.util.IntervalTree
  Return an iterator over the entire tree that returns intervals in reverse order.
reverseIterator(int, int) - Method in class htsjdk.samtools.util.IntervalTree
  Return an iterator over all intervals less than or equal to the specified interval, in reverse order.
reverseQualities(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
  Reverses the quals in place.
reverseQualities(ByteBuffer, int, FQZState) - Static method in class htsjdk.samtools.cram.compression.fqzcomp.FQZCompDecode
  Reverse quality score arrays for records that were flagged for reversal during encoding.
reverseString(String) - Static method in class htsjdk.samtools.util.StringUtil
  Reverse the given string.
RevIterator(IntervalTree.Node) - Constructor for class htsjdk.samtools.util.IntervalTree.RevIterator
RF - Enum constant in enum class htsjdk.samtools.SamPairUtil.PairOrientation
RG - Enum constant in enum class htsjdk.samtools.SAMTag
RG - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
RG_ReadGroup - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
RI_RefId - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
RL_ReadLength - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
RLE_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.range.RangeParams
RLE_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
rmAttribute(String) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Removes key if present in the attributes
rmAttributes(List) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Removes list of keys if present in the attributes
RMS_BASE_QUALITY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
RMS_MAPPING_QUALITY_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
RN_ReadName - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
RNAME - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
RNEXT - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
RS_RefSkip - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
RT - Enum constant in enum class htsjdk.samtools.SAMTag
  Deprecated.
  use BC instead, for backwards compatibilty only
RT - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
run(String[]) - Static method in class htsjdk.samtools.cram.CramComparison
  Run the comparison and return the exit code (0=match, 1=mismatch, 2=error).
RunningStat() - Constructor for class htsjdk.tribble.util.MathUtils.RunningStat
RuntimeEOFException - Exception Class in htsjdk.samtools.util
  Thrown by various codecs to indicate EOF without having to clutter the API with throws clauses
RuntimeEOFException() - Constructor for exception class htsjdk.samtools.util.RuntimeEOFException
RuntimeEOFException(String) - Constructor for exception class htsjdk.samtools.util.RuntimeEOFException
RuntimeEOFException(String, Throwable) - Constructor for exception class htsjdk.samtools.util.RuntimeEOFException
RuntimeEOFException(Throwable) - Constructor for exception class htsjdk.samtools.util.RuntimeEOFException
RuntimeIOException - Exception Class in htsjdk.samtools.util
  Thrown by various IO classes to indicate IOException without having to clutter the API with throws clauses
RuntimeIOException() - Constructor for exception class htsjdk.samtools.util.RuntimeIOException
RuntimeIOException(String) - Constructor for exception class htsjdk.samtools.util.RuntimeIOException
RuntimeIOException(String, Throwable) - Constructor for exception class htsjdk.samtools.util.RuntimeIOException
RuntimeIOException(Throwable) - Constructor for exception class htsjdk.samtools.util.RuntimeIOException
RuntimeScriptException - Exception Class in htsjdk.samtools.util
  Thrown by classes handling script engines like the javascript-based filters for SAM/VCF
RuntimeScriptException() - Constructor for exception class htsjdk.samtools.util.RuntimeScriptException
RuntimeScriptException(String) - Constructor for exception class htsjdk.samtools.util.RuntimeScriptException
RuntimeScriptException(String, Throwable) - Constructor for exception class htsjdk.samtools.util.RuntimeScriptException
RuntimeScriptException(Throwable) - Constructor for exception class htsjdk.samtools.util.RuntimeScriptException
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMCodecV1_0
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.reads.cram.CRAMCodec
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMCodecV1_0
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFCodecV3_2
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFCodecV3_3
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFCodecV4_0
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFCodecV4_1
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFCodecV4_2
runVersionUpgrade(HtsVersion, HtsVersion) - Method in class htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFCodecV4_3
runVersionUpgrade(HtsVersion, HtsVersion) - Method in interface htsjdk.beta.plugin.Upgradeable
runWithIndex(File, FeatureCodec, int) - Static method in class htsjdk.tribble.example.CountRecords
RX - Enum constant in enum class htsjdk.samtools.SAMTag
RX - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.

## S

S - Enum constant in enum class htsjdk.samtools.CigarOperator
  Soft clip.
S1 - Enum constant in enum class htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS
S2 - Enum constant in enum class htsjdk.samtools.SAMTag
  Deprecated.
  for backwards compatibility only
S2 - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
S5 - Enum constant in enum class htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS
SA - Enum constant in enum class htsjdk.samtools.SAMTag
SA - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
SAM - Enum constant in enum class htsjdk.samtools.util.QualityEncodingDetector.FileContext
SAM - Static variable in class htsjdk.beta.plugin.reads.ReadsFormats
  SAM file format.
SAM - Static variable in class htsjdk.samtools.util.FileExtensions
  extensions for alignment files SAM, BAM, CRAM.
SAM - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
SAM_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  since June 2019 Use `FileExtensions.SAM` instead.
SAM_FLAG_FIELD_FORMAT - Static variable in class htsjdk.samtools.Defaults
  The output format of the flag field when writing SAM text.
SAM_FLAGS - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
SAM_TYPE - Static variable in class htsjdk.samtools.SamReader.Type
SAMBinaryTagAndUnsignedArrayValue - Class in htsjdk.samtools
  Simple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because signedness cannot be determined by introspection of value.
SAMBinaryTagAndUnsignedArrayValue(short, Object) - Constructor for class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue
SAMBinaryTagAndValue - Class in htsjdk.samtools
  Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.
SAMBinaryTagAndValue(short, Object) - Constructor for class htsjdk.samtools.SAMBinaryTagAndValue
SAMCodec - Class in htsjdk.beta.codecs.reads.sam
  InternalAPI Base class for `BundleResourceType.FMT_READS_SAM` codecs.
SAMCodec() - Constructor for class htsjdk.beta.codecs.reads.sam.SAMCodec
SAMCodecV1_0 - Class in htsjdk.beta.codecs.reads.sam.samV1_0
  SAM v1.0 codec.
SAMCodecV1_0() - Constructor for class htsjdk.beta.codecs.reads.sam.samV1_0.SAMCodecV1_0
SamConstants - Class in htsjdk.samtools.util
  A set of constants defined in the sam-spec (https://github.com/samtools/hts-specs) that need to be referenced in code.
SAMDecoder - Class in htsjdk.beta.codecs.reads.sam
  InternalAPI Base class for `BundleResourceType.FMT_READS_SAM` decoders.
SAMDecoder(Bundle, ReadsDecoderOptions) - Constructor for class htsjdk.beta.codecs.reads.sam.SAMDecoder
  Create a SAM decoder for the given input bundle.
SAMDecoderV1_0 - Class in htsjdk.beta.codecs.reads.sam.samV1_0
  SAM v1.0 decoder.
SAMDecoderV1_0(Bundle, ReadsDecoderOptions) - Constructor for class htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0
  Create a V1.0 SAM decoder for the given input bundle.
sameGenotype(Genotype) - Method in class htsjdk.variant.variantcontext.Genotype
sameGenotype(Genotype, boolean) - Method in class htsjdk.variant.variantcontext.Genotype
sameLineTypeAndName(VCFCompoundHeaderLine) - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
SAMEncoder - Class in htsjdk.beta.codecs.reads.sam
  InternalAPI Base class for `BundleResourceType.FMT_READS_SAM` encoders.
SAMEncoder(Bundle, ReadsEncoderOptions) - Constructor for class htsjdk.beta.codecs.reads.sam.SAMEncoder
  InternalAPI Create a SAM encoder for the given output bundle.
SAMEncoderV1_0 - Class in htsjdk.beta.codecs.reads.sam.samV1_0
  SAM v1.0 encoder.
SAMEncoderV1_0(Bundle, ReadsEncoderOptions) - Constructor for class htsjdk.beta.codecs.reads.sam.samV1_0.SAMEncoderV1_0
  Create a V1.0 SAM encoder for the given output bundle.
SAMException - Exception Class in htsjdk.samtools
SAMException() - Constructor for exception class htsjdk.samtools.SAMException
SAMException(String) - Constructor for exception class htsjdk.samtools.SAMException
SAMException(String, Throwable) - Constructor for exception class htsjdk.samtools.SAMException
SAMException(Throwable) - Constructor for exception class htsjdk.samtools.SAMException
SAMFileHeader - Class in htsjdk.samtools
  Header information from a SAM or BAM file.
SAMFileHeader() - Constructor for class htsjdk.samtools.SAMFileHeader
SAMFileHeader(SAMSequenceDictionary) - Constructor for class htsjdk.samtools.SAMFileHeader
  Constructor that initializes the sequence dictionary with the provided one.
SAMFileHeader.GroupOrder - Enum Class in htsjdk.samtools
SAMFileHeader.PgIdGenerator - Class in htsjdk.samtools
  Little class to generate program group IDs
SAMFileHeader.SortOrder - Enum Class in htsjdk.samtools
  Ways in which a SAM or BAM may be sorted.
SamFileHeaderMerger - Class in htsjdk.samtools
  Merges SAMFileHeaders that have the same sequences into a single merged header object while providing read group translation for cases where read groups clash across input headers.
SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean) - Constructor for class htsjdk.samtools.SamFileHeaderMerger
  Create SAMFileHeader with additional information..
SamFileHeaderMerger(Collection, SAMFileHeader.SortOrder) - Constructor for class htsjdk.samtools.SamFileHeaderMerger
  Deprecated.
  replaced by `SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)`
SamFileHeaderMerger(Collection, SAMFileHeader.SortOrder, boolean) - Constructor for class htsjdk.samtools.SamFileHeaderMerger
  Deprecated.
  replaced by `SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)`
SamFiles - Class in htsjdk.samtools
SamFiles() - Constructor for class htsjdk.samtools.SamFiles
SAMFileSource - Class in htsjdk.samtools
  Represents the origin of a SAM record.
SAMFileSource(SamReader, SAMFileSpan) - Constructor for class htsjdk.samtools.SAMFileSource
  Create a new SAMFileSource with the given reader and file pointer.
SAMFileSpan - Interface in htsjdk.samtools
  A interface representing a collection of (possibly) discontinuous segments in the BAM file, possibly representing the results of an index query.
SamFileValidator - Class in htsjdk.samtools
  Validates SAM files as follows: checks sam file header for sequence dictionary checks sam file header for read groups for each sam record reports error detected by SAMRecord.isValid() validates NM (nucleotide differences) exists and matches reality validates mate fields agree with data in the mate record
SamFileValidator(PrintWriter, int) - Constructor for class htsjdk.samtools.SamFileValidator
SamFileValidator.ValidationMetrics - Class in htsjdk.samtools
SAMFileWriter - Interface in htsjdk.samtools
  Interface for SAMText and BAM file writers.
SAMFileWriterFactory - Class in htsjdk.samtools
  Create a writer for writing SAM, BAM, or CRAM files.
SAMFileWriterFactory() - Constructor for class htsjdk.samtools.SAMFileWriterFactory
  simple constructor
SAMFileWriterFactory(SAMFileWriterFactory) - Constructor for class htsjdk.samtools.SAMFileWriterFactory
  copy constructor
SAMFileWriterImpl - Class in htsjdk.samtools
  Base class for implementing SAM writer with any underlying format.
SAMFileWriterImpl() - Constructor for class htsjdk.samtools.SAMFileWriterImpl
SAMFlag - Enum Class in htsjdk.samtools
  SAM flags as enum, to be used in GUI, menu, etc...
SamFlagField - Enum Class in htsjdk.samtools
  This determines how flag fields are represented in the SAM file.
SAMFormatException - Exception Class in htsjdk.samtools
  Thrown when a SAM file being read or decoded (text or binary) looks bad.
SAMFormatException() - Constructor for exception class htsjdk.samtools.SAMFormatException
SAMFormatException(String) - Constructor for exception class htsjdk.samtools.SAMFormatException
SAMFormatException(String, Throwable) - Constructor for exception class htsjdk.samtools.SAMFormatException
SAMFormatException(Throwable) - Constructor for exception class htsjdk.samtools.SAMFormatException
SAMHeaderRecordComparator<T> - Class in htsjdk.samtools
  Provides ordering based on SAM header records' attribute values.
SAMHeaderRecordComparator(String...) - Constructor for class htsjdk.samtools.SAMHeaderRecordComparator
samHeaderToByteArray(SAMFileHeader) - Static method in class htsjdk.samtools.cram.build.CramIO
SamIndexes - Enum Class in htsjdk.samtools
  A helper class to read BAI and CRAI indexes.
SamInputResource - Class in htsjdk.samtools
  Describes a SAM-like resource, including its data (where the records are), and optionally an index.
SAMJDK_PREFIX - Static variable in class htsjdk.samtools.Defaults
SAMLineParser - Class in htsjdk.samtools
  This class enables creation of a SAMRecord object from a String in SAM text format.
SAMLineParser(SAMFileHeader) - Constructor for class htsjdk.samtools.SAMLineParser
  Public constructor.
SAMLineParser(SAMFileHeader, SamReader, File) - Constructor for class htsjdk.samtools.SAMLineParser
  Public constructor.
SAMLineParser(SAMRecordFactory, ValidationStringency, SAMFileHeader, SamReader, File) - Constructor for class htsjdk.samtools.SAMLineParser
  Public constructor.
SAMLocusAndReference(SamLocusIterator.LocusInfo, byte) - Constructor for class htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference
SamLocusAndReferenceIterator - Class in htsjdk.samtools.reference
  Iterator that traverses a SAM File and a ReferenceFile, accumulating information on a per-locus basis.
SamLocusAndReferenceIterator(ReferenceSequenceFileWalker, SamLocusIterator) - Constructor for class htsjdk.samtools.reference.SamLocusAndReferenceIterator
  Constructor that takes a `ReferenceSequenceFile` and a `SamLocusIterator`.
SamLocusAndReferenceIterator.SAMLocusAndReference - Class in htsjdk.samtools.reference
  Small class to hold together a `SamLocusIterator.LocusInfo` and the reference base over that locus.
SamLocusIterator - Class in htsjdk.samtools.util
  Iterator that traverses a SAM File, accumulating information on a per-locus basis.
SamLocusIterator(SamReader) - Constructor for class htsjdk.samtools.util.SamLocusIterator
  Prepare to iterate through the given SAM records, skipping non-primary alignments.
SamLocusIterator(SamReader, IntervalList) - Constructor for class htsjdk.samtools.util.SamLocusIterator
  Prepare to iterate through the given SAM records, skipping non-primary alignments.
SamLocusIterator(SamReader, IntervalList, boolean) - Constructor for class htsjdk.samtools.util.SamLocusIterator
  Prepare to iterate through the given SAM records, skipping non-primary alignments
SamLocusIterator.LocusInfo - Class in htsjdk.samtools.util
  The unit of iteration.
SamLocusIterator.RecordAndOffset - Class in htsjdk.samtools.util
  Implementation of `AbstractRecordAndOffset` class for `SamLocusIterator`.
SamPairUtil - Class in htsjdk.samtools
  Utility methods for pairs of SAMRecords
SamPairUtil() - Constructor for class htsjdk.samtools.SamPairUtil
SamPairUtil.PairOrientation - Enum Class in htsjdk.samtools
  The possible orientations of paired reads.
SamPairUtil.SetMateInfoIterator - Class in htsjdk.samtools
  A class to iterate through SAMRecords and set mate information on the given records, and optionally set the mate cigar tag (true by default).
SAMPLE_HEADER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
SAMPLE_HEADER_OFFSET - Static variable in class htsjdk.variant.vcf.VCFConstants
SAMPLE_HEADER_START - Static variable in class htsjdk.variant.vcf.VCFConstants
SAMPLE_NUMBER_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
sampleNamesInOrder - Variable in class htsjdk.variant.variantcontext.GenotypesContext
  sampleNamesInOrder a list of sample names, one for each genotype in genotypes, sorted in alphabetical order
sampleNameToOffset - Variable in class htsjdk.variant.variantcontext.GenotypesContext
  a map optimized for efficient lookup.
samplesWereAlreadySorted() - Method in class htsjdk.variant.vcf.VCFHeader
  were the input samples sorted originally?
SAMProgramRecord - Class in htsjdk.samtools
  In-memory representation of @PG SAM header record.
SAMProgramRecord(String) - Constructor for class htsjdk.samtools.SAMProgramRecord
SAMProgramRecord(String, SAMProgramRecord) - Constructor for class htsjdk.samtools.SAMProgramRecord
SamReader - Interface in htsjdk.samtools
  Describes functionality for objects that produce `SAMRecord`s and associated information.
SamReader.AssertingIterator - Class in htsjdk.samtools
SamReader.Indexing - Interface in htsjdk.samtools
  Facet for index-related operations.
SamReader.PrimitiveSamReader - Interface in htsjdk.samtools
  The minimal subset of functionality needed for a `SAMRecord` data source.
SamReader.PrimitiveSamReaderToSamReaderAdapter - Class in htsjdk.samtools
  Decorator for a `SamReader.PrimitiveSamReader` that expands its functionality into a `SamReader`, given the backing `SamInputResource`.
SamReader.ReaderImplementation - Class in htsjdk.samtools
  Internal interface for SAM/BAM/CRAM file reader implementations, as distinct from non-file-based readers.
SamReader.Type - Class in htsjdk.samtools
  Describes a type of SAM file.
SamReaderFactory - Class in htsjdk.samtools
  Describes the functionality for producing `SamReader`, and offers a handful of static generators.
SamReaderFactory() - Constructor for class htsjdk.samtools.SamReaderFactory
SamReaderFactory.Option - Enum Class in htsjdk.samtools
  A collection of binary `SamReaderFactory` options.
SAMReadGroupRecord - Class in htsjdk.samtools
  Header information about a read group.
SAMReadGroupRecord(String) - Constructor for class htsjdk.samtools.SAMReadGroupRecord
SAMReadGroupRecord(String, SAMReadGroupRecord) - Constructor for class htsjdk.samtools.SAMReadGroupRecord
SAMReadGroupRecord.PlatformValue - Enum Class in htsjdk.samtools
SAMRecord - Class in htsjdk.samtools
  Java binding for a SAM file record.
SAMRecord(SAMFileHeader) - Constructor for class htsjdk.samtools.SAMRecord
SAMRecord.SAMTagAndValue - Class in htsjdk.samtools
  Tag name and value of an attribute, for getAttributes() method.
SAMRecordComparator - Interface in htsjdk.samtools
  Interface for comparators that define the various SAM sort orders.
SAMRecordCoordinateComparator - Class in htsjdk.samtools
  Comparator for sorting SAMRecords by coordinate.
SAMRecordCoordinateComparator() - Constructor for class htsjdk.samtools.SAMRecordCoordinateComparator
SAMRecordDuplicateComparator - Class in htsjdk.samtools
  Compares records based on if they should be considered PCR Duplicates (see MarkDuplicates).
SAMRecordDuplicateComparator() - Constructor for class htsjdk.samtools.SAMRecordDuplicateComparator
SAMRecordDuplicateComparator(SAMFileHeader) - Constructor for class htsjdk.samtools.SAMRecordDuplicateComparator
SAMRecordDuplicateComparator(List) - Constructor for class htsjdk.samtools.SAMRecordDuplicateComparator
  Deprecated.
samRecordFactory(SAMRecordFactory) - Method in class htsjdk.samtools.SamReaderFactory
  Set this factory's `SAMRecordFactory` to the provided one, then returns itself.
SAMRecordFactory - Interface in htsjdk.samtools
  Factory interface which allows plugging in of different classes for generating instances of SAMRecord and BAMRecord when reading from SAM/BAM files.
SamRecordFilter - Interface in htsjdk.samtools.filter
  API for filtering SAMRecords $Id$
SamRecordIntervalIteratorFactory - Class in htsjdk.samtools.util
  Create an iterator over a `SamReader` that only returns reads that overlap one of the intervals in an interval list.
SamRecordIntervalIteratorFactory() - Constructor for class htsjdk.samtools.util.SamRecordIntervalIteratorFactory
SAMRecordIterator - Interface in htsjdk.samtools
  A general interface that adds functionality to a CloseableIterator of SAMRecords.
SAMRecordPrefetchingIterator - Class in htsjdk.samtools.util
  Iterator that uses a dedicated background thread to prefetch SAMRecords, reading ahead by a set number of bases to improve throughput.
SAMRecordPrefetchingIterator(CloseableIterator, int) - Constructor for class htsjdk.samtools.util.SAMRecordPrefetchingIterator
  Creates a new iterator that traverses the given iterator on a background thread
SAMRecordQueryHashComparator - Class in htsjdk.samtools
  SAMRecord comparator that provides an ordering based on a hash of the queryname.
SAMRecordQueryHashComparator() - Constructor for class htsjdk.samtools.SAMRecordQueryHashComparator
SAMRecordQueryNameComparator - Class in htsjdk.samtools
  Comparator for "queryname" ordering of SAMRecords.
SAMRecordQueryNameComparator() - Constructor for class htsjdk.samtools.SAMRecordQueryNameComparator
SAMRecordSetBuilder - Class in htsjdk.samtools
  Factory class for creating SAMRecords for testing purposes.
SAMRecordSetBuilder() - Constructor for class htsjdk.samtools.SAMRecordSetBuilder
  Constructs a new SAMRecordSetBuilder with all the data needed to keep the records sorted in coordinate order.
SAMRecordSetBuilder(boolean, SAMFileHeader.SortOrder) - Constructor for class htsjdk.samtools.SAMRecordSetBuilder
  Construct a new SAMRecordSetBuilder.
SAMRecordSetBuilder(boolean, SAMFileHeader.SortOrder, boolean) - Constructor for class htsjdk.samtools.SAMRecordSetBuilder
SAMRecordSetBuilder(boolean, SAMFileHeader.SortOrder, boolean, int) - Constructor for class htsjdk.samtools.SAMRecordSetBuilder
SAMRecordSetBuilder(boolean, SAMFileHeader.SortOrder, boolean, int, DuplicateScoringStrategy.ScoringStrategy) - Constructor for class htsjdk.samtools.SAMRecordSetBuilder
SamRecordTrackingBuffer<T> - Class in htsjdk.samtools.util
  This class stores SAMRecords for return.
SamRecordTrackingBuffer(int, int, List, SAMFileHeader, Class) - Constructor for class htsjdk.samtools.util.SamRecordTrackingBuffer
SamRecordWithOrdinal - Class in htsjdk.samtools.util
  A little class to store the unique index associated with this record.
SamRecordWithOrdinal() - Constructor for class htsjdk.samtools.util.SamRecordWithOrdinal
SamRecordWithOrdinal(SAMRecord, long) - Constructor for class htsjdk.samtools.util.SamRecordWithOrdinal
SAMSequenceDictionary - Class in htsjdk.samtools
  Collection of SAMSequenceRecords.
SAMSequenceDictionary() - Constructor for class htsjdk.samtools.SAMSequenceDictionary
SAMSequenceDictionary(List) - Constructor for class htsjdk.samtools.SAMSequenceDictionary
SAMSequenceDictionaryCodec - Class in htsjdk.samtools
  "On the fly" codec SAMSequenceDictionaryCodec.
SAMSequenceDictionaryCodec(Writer) - Constructor for class htsjdk.samtools.SAMSequenceDictionaryCodec
SAMSequenceDictionaryExtractor - Class in htsjdk.variant.utils
  Small class for loading a SAMSequenceDictionary from a file
SAMSequenceDictionaryExtractor() - Constructor for class htsjdk.variant.utils.SAMSequenceDictionaryExtractor
SAMSequenceRecord - Class in htsjdk.samtools
  Header information about a reference sequence.
SAMSequenceRecord(String) - Constructor for class htsjdk.samtools.SAMSequenceRecord
  Deprecated.
  Use `SAMSequenceRecord(String, int)` instead. sequenceLength is required for the object to be considered valid.
SAMSequenceRecord(String, int) - Constructor for class htsjdk.samtools.SAMSequenceRecord
SAMSortOrderChecker - Class in htsjdk.samtools
  Encapsulates simple check for SAMRecord order.
SAMSortOrderChecker(SAMFileHeader.SortOrder) - Constructor for class htsjdk.samtools.SAMSortOrderChecker
SamStreams - Class in htsjdk.samtools
  Utilities related to processing of `InputStream`s encoding SAM data
SamStreams() - Constructor for class htsjdk.samtools.SamStreams
SAMTag - Enum Class in htsjdk.samtools
  The standard tags for a SAM record that are defined in the SAM spec.
SAMTagAndValue(String, Object) - Constructor for class htsjdk.samtools.SAMRecord.SAMTagAndValue
SAMTagUtil - Class in htsjdk.samtools
  Deprecated.
  as of 11/2018, the functions in this class have been absorbed by the `SAMTag` enum.
SAMTagUtil() - Constructor for class htsjdk.samtools.SAMTagUtil
  Deprecated.
SAMTestUtil - Class in htsjdk.samtools
  Misc methods for SAM-related unit tests.
SAMTestUtil() - Constructor for class htsjdk.samtools.SAMTestUtil
SAMTestUtil.SanityCheckFailedException - Exception Class in htsjdk.samtools
  Indicates that a required sanity-check condition was not met.
SAMTextHeaderCodec - Class in htsjdk.samtools
  Parser for a SAM text header, and a generator of SAM text header.
SAMTextHeaderCodec() - Constructor for class htsjdk.samtools.SAMTextHeaderCodec
SAMTextWriter - Class in htsjdk.samtools
  Writer for text-format SAM files.
SAMTextWriter(File) - Constructor for class htsjdk.samtools.SAMTextWriter
  Constructs a SAMTextWriter that writes to a File.
SAMTextWriter(File, SamFlagField) - Constructor for class htsjdk.samtools.SAMTextWriter
  Constructs a SAMTextWriter that writes to a File.
SAMTextWriter(OutputStream) - Constructor for class htsjdk.samtools.SAMTextWriter
  Constructs a SAMTextWriter that writes to an OutputStream.
SAMTextWriter(OutputStream, SamFlagField) - Constructor for class htsjdk.samtools.SAMTextWriter
  Constructs a SAMTextWriter that writes to an OutputStream.
SAMTextWriter(Writer) - Constructor for class htsjdk.samtools.SAMTextWriter
  Constructs a SAMTextWriter that outputs to a Writer.
SAMTextWriter(Writer, SamFlagField) - Constructor for class htsjdk.samtools.SAMTextWriter
  Constructs a SAMTextWriter that outputs to a Writer.
SAMUtils - Class in htsjdk.samtools
  Utilty methods.
SAMUtils() - Constructor for class htsjdk.samtools.SAMUtils
SAMValidationError - Class in htsjdk.samtools
  Class that encapsulates a validation error message as well as a type code so that errors can be aggregated by type.
SAMValidationError(SAMValidationError.Type, String, String) - Constructor for class htsjdk.samtools.SAMValidationError
  Construct a SAMValidationError with unknown record number.
SAMValidationError(SAMValidationError.Type, String, String, long) - Constructor for class htsjdk.samtools.SAMValidationError
  Construct a SAMValidationError with possibly-known record number.
SAMValidationError.Severity - Enum Class in htsjdk.samtools
SAMValidationError.Type - Enum Class in htsjdk.samtools
sanityCheckDictionaryAgainstIndex(String, SAMSequenceDictionary, FastaSequenceIndex) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Do some basic checking to make sure the dictionary and the index match.
sanityCheckDictionaryAgainstIndex(String, SAMSequenceDictionary, FastaSequenceIndex) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Do some basic checking to make sure the dictionary and the index match.
SanityCheckFailedException(String) - Constructor for exception class htsjdk.samtools.SAMTestUtil.SanityCheckFailedException
SBI - Static variable in class htsjdk.samtools.util.FileExtensions
SBIIndex - Class in htsjdk.samtools
  SBI is an index into BGZF-compressed data files, which has an entry for the file position of the start of every nth record.
SBIIndex(SBIIndex.Header, long[]) - Constructor for class htsjdk.samtools.SBIIndex
  Create an in-memory SBI with the given virtual offsets.
SBIIndex.Header - Class in htsjdk.samtools
SBIIndexMerger - Class in htsjdk.samtools
  Merges SBI files for parts of a file that have been concatenated.
SBIIndexMerger(OutputStream, long) - Constructor for class htsjdk.samtools.SBIIndexMerger
  Prepare to merge SBI indexes.
SBIIndexWriter - Class in htsjdk.samtools
  Writes SBI files as understood by `SBIIndex`.
SBIIndexWriter(OutputStream) - Constructor for class htsjdk.samtools.SBIIndexWriter
  Prepare to write an SBI index with the default granularity.
SBIIndexWriter(OutputStream, long) - Constructor for class htsjdk.samtools.SBIIndexWriter
  Prepare to write an SBI index.
SC_SoftClip - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
scanDir(File, String) - Method in class htsjdk.utils.ClassFinder
  Scans a directory on the filesystem for classes.
scanJar(File, String) - Method in class htsjdk.utils.ClassFinder
  Scans the entries in a ZIP/JAR file for classes under the parent package.
scoreIndexes(double, Map, int, IndexFactory.IndexBalanceApproach) - Static method in class htsjdk.tribble.index.DynamicIndexCreator
  score the available indexes for the specified density and feature lengths The scoring method is trying to determine how many features would be returned for a sample one base query; or: (features/seek).
Scores - Class in htsjdk.samtools.cram.encoding.readfeatures
  A read feature representing a contiguous stretch of quality scores in a read.
Scores(int, byte[]) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Scores
SD - Enum constant in enum class htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS
SECOND_OF_PAIR - Enum constant in enum class htsjdk.samtools.SAMFlag
SECOND_OF_PAIR - Static variable in class htsjdk.samtools.fastq.FastqConstants
SECONDARY_ALIGNMENT - Enum constant in enum class htsjdk.samtools.SAMFlag
SecondaryAlignmentFilter - Class in htsjdk.samtools.filter
  SamRecordFilter that filters out secondary alignments, but not supplemental alignments.
SecondaryAlignmentFilter() - Constructor for class htsjdk.samtools.filter.SecondaryAlignmentFilter
SecondaryAlignmentSkippingIterator - Class in htsjdk.samtools
  Wrapper around SAMRecord iterator that skips over secondary elements.
SecondaryAlignmentSkippingIterator(CloseableIterator) - Constructor for class htsjdk.samtools.SecondaryAlignmentSkippingIterator
SecondaryOrSupplementaryFilter - Class in htsjdk.samtools.filter
  Filter out SAMRecords with Secondary or Supplementary flag set This class should be viewed as a replacement for `NotPrimarySkippingIterator`, in that we did not want to change the functionality of NPSI to no longer match its name $Id$
SecondaryOrSupplementaryFilter() - Constructor for class htsjdk.samtools.filter.SecondaryOrSupplementaryFilter
SecondaryOrSupplementarySkippingIterator - Class in htsjdk.samtools
  Wrapper around SAMRecord iterator that skips over secondary and supplementary elements.
SecondaryOrSupplementarySkippingIterator(CloseableIterator) - Constructor for class htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
seek(long) - Method in class htsjdk.samtools.AbstractBAMFileIndex
seek(long) - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableMemoryStream
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
seek(long) - Method in class htsjdk.samtools.seekablestream.SeekableStream
  Seeks the stream to the provided position.
seek(long) - Method in class htsjdk.samtools.util.BlockCompressedInputStream
  Seek to the given position in the file.
SeekableBufferedStream - Class in htsjdk.samtools.seekablestream
  A wrapper class to provide buffered read access to a SeekableStream.
SeekableBufferedStream(SeekableStream) - Constructor for class htsjdk.samtools.seekablestream.SeekableBufferedStream
SeekableBufferedStream(SeekableStream, int) - Constructor for class htsjdk.samtools.seekablestream.SeekableBufferedStream
SeekableFileStream - Class in htsjdk.samtools.seekablestream
SeekableFileStream(File) - Constructor for class htsjdk.samtools.seekablestream.SeekableFileStream
SeekableFTPStream - Class in htsjdk.samtools.seekablestream
  Unfortunately the seekable stream classes exist for both Tribble and Picard, and we need both.
SeekableFTPStream(URL) - Constructor for class htsjdk.samtools.seekablestream.SeekableFTPStream
SeekableFTPStream(URL, UserPasswordInput) - Constructor for class htsjdk.samtools.seekablestream.SeekableFTPStream
SeekableFTPStreamHelper - Class in htsjdk.samtools.seekablestream
SeekableHTTPStream - Class in htsjdk.samtools.seekablestream
SeekableHTTPStream(URL) - Constructor for class htsjdk.samtools.seekablestream.SeekableHTTPStream
SeekableHTTPStream(URL, Proxy) - Constructor for class htsjdk.samtools.seekablestream.SeekableHTTPStream
SeekableMemoryStream - Class in htsjdk.samtools.seekablestream
SeekableMemoryStream(byte[], String) - Constructor for class htsjdk.samtools.seekablestream.SeekableMemoryStream
SeekablePathStream - Class in htsjdk.samtools.seekablestream
  An implementation of `SeekableStream` for `Path`.
SeekablePathStream(Path) - Constructor for class htsjdk.samtools.seekablestream.SeekablePathStream
SeekablePathStream(Path, Function) - Constructor for class htsjdk.samtools.seekablestream.SeekablePathStream
SeekableStream - Class in htsjdk.samtools.seekablestream
  InputStream with random access support (seek).
SeekableStream() - Constructor for class htsjdk.samtools.seekablestream.SeekableStream
SeekableStreamFactory - Class in htsjdk.samtools.seekablestream
  Singleton class for getting `SeekableStream`s from URL/paths Applications using this library can set their own factory
SeekableStreamResource - Class in htsjdk.beta.io.bundle
  A `BundleResource` backed by a `SeekableStream`.
SeekableStreamResource(SeekableStream, String, String) - Constructor for class htsjdk.beta.io.bundle.SeekableStreamResource
  Create a `BundleResource` backed by an SeekableStream, specifying a display name and content type.
SeekableStreamResource(SeekableStream, String, String, String) - Constructor for class htsjdk.beta.io.bundle.SeekableStreamResource
  Create a `BundleResource` backed by an SeekableStream, specifying a display name, content type and format.
SELECTOR_TABLE_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.fqzcomp.FQZGlobalFlags
SEPARATOR - Static variable in class htsjdk.samtools.metrics.MetricsFile
SEQ - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
SEQUENCE_HEADER - Static variable in class htsjdk.samtools.fastq.FastqConstants
SEQUENCE_LENGTH_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
SEQUENCE_NAME_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
SEQUENCE_REGION_DIRECTIVE - Enum constant in enum class htsjdk.tribble.gff.Gff3Codec.Gff3Directive
sequenceColumn - Variable in class htsjdk.tribble.index.tabix.TabixFormat
  One-based index of the column in the file being indexed containing the sequence name
SequenceHeader - Enum constant in enum class htsjdk.samtools.fastq.FastqReader.LineType
SequenceLine - Enum constant in enum class htsjdk.samtools.fastq.FastqReader.LineType
SequenceListsDifferException() - Constructor for exception class htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException
SequenceListsDifferException(String) - Constructor for exception class htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException
SequenceListsDifferException(String, Throwable) - Constructor for exception class htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException
SequenceListsDifferException(Throwable) - Constructor for exception class htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException
SequenceRegion - Class in htsjdk.tribble.gff
  Represents a sequence region feature in a gff3 file.
SequenceUtil - Class in htsjdk.samtools.util
SequenceUtil() - Constructor for class htsjdk.samtools.util.SequenceUtil
SequenceUtil.SequenceListsDifferException - Exception Class in htsjdk.samtools.util
SEQUENCING_CENTER_TAG - Static variable in class htsjdk.samtools.SAMReadGroupRecord
serializeAndDeserialize(T) - Static method in class htsjdk.samtools.util.TestUtil
  Serialize and Deserialize an object Useful for testing if serialization is correctly handled for a class.
serialVersionUID - Static variable in class htsjdk.samtools.AbstractSAMHeaderRecord
serialVersionUID - Static variable in class htsjdk.samtools.AlignmentBlock
serialVersionUID - Static variable in class htsjdk.samtools.Cigar
serialVersionUID - Static variable in class htsjdk.samtools.CigarElement
serialVersionUID - Static variable in class htsjdk.samtools.SAMBinaryTagAndValue
serialVersionUID - Static variable in class htsjdk.samtools.SAMRecord
serialVersionUID - Static variable in class htsjdk.samtools.SAMSequenceDictionary
serialVersionUID - Static variable in class htsjdk.samtools.SAMSequenceRecord
serialVersionUID - Static variable in class htsjdk.samtools.SAMValidationError
serialVersionUID - Static variable in class htsjdk.variant.variantcontext.CommonInfo
serialVersionUID - Static variable in class htsjdk.variant.variantcontext.Genotype
serialVersionUID - Static variable in class htsjdk.variant.variantcontext.GenotypesContext
serialVersionUID - Static variable in class htsjdk.variant.variantcontext.VariantContext
serialVersionUID - Static variable in class htsjdk.variant.vcf.VCFHeader
serialVersionUID - Static variable in class htsjdk.variant.vcf.VCFHeaderLine
set(int, int) - Method in class htsjdk.samtools.cram.compression.rans.RANSDecodingSymbol
  Set the decoding parameters for this symbol.
set(int, int, int) - Method in class htsjdk.samtools.cram.compression.rans.RANSEncodingSymbol
  Initialize encoding parameters for a symbol given its position in the frequency table.
set(int, Genotype) - Method in class htsjdk.variant.variantcontext.GenotypesContext
set(String, Object) - Method in class htsjdk.variant.variantcontext.GenotypeJEXLContext
setAlignmentStart(int) - Method in class htsjdk.samtools.SAMRecord
setAll(Feature) - Method in class htsjdk.tribble.MutableFeature
setAllowFieldsMissingFromHeader(boolean) - Method in class htsjdk.beta.plugin.variants.VariantsEncoderOptions
  Set whether writing fields that are missing from the header is allowed.
setAllowMissingFieldsInHeader(boolean) - Method in class htsjdk.variant.vcf.VCFEncoder
  Deprecated.
  since 10/24/13 use the constructor
setAlternativeSequenceName(Collection) - Method in class htsjdk.samtools.SAMSequenceRecord
  Sets the alternative sequence names in the order provided by iteration, removing the previous values.
setAssembly(String) - Method in class htsjdk.samtools.SAMSequenceRecord
setAsyncIO(boolean) - Method in class htsjdk.beta.codecs.reads.bam.BAMDecoderOptions
  Set whether async IO is enable for these options.
setAsyncIO(boolean) - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Set whether to enable async IO for these options.
setAsyncIO(boolean) - Method in class htsjdk.beta.plugin.variants.VariantsEncoderOptions
  Set whether to enable async IO for these options.
setAsyncOutputBufferSize(int) - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Get the async output buffer size used for these options.
setAsyncOutputBufferSize(int) - Method in class htsjdk.samtools.SAMFileWriterFactory
  If and only if using asynchronous IO then sets the maximum number of records that can be buffered per SAMFileWriter before producers will block when trying to write another SAMRecord.
setAttribute(short, Object) - Method in class htsjdk.samtools.SAMRecord
setAttribute(short, Object, boolean) - Method in class htsjdk.samtools.BAMRecord
setAttribute(short, Object, boolean) - Method in class htsjdk.samtools.SAMRecord
setAttribute(SAMTag, Object) - Method in class htsjdk.samtools.SAMRecord
setAttribute(SAMTag, Object, boolean) - Method in class htsjdk.samtools.SAMRecord
setAttribute(SAMTag, String) - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
  Set the given value for the SAMTag 'tag'.
setAttribute(String, Object) - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
  Deprecated.
  Use `AbstractSAMHeaderRecord.setAttribute(String, String)` instead
setAttribute(String, Object) - Method in class htsjdk.samtools.SAMFileHeader
  Deprecated.
  Use `SAMFileHeader.setAttribute(String, String)` instead
setAttribute(String, Object) - Method in class htsjdk.samtools.SAMRecord
  Set a named attribute onto the SAMRecord.
setAttribute(String, String) - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
  Set the given value for the attribute named 'key'.
setAttribute(String, String) - Method in class htsjdk.samtools.SAMFileHeader
  Set the given value for the attribute named 'key'.
setAttributes(SAMBinaryTagAndValue) - Method in class htsjdk.samtools.SAMRecord
  Replace any existing attributes with the given linked item.
setAttributes(Map) - Method in class htsjdk.variant.variantcontext.CommonInfo
setBAMDecoderOptions(BAMDecoderOptions) - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Set the `BAMDecoderOptions` used for these options.
setBAMEncoderOptions(BAMEncoderOptions) - Method in class htsjdk.beta.plugin.reads.ReadsEncoderOptions
  Set the `BAMEncoderOptions` for these ReadsEncoderOptions.
setBarcodes(List) - Method in class htsjdk.samtools.SAMReadGroupRecord
  Set the barcodes associated with this ReadGroup.
setBase(byte) - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
setBaseQualities(byte[]) - Method in class htsjdk.samtools.BAMRecord
setBaseQualities(byte[]) - Method in class htsjdk.samtools.SAMRecord
setBaseQualityString(String) - Method in class htsjdk.samtools.SAMRecord
setBases(byte[]) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
setBases(int) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
setBasesPerLine(int) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Sets the number of bases each line of the fasta file will have.
setBasesPerSlice(long) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Set the maximum accumulated bases per slice.
setBinLabel(String) - Method in class htsjdk.samtools.util.Histogram
setBisulfiteSequenced(boolean) - Method in class htsjdk.samtools.SamFileValidator
setBuffer(int) - Method in class htsjdk.beta.plugin.variants.VariantsEncoderOptions
  Set an output buffer size to use when writing to an `IOPathResource`.
setBuffer(int) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set a buffer size for the file output stream passed to the next `VariantContextWriter` created by this builder.
setBufferSize(int) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Controls size of write buffer.
setByteOffsetOfSliceHeaderBlock(int) - Method in class htsjdk.samtools.cram.structure.Slice
setByteSizeOfSliceBlocks(int) - Method in class htsjdk.samtools.cram.structure.Slice
setCachedPath(Path) - Method in class htsjdk.io.HtsPath
setCheckCrcs(boolean) - Method in class htsjdk.samtools.util.BlockCompressedInputStream
  Determines whether or not the inflater will re-calculated the CRC on the decompressed data and check it against the value stored in the GZIP header.
setCheckCrcs(boolean) - Method in class htsjdk.samtools.util.BlockGunzipper
  Allows the caller to decide whether or not to check CRCs on when uncompressing blocks.
setCheckCrcs(boolean) - Method in class htsjdk.samtools.util.GzipCodec
  Enable or disable CRC32 validation during decompression.
setChr(String) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
setChrIndex(List) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex
setChunkEnd(long) - Method in class htsjdk.samtools.Chunk
setChunkList(List) - Method in class htsjdk.samtools.Bin
  Sets the chunks associated with this bin
setChunkStart(long) - Method in class htsjdk.samtools.Chunk
setCigar(Cigar) - Method in class htsjdk.samtools.BAMRecord
setCigar(Cigar) - Method in class htsjdk.samtools.SAMRecord
  For setting the Cigar string when changed.
setCigarString(String) - Method in class htsjdk.samtools.BAMRecord
setCigarString(String) - Method in class htsjdk.samtools.SAMRecord
setCode(byte) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
setCodingEnd(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
  Method description
setCodingEnd(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
  Method description
setCodingStart(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
  Method description
setCodingStart(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
  Method description
setColor(Color) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
setCombineAbutting(boolean) - Method in class htsjdk.samtools.util.IntervalUtil.IntervalCombiner
setCommandLine(String) - Method in class htsjdk.samtools.SAMProgramRecord
setComments(Collection) - Method in class htsjdk.samtools.SAMFileHeader
  Replace existing comments with the contents of the given collection.
setComponentMethods(AbstractFeatureReader.ComponentMethods) - Static method in class htsjdk.tribble.AbstractFeatureReader
setCompressionLevel(int) - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Set the compression level for these options.
setCompressionLevel(int) - Method in class htsjdk.samtools.SAMFileWriterFactory
  set compression level 0!none 9: max
setCompressionLevel(int) - Static method in class htsjdk.samtools.util.IOUtil
  Sets the GZip compression level for subsequent GZIPOutputStream object creation.
setCompressorMap(EnumMap) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Set the per-DataSeries compressor map.
setConcatenateNames(boolean) - Method in class htsjdk.samtools.util.IntervalUtil.IntervalCombiner
setContainerBlocksByteSize(int) - Method in class htsjdk.samtools.cram.structure.ContainerHeader
setContext(int) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
setContig(String) - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
  Sometimes contigs need to be adjusted on-the-fly to match sequence dictionary entries.
setCRAMDecoderOptions(CRAMDecoderOptions) - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Set the `CRAMDecoderOptions` for these ReadsDecoderOptions.
setCRAMEncoderOptions(CRAMEncoderOptions) - Method in class htsjdk.beta.plugin.reads.ReadsEncoderOptions
  Set the `CRAMEncoderOptions` for these ReadsEncoderOptions.
setCRAMEncodingStrategy(CRAMEncodingStrategy) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Set the `CRAMEncodingStrategy` to use when creating CRAM writers.
setCramVersion(CRAMVersion) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Set the CRAM version to write.
setCreateIndex(boolean) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Convenience method allowing newSAMFileWriterFactory().setCreateIndex(true); Equivalent to SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true); newSAMFileWriterFactory(); If a BAM or CRAM (not SAM) file is created, the setting is true, and the file header specifies coordinate order, then a BAM index file will be written along with the BAM file.
setCreateMd5(boolean) - Method in class htsjdk.samtools.fastq.FastqWriterFactory
  If true, compute MD5 and write appropriately-named file when file is closed.
setCreateMD5() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Create an MD5 digest file for the next `VariantContextWriter` created by this builder.
setCreateMD5(boolean) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Choose whether to also create an MD5 digest file for the next `VariantContextWriter` created by this builder.
setCreateMd5File(boolean) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Sets whether to create md5Files for BAMs from this factory.
setCustomCompressionHeaderEncodingMap(CompressionHeaderEncodingMap) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Set a pre-built `CompressionHeaderEncodingMap` that bypasses the compressor map.
setDataClass(HtsgetClass) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
setDate(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
setDecodeEagerly(boolean) - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Set the eagerly decoding state used for these options.
setDefaultCompressionLevel(int) - Static method in class htsjdk.samtools.util.BlockCompressedOutputStream
  Sets the GZip compression level for subsequent BlockCompressedOutputStream object creation that do not specify the compression level.
setDefaultCreateIndexWhileWriting(boolean) - Static method in class htsjdk.samtools.SAMFileWriterFactory
  Sets the default for subsequent SAMFileWriterFactories that do not specify whether to create an index.
setDefaultCreateMd5File(boolean) - Static method in class htsjdk.samtools.SAMFileWriterFactory
  Sets the default for whether to create md5Files for BAM files this factory.
setDefaultDeflaterFactory(DeflaterFactory) - Static method in class htsjdk.samtools.util.BlockCompressedOutputStream
  Sets the default `DeflaterFactory` that will be used for all instances unless specified otherwise in the constructor.
setDefaultInflaterFactory(InflaterFactory) - Static method in class htsjdk.samtools.util.BlockGunzipper
  Sets the default `InflaterFactory` that will be used for all instances unless specified otherwise in the constructor.
setDefaultMaxRecordsInRam(int) - Static method in class htsjdk.samtools.SAMFileWriterImpl
  When writing records that are not presorted, specify the number of records stored in RAM before spilling to disk.
setDefaultOption(Options) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Add one option to the set of default `Options` that will be used as the initial set of options for all VariantContextWriterBuilders created after this call.
setDefaultValidationStringency(ValidationStringency) - Static method in class htsjdk.samtools.SamReaderFactory
setDeflaterFactory(DeflaterFactory) - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Set the `DeflaterFactory` for these options for these options.
setDeflaterFactory(DeflaterFactory) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Set the deflater factory used by BAM writers created by this writer factory.
setDelta(int) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
setDescription(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
setDescription(String) - Method in class htsjdk.samtools.SAMSequenceRecord
setDescription(String) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
setDestructiveIteration(boolean) - Method in class htsjdk.samtools.util.SortingCollection
  Tell this collection that it is allowed to discard data during iteration in order to reduce memory footprint, precluding a second iteration.
setDetached(boolean) - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Set or clear the detached CRAM flag (mate info stored explicitly).
setDictFile(Path) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Set the output dictionary file to write to.
setDictOutput(OutputStream) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Set the output stream for writing the dictionary.
setDownloadTriesBeforeFailing(int) - Method in class htsjdk.samtools.cram.ref.ReferenceSource
setDuplicateFlag(boolean) - Method in class htsjdk.samtools.DuplicateSet
  Controls if we should update the duplicate flag of the records in this set.
setDuplicateReadFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  the read is either a PCR duplicate or an optical duplicate.
setEagerDecode(boolean) - Method in class htsjdk.samtools.BAMFileReader
setEagerDecode(boolean) - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Set whether to eagerly decode subsequent SAMRecord reads.
setEmbeddedReferenceBases(byte[], int, int) - Method in class htsjdk.samtools.cram.build.CRAMReferenceRegion
  Set this `CRAMReferenceRegion` to use an embedded reference.
setEmbeddedReferenceBlock(Block) - Method in class htsjdk.samtools.cram.structure.Slice
setEmbeddedReferenceContentID(int) - Method in class htsjdk.samtools.cram.structure.Slice
  Set the content ID of the embedded reference block.
setEmitMd5(boolean) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
setEmitUncoveredLoci(boolean) - Method in class htsjdk.samtools.util.AbstractLocusIterator
setEmitUncoveredLoci(boolean) - Method in class htsjdk.samtools.util.EdgeReadIterator
  For correct work of `EdgeReadIterator` value `emitUncoveredLoci` must be true.
setEnd(int) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
setEndPosition(long) - Method in class htsjdk.tribble.index.Block
  This method is used to aid in consolidating blocks.
setEnforceSameStrand(boolean) - Method in class htsjdk.samtools.util.IntervalUtil.IntervalCombiner
setErrorsToIgnore(Collection) - Method in class htsjdk.samtools.SamFileValidator
  Sets one or more error types that should not be reported on.
setExons(List) - Method in class htsjdk.tribble.bed.FullBEDFeature
setFastaFile(Path) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Set the output fasta file to write to.
setFastaOutput(OutputStream) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Set the output stream for writing the reference.
setFileBasedIndexCached(boolean) - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Set id file based index caching is enabled for these options.
setFileSource(SAMFileSource) - Method in class htsjdk.samtools.SAMRecord
  Sets a marker providing the source reader for this file and the position in the file from which the read originated.
setFileSource(SamReader) - Method in class htsjdk.samtools.CRAMIterator
setFirstOfPairFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  the read is the first read in a pair.
setFixedLen(int) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZParam
setFlags(int) - Method in class htsjdk.samtools.SAMRecord
setFlowOrder(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
setFormat(HtsgetFormat) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
setGlobalLogLevel(Log.LogLevel) - Static method in class htsjdk.samtools.util.Log
  Set the log level.
setGlobalPrintStream(PrintStream) - Static method in class htsjdk.samtools.util.Log
  Set the `PrintStream` for writing.
setGroupOrder(SAMFileHeader.GroupOrder) - Method in class htsjdk.samtools.SAMFileHeader
setGziIndexFile(Path) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Set the output gzi index file to write to.
setGziIndexOutput(OutputStream) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Set the output stream for writing the index.
setGZIPCompressionLevel(int) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Set the GZIP compression level used for data series compressed with GZIP.
setHeader(H) - Method in interface htsjdk.beta.plugin.HtsEncoder
  Set the file format header for this decoder, of type `H`.
setHeader(SAMFileHeader) - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMEncoderV1_0
setHeader(SAMFileHeader) - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoder
setHeader(SAMFileHeader) - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMEncoderV1_0
setHeader(SAMFileHeader) - Method in class htsjdk.samtools.SAMFileWriterImpl
  Must be called before addAlignment.
setHeader(SAMFileHeader) - Method in class htsjdk.samtools.SAMRecord
  Sets the SAMFileHeader for this record.
setHeader(SAMFileHeader) - Method in class htsjdk.samtools.SAMRecordSetBuilder
setHeader(VCFHeader) - Method in class htsjdk.beta.codecs.variants.vcf.VCFEncoder
setHeader(VCFHeader) - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
setHeader(VCFHeader) - Method in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
setHeader(VCFHeader) - Method in interface htsjdk.variant.variantcontext.writer.VariantContextWriter
  Sets the VCF header so that data blocks can be written without writing the header Exactly one of writeHeader() or setHeader() should be called when using a writer
setHeaderStrict(SAMFileHeader) - Method in class htsjdk.samtools.SAMRecord
  Establishes the SAMFileHeader for this record and forces resolution of the record's reference and mate reference names against the header using the sequence dictionary in the new header.
setHistogram(Histogram) - Method in class htsjdk.samtools.metrics.MetricsFile
  Sets the histogram contained in the metrics file.
setHost(String) - Method in interface htsjdk.samtools.seekablestream.UserPasswordInput
setHours(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
setIgnoreWarnings(boolean) - Method in class htsjdk.samtools.SamFileValidator
setIncludeIndels(boolean) - Method in class htsjdk.samtools.util.AbstractLocusIterator
setIncludeIndels(boolean) - Method in class htsjdk.samtools.util.EdgeReadIterator
setIncludeNonPfReads(boolean) - Method in class htsjdk.samtools.util.AbstractLocusIterator
setIndex(byte) - Method in class htsjdk.samtools.cram.structure.ReadTag
setIndexChannelTransformer(Function) - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Set the channel transformer for the index resource.
setIndexChannelTransformer(Function) - Method in class htsjdk.beta.plugin.variants.VariantsDecoderOptions
  Set the channel transformer for the index resource.
setIndexCreator(IndexCreator) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set an IndexCreator for the next `VariantContextWriter` created by this builder.
setIndexFile(Path) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Set the output fai index file to write to.
setIndexOutput(OutputStream) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Set the output stream for writing the index.
setIndexSequenceDictionary(SAMSequenceDictionary) - Method in interface htsjdk.tribble.index.IndexCreator
  Set the sequence dictionary for the index.
setIndexSequenceDictionary(SAMSequenceDictionary) - Method in class htsjdk.tribble.index.TribbleIndexCreator
  Set the sequence dictionary entries for the index property list.
setIndexValidationStringency(BamIndexValidator.IndexValidationStringency) - Method in class htsjdk.samtools.SamFileValidator
setInferredInsertSize(int) - Method in class htsjdk.samtools.SAMRecord
setInflaterFactory(InflaterFactory) - Method in class htsjdk.beta.codecs.reads.bam.BAMDecoderOptions
  Set the `InflaterFactory` to use for these options.
setInputFileName(String) - Method in class htsjdk.samtools.util.BinaryCodec
setInputStream(InputStream) - Method in class htsjdk.samtools.BAMRecordCodec
  Sets the input stream that records will be read from.
setInputStream(InputStream) - Method in interface htsjdk.samtools.CoordinateSortedPairInfoMap.Codec
  Where to read encoded input from
setInputStream(InputStream) - Method in class htsjdk.samtools.util.BinaryCodec
setInputStream(InputStream) - Method in class htsjdk.samtools.util.IntervalCodec
  Sets the input stream that records will be read from.
setInputStream(InputStream) - Method in interface htsjdk.samtools.util.SortingCollection.Codec
  Where to read encoded input from
setInputStream(InputStream) - Method in class htsjdk.variant.vcf.VCFRecordCodec
setInputStream(InputStream, String) - Method in class htsjdk.samtools.BAMRecordCodec
  Sets the input stream that records will be read from.
setInputStream(InputStream, String) - Method in class htsjdk.samtools.util.IntervalCodec
  Sets the input stream that records will be read from.
setInstance(CustomReaderFactory) - Static method in class htsjdk.samtools.CustomReaderFactory
setInstance(ISeekableStreamFactory) - Static method in class htsjdk.samtools.seekablestream.SeekableStreamFactory
setInterval(Locatable) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
setInterval(Locatable) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
setIsDuplicate(boolean) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
setKeySequence(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
setLandmarkIndex(int) - Method in class htsjdk.samtools.cram.structure.Slice
setLandmarks(List) - Method in class htsjdk.samtools.cram.structure.ContainerHeader
setLastChunk(Chunk) - Method in class htsjdk.samtools.Bin
  Optimization to keep lastChunk instead of iterating over all chunks repeatedly
setLibrary(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
setLiftOverMinMatch(double) - Method in class htsjdk.samtools.liftover.LiftOver
  Set minimum fraction of bases that must remap.
setLink(String) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
setLog10PError(double) - Method in class htsjdk.variant.variantcontext.CommonInfo
setMakeDictOutput(boolean) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Sets whether to automatically generate an dictionary file from the name of the fasta-file (assuming it is given as a file).
setMakeFaiOutput(boolean) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Sets whether to automatically generate an index file from the name of the fasta-file (assuming it is given as a file).
setMakeGziOutput(boolean) - Method in class htsjdk.samtools.reference.FastaReferenceWriterBuilder
  Sets whether to automatically generate a gzi index file using an index file name derived from the name of the fasta-file (assuming the fasta file is a valid bgzipped file).
setMappingQuality(int) - Method in class htsjdk.samtools.SAMRecord
setMappingQualityScoreCutoff(int) - Method in class htsjdk.samtools.util.AbstractLocusIterator
setMateAlignmentStart(int) - Method in class htsjdk.samtools.SAMRecord
setMateInfo(SAMRecord, SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil
  Write the mate info for two SAMRecords.
setMateInfo(SAMRecord, SAMRecord, boolean) - Static method in class htsjdk.samtools.SamPairUtil
  Write the mate info for two SAMRecords
setMateInfo(SAMRecord, SAMRecord, SAMFileHeader) - Static method in class htsjdk.samtools.SamPairUtil
  Deprecated.
  use `SamPairUtil.setMateInfo(SAMRecord, SAMRecord)` instead
setMateInfo(SAMRecord, SAMRecord, SAMFileHeader, boolean) - Static method in class htsjdk.samtools.SamPairUtil
  Deprecated.
  use `SamPairUtil.setMateInfo(SAMRecord, SAMRecord, boolean)` instead
SetMateInfoIterator(Iterator) - Constructor for class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
  By default, the mate cigar tag is set
SetMateInfoIterator(Iterator, boolean) - Constructor for class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
SetMateInfoIterator(Iterator, boolean, boolean) - Constructor for class htsjdk.samtools.SamPairUtil.SetMateInfoIterator
setMateInformationOnSupplementalAlignment(SAMRecord, SAMRecord) - Static method in class htsjdk.samtools.SamPairUtil
  Sets mate pair information appropriately on a supplemental SAMRecord (e.g.
setMateInformationOnSupplementalAlignment(SAMRecord, SAMRecord, boolean) - Static method in class htsjdk.samtools.SamPairUtil
  Sets mate pair information appropriately on a supplemental SAMRecord (e.g.
setMateNegativeStrandFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  strand of the mate (false for forward; true for reverse strand).
setMateReferenceIndex(int) - Method in class htsjdk.samtools.SAMRecord
  Updates the mate reference index.
setMateReferenceName(String) - Method in class htsjdk.samtools.SAMRecord
  Sets the mate reference name for this record.
setMateUnmappedFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  the mate is unmapped.
setMaxReadsToAccumulatePerLocus(int) - Method in class htsjdk.samtools.util.AbstractLocusIterator
  If set, this will cap the number of reads we accumulate for any given position.
setMaxReadsToAccumulatePerLocus(int) - Method in class htsjdk.samtools.util.EdgeReadIterator
  This method isn't supported in current implementation.
setMaxRecordsInRam(int) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Before creating a writer that is not presorted, this method may be called in order to override the default number of SAMRecords stored in RAM before spilling to disk (c.f.
setMaxRecordsInRam(int) - Method in class htsjdk.samtools.SAMFileWriterImpl
  When writing records that are not presorted, specify the number of records stored in RAM before spilling to disk.
setMaxRecordsInRAM(int) - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Get the maximum records kept in RAM before spilling to disk for these options.
setMd5(String) - Method in class htsjdk.samtools.SAMSequenceRecord
setMD5(String) - Method in class htsjdk.tribble.index.AbstractIndex
setMemoryMapIndexes(boolean) - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Set whether memory mapping indexes is enabled.
setMethod(BlockCompressionMethod) - Method in class htsjdk.samtools.cram.compression.ExternalCompressor
  Set the compression method.
setMinimumSingleReferenceSliceSize(int) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  The minimum number of reads we need to have seen to emit a single-reference slice.
setMinutes(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
setMonth(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
setMrnaBase(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
setMrnaBase(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
setName(String) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
setName(String) - Method in interface htsjdk.tribble.NameAwareCodec
setName(String) - Method in class htsjdk.variant.variantcontext.CommonInfo
  Sets the name
setName(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  set the name of this codec
setNextSegment(CRAMCompressionRecord) - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
setNotPrimaryAlignmentFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  Deprecated.
  use `SAMRecord.setSecondaryAlignment(boolean)` instead.
setNumber(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
setNumber(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
setNumberToUnbounded() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
setOption(SamReaderFactory.Option, boolean) - Method in class htsjdk.samtools.SamReaderFactory
  Sets a specific Option to a boolean value.
setOption(Options) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Add one option to the set of `Options` for the `VariantContextWriterBuilder`, if it's not already present.
setOptions(EnumSet) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Replace the set of `Options` for the `VariantContextWriterBuilder` with a new set.
setOriginalBaseQualities(byte[]) - Method in class htsjdk.samtools.SAMRecord
  Sets the original base quality scores into the "OQ" tag as a String.
setOutput(byte[], int) - Method in class htsjdk.samtools.cram.compression.range.RangeCoder
  Set the output buffer for encoding.
setOutputBCFStream(OutputStream) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set the output BCF stream for the next `VariantContextWriter` created by this builder.
setOutputBufferSize(int) - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Set the buffer size for these options.
setOutputFile(File) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set the output file for the next `VariantContextWriter` created by this builder.
setOutputFile(String) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set the output file for the next `VariantContextWriter` created by this builder.
setOutputFileName(String) - Method in class htsjdk.samtools.util.BinaryCodec
setOutputFileType(VariantContextWriterBuilder.OutputType) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set the output file type for the next `VariantContextWriter` created by this builder.
setOutputPath(Path) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set the output file for the next `VariantContextWriter` created by this builder.
setOutputStream(OutputStream) - Method in class htsjdk.samtools.BAMRecordCodec
  Sets the output stream that records will be written to.
setOutputStream(OutputStream) - Method in interface htsjdk.samtools.CoordinateSortedPairInfoMap.Codec
  Where to write encoded output
setOutputStream(OutputStream) - Method in class htsjdk.samtools.util.BinaryCodec
setOutputStream(OutputStream) - Method in class htsjdk.samtools.util.IntervalCodec
  Sets the output stream that records will be written to.
setOutputStream(OutputStream) - Method in interface htsjdk.samtools.util.SortingCollection.Codec
  Where to write encoded output
setOutputStream(OutputStream) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set the output stream (VCF, by default) for the next `VariantContextWriter` created by this builder.
setOutputStream(OutputStream) - Method in class htsjdk.variant.vcf.VCFRecordCodec
setOutputStream(OutputStream, String) - Method in class htsjdk.samtools.BAMRecordCodec
  Sets the output stream that records will be written to.
setOutputStream(OutputStream, String) - Method in class htsjdk.samtools.util.IntervalCodec
  Sets the output stream that records will be written to.
setOutputVCFStream(OutputStream) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set the output VCF stream for the next `VariantContextWriter` created by this builder.
setPhase(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
  Method description
setPhase(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
  Method description
setPlatform(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
setPlatformModel(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
setPlatformUnit(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
setPredictedMedianInsertSize(Integer) - Method in class htsjdk.samtools.SAMReadGroupRecord
setPreSorted(boolean) - Method in class htsjdk.beta.plugin.reads.ReadsEncoderOptions
  Set the preSorted setting for these options.
setPreviousProgramGroupId(String) - Method in class htsjdk.samtools.SAMProgramRecord
setPreviousQuality(int) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
setPreviousSegment(CRAMCompressionRecord) - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
setProgramGroup(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
setProgramName(String) - Method in class htsjdk.samtools.SAMProgramRecord
setProgramRecord(SAMProgramRecord) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Adds the given program record to the header, and assigns the PG tag to any SAMRecords created after it has been added.
setProgramRecords(List) - Method in class htsjdk.samtools.SAMFileHeader
  Replace entire list of program records
setProgramVersion(String) - Method in class htsjdk.samtools.SAMProgramRecord
setProgressLogger(ProgressLoggerInterface) - Method in interface htsjdk.samtools.SAMFileWriter
  Sets a ProgressLogger on this writer.
setProgressLogger(ProgressLoggerInterface) - Method in class htsjdk.samtools.SAMFileWriterImpl
  Sets the progress logger used by this implementation.
setProperPairAndMateInfo(SAMRecord, SAMRecord, SAMFileHeader, List) - Static method in class htsjdk.samtools.SamPairUtil
  Deprecated.
  use `SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, List)` instead
setProperPairAndMateInfo(SAMRecord, SAMRecord, SAMFileHeader, List, boolean) - Static method in class htsjdk.samtools.SamPairUtil
  Deprecated.
  use `SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, List, boolean)`
setProperPairAndMateInfo(SAMRecord, SAMRecord, List) - Static method in class htsjdk.samtools.SamPairUtil
  This method will clear any mate cigar already present.
setProperPairAndMateInfo(SAMRecord, SAMRecord, List, boolean) - Static method in class htsjdk.samtools.SamPairUtil
setProperPairFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
setProperPairFlags(SAMRecord, SAMRecord, List) - Static method in class htsjdk.samtools.SamPairUtil
setProxy(Proxy) - Static method in class htsjdk.tribble.util.HTTPHelper
setQualityContext(int) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
setQualityScoreCutoff(int) - Method in class htsjdk.samtools.util.AbstractLocusIterator
setQualityScoreCutoff(int) - Method in class htsjdk.samtools.util.EdgeReadIterator
  This method isn't supported in current implementation.
setRandomSeed(long) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Set the seed of the random number generator for cases in which repeatable result is desired.
setReadBases(byte[]) - Method in class htsjdk.samtools.BAMRecord
setReadBases(byte[]) - Method in class htsjdk.samtools.SAMRecord
setReadFailsVendorQualityCheckFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  the read fails platform/vendor quality checks.
setReadGroup(SAMReadGroupRecord) - Method in class htsjdk.samtools.SAMRecordSetBuilder
setReadGroups(List) - Method in class htsjdk.samtools.SAMFileHeader
  Replace entire list of read groups.
setReadingFrame(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
  Method description
setReadingFrame(int) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
  Method description
setReadLength(int) - Method in class htsjdk.samtools.SAMRecordSetBuilder
setReadName(String) - Method in class htsjdk.samtools.BAMRecord
setReadName(String) - Method in class htsjdk.samtools.SAMRecord
setReadNegativeStrandFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  strand of the query (false for forward; true for reverse strand).
setReadOrdinal(int) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
setReadPairedFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  the read is paired in sequencing, no matter whether it is mapped in a pair.
setReadsChannelTransformer(Function) - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Set the channel transformer for the reads resource.
setReadsPerSlice(int) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Set number of reads per slice.
setReadString(String) - Method in class htsjdk.samtools.SAMRecord
setReadUmappedFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  Deprecated.
setReadUnmappedFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  the query sequence itself is unmapped.
setRecord(SAMRecord) - Method in class htsjdk.samtools.util.SamRecordWithOrdinal
setRecordBytes(byte[]) - Method in class htsjdk.variant.bcf2.BCF2Decoder
  Use the recordBytes[] to read BCF2 records from now on
setRecordLength(int) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
setRecordNumber(long) - Method in class htsjdk.samtools.SAMValidationError
setRecordOrdinal(long) - Method in class htsjdk.samtools.util.SamRecordWithOrdinal
setReferenceDictionary(SAMSequenceDictionary) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Set the reference dictionary to be used by `VariantContextWriter`s created by this builder.
setReferenceIndex(int) - Method in class htsjdk.samtools.SAMRecord
  Updates the reference index.
setReferenceMD5(CRAMReferenceRegion) - Method in class htsjdk.samtools.cram.structure.Slice
setReferenceName(String) - Method in class htsjdk.samtools.SAMRecord
  Sets the reference name for this record.
setReferencePath(IOPath) - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoderOptions
  Set the reference path for these options.
setReferencePath(IOPath) - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoderOptions
  Set the reference path for these options.
setReferenceSource(CRAMReferenceSource) - Method in class htsjdk.beta.codecs.reads.cram.CRAMDecoderOptions
  Set the `CRAMReferenceSource` for these options.
setReferenceSource(CRAMReferenceSource) - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoderOptions
  Set the `CRAMReferenceSource` for these options.
setRemappedSampleName(String) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  Replaces the sample name read from the VCF header with the remappedSampleName.
setRestPosition(long) - Method in class htsjdk.samtools.util.ftp.FTPClient
setResultState(boolean) - Method in class htsjdk.samtools.util.SamRecordWithOrdinal
  Set the result state on this record.
setResultState(SamRecordWithOrdinal, boolean) - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer
  Mark the current samRecordWithOrdinal as having been examined.
setRunDate(Date) - Method in class htsjdk.samtools.SAMReadGroupRecord
  Converts to Iso8601Date if not already in that form.
setSamFilters(List) - Method in class htsjdk.samtools.util.AbstractLocusIterator
  Controls which, if any, SAMRecords are filtered.
setSamFlagFieldOutput(SamFlagField) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Set the flag output format only when writing text.
setSample(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
setSAMRecordFactory(SAMRecordFactory) - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Set SAMRecordFactory for subsequent SAMRecord reads.
setScore(float) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
setScores(byte[]) - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy) - Method in class htsjdk.samtools.DuplicateSetIterator
  Deprecated.
setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy) - Method in class htsjdk.samtools.SAMRecordDuplicateComparator
setSecondaryAlignment(boolean) - Method in class htsjdk.samtools.SAMRecord
  set whether this alignment is secondary (an alternative alignment of the read).
setSecondOfPairFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  the read is the second read in a pair.
setSeconds(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
setSelector(int) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
setSelectorTable(int) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZState
setSentinel(V) - Method in class htsjdk.samtools.util.IntervalTree
  Set the special sentinel value that will be used to signal novelty when putting a new interval into the tree, or to signal "not found" when removing an interval.
setSequence(byte[]) - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
setSequenceDictionary(SAMSequenceDictionary) - Method in class htsjdk.samtools.SAMFileHeader
  Replace entire sequence dictionary.
setSequenceDictionary(SAMSequenceDictionary) - Method in class htsjdk.variant.vcf.VCFHeader
  Completely replaces the contig records in this header with those in the given SAMSequenceDictionary.
setSequenceIndex(int) - Method in class htsjdk.samtools.SAMSequenceRecord
setSequenceIndexes(int) - Method in class htsjdk.samtools.AbstractBAMFileIndex
setSequenceLength(int) - Method in class htsjdk.samtools.SAMSequenceRecord
setSequences(List) - Method in class htsjdk.samtools.SAMSequenceDictionary
  Replaces the existing list of SAMSequenceRecords with the given list.
setSequencingCenter(String) - Method in class htsjdk.samtools.SAMReadGroupRecord
setShouldLogFailedIntervalsBelowThreshold(boolean) - Method in class htsjdk.samtools.liftover.LiftOver
  By default any lifted interval that falls below liftOverMinMatch will be logged.
setSkipMateValidation(boolean) - Method in class htsjdk.samtools.SamFileValidator
  Sets whether or not we should run mate validation beyond the mate cigar check, which is useful in extreme edge cases that would require a lot of memory to do the validation.
setSlicesPerContainer(int) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Set the number of slices per container.
setSortOrder(SAMFileHeader.SortOrder) - Method in class htsjdk.samtools.SAMFileHeader
setSortOrder(SAMFileHeader.SortOrder, boolean) - Method in class htsjdk.samtools.SAMFileWriterImpl
  Must be called before calling setHeader().
setSortOrderChecking(boolean) - Method in interface htsjdk.samtools.SAMFileWriter
  If true writers that are writing pre-sorted records should check the order during writing.
setSortOrderChecking(boolean) - Method in class htsjdk.samtools.SAMFileWriterImpl
setSource(String) - Method in class htsjdk.samtools.SAMValidationError
setSource(String) - Method in exception class htsjdk.tribble.TribbleException
  set the source for the file; where we got lines from
setSource(String) - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
  Specify annotation source
setSpecies(String) - Method in class htsjdk.samtools.SAMSequenceRecord
setStart(int) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
setStoreMD(boolean) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Set whether to store the MD:Z tag verbatim.
setStoreNM(boolean) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Set whether to store the NM:i tag verbatim.
setStrand(Strand) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
setSubstitutionMatrix(SubstitutionMatrix) - Method in class htsjdk.samtools.cram.structure.CompressionHeader
setSupplementaryAlignmentFlag(boolean) - Method in class htsjdk.samtools.SAMRecord
  set whether this alignment is supplementary (a split alignment such as a chimeric alignment).
setTagIdDictionary(byte[][][]) - Method in class htsjdk.samtools.cram.structure.CompressionHeader
setTagIdsIndex(MutableInt) - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
setTempDirectory(File) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Set the temporary directory to use when sort data.
setTempDirectory(File) - Method in class htsjdk.samtools.SAMFileWriterImpl
  When writing records that are not presorted, specify the path of the temporary directory for spilling to disk.
setTemporaryDirectory(IOPath) - Method in class htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  Get the temporary directory path for these options.
setTextHeader(String) - Method in class htsjdk.samtools.SAMFileHeader
  Deprecated.
  since May 1st 2019 - text version of header is no longer stored.
setTime(long) - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
setTimeoutSeconds(int) - Method in class htsjdk.io.AsyncWriterPool
  Set the `timeoutSeconds` value.
setToDetachedState() - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Mark this record as detached — mate info stored explicitly via MF, NS, NP, TS data series.
setTransientAttribute(Object, Object) - Method in class htsjdk.samtools.SAMRecord
  Sets the value of a transient attribute, and returns the previous value if defined.
setTrialCandidatesMap(EnumMap) - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  Set additional trial compression candidates per DataSeries.
setTS(long) - Method in class htsjdk.tribble.index.linear.LinearIndex
setType(String) - Method in class htsjdk.tribble.bed.SimpleBEDFeature
setUnmappedHasBasesAndQualities(boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder
setUnsignedArrayAttribute(String, Object) - Method in class htsjdk.samtools.SAMRecord
  Because Java does not support unsigned integer types, we think it is a bad idea to encode them in SAM files.
setup(VCFHeader, BCF2Encoder, Map) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager
  Setup the FieldWriters appropriate to each INFO and FORMAT in the VCF header Must be called before any of the getter methods will work
setURLHelperFactory(URLHelperFactory) - Static method in class htsjdk.tribble.util.ParsingUtils
  Set the factory object for providing URLHelpers.
setUseAsyncIo(boolean) - Method in class htsjdk.samtools.fastq.FastqWriterFactory
  Sets whether or not to use async io (i.e.
setUseAsyncIo(boolean) - Method in class htsjdk.samtools.SAMFileWriterFactory
  Turn on or off the use of asynchronous IO for writing output SAM and BAM files.
setUseAsyncIo(boolean) - Method in class htsjdk.samtools.SamReaderFactory
  Set whether readers created by this factory will use asynchronous IO.
setUseBamFile(boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Determine whether the class will use a bam (default) or a sam file to hold the records when providing a reader to them.
setUseNmFlag(boolean) - Method in class htsjdk.samtools.SAMRecordSetBuilder
setUsingPOST(boolean) - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Force the source to attempt to use the POST api when requesting multiple intervals.
setUTR(boolean) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon
  Flag indicating that the entire exon is the UTR.
setUTR(boolean) - Method in class htsjdk.tribble.bed.FullBEDFeature.Exon2
  Flag indicating that the entire exon is the UTR.
setValidateCRCChecksums(boolean) - Method in class htsjdk.beta.codecs.reads.bam.BAMDecoderOptions
  Set whether validation of CRC checksums should be enabled for these options.
setValidateIndex(boolean) - Method in class htsjdk.samtools.SamFileValidator
  Deprecated.
  use `SamFileValidator.setIndexValidationStringency(BamIndexValidator.IndexValidationStringency)` instead
setValidationErrors(Collection) - Method in class htsjdk.samtools.SAMFileHeader
  Replace list of validation errors with the elements of the given list.
setValidationStringency(ValidationStringency) - Method in class htsjdk.beta.plugin.reads.ReadsDecoderOptions
  Set the `ValidationStringency` used for these options.
setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.CRAMIterator
setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.HtsgetBAMFileReader
  Set error-checking level for subsequent SAMRecord reads.
setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.SAMRecord
  Control validation of lazily-decoded elements.
setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.SAMSequenceDictionaryCodec
setValidationStringency(ValidationStringency) - Method in class htsjdk.samtools.SAMTextHeaderCodec
setValue(String) - Method in class htsjdk.samtools.metrics.StringHeader
setValue(V1) - Method in class htsjdk.samtools.util.IntervalTree.Node
setValueLabel(String) - Method in class htsjdk.samtools.util.Histogram
setVariantsChannelTransformer(Function) - Method in class htsjdk.beta.plugin.variants.VariantsDecoderOptions
  Set the channel transformer for the variants resource.
setVCFHeader(VCFHeader) - Method in class htsjdk.variant.vcf.VCFEncoder
  Deprecated.
  since 10/24/13 use the constructor
setVCFHeader(VCFHeader, VCFHeaderVersion) - Method in class htsjdk.variant.vcf.AbstractVCFCodec
  Explicitly set the VCFHeader on this codec.
setVCFHeaderVersion(VCFHeaderVersion) - Method in class htsjdk.variant.vcf.VCFHeader
  Establish the header version for this header.
setVerbose(boolean, int) - Method in class htsjdk.samtools.SamFileValidator
  Control verbosity
setVersion(String) - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
  Specify annotation version
setVersionedItem(String) - Method in class htsjdk.samtools.metrics.VersionHeader
setVersionString(String) - Method in class htsjdk.samtools.metrics.VersionHeader
setWriteCommandLine(boolean) - Method in class htsjdk.variant.vcf.VCFHeader
  If true, and isWriteEngineHeaders also returns true, the command line will be written to the VCF.
setWriteEngineHeaders(boolean) - Method in class htsjdk.variant.vcf.VCFHeader
  If true additional engine headers will be written to the VCF, otherwise only the walker headers will be output.
setWriteFullFormatField(boolean) - Method in class htsjdk.beta.plugin.variants.VariantsEncoderOptions
  Set whether full format fields should always be written (suppress trimming of trailing missing values).
setWriteSitesOnly(boolean) - Method in class htsjdk.beta.plugin.variants.VariantsEncoderOptions
  Set whether only sites are written, without genotypes suppressed.
setWrittenCount(long) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
setYear(int) - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Deprecated.
severity - Variable in enum class htsjdk.samtools.SAMValidationError.Type
shadowBCF(File) - Static method in class htsjdk.variant.bcf2.BCF2Utils
  Returns a good name for a shadow BCF file for vcfFile.
SHALLOW - Enum constant in enum class htsjdk.tribble.gff.Gff3Codec.DecodeDepth
shift(long, long) - Static method in class htsjdk.samtools.util.BlockCompressedFilePointerUtil
  Move a virtual file pointer by a given (non-virtual) offset.
shouldBeAddedToDictionary() - Method in class htsjdk.variant.vcf.VCFFilterHeaderLine
shouldBeAddedToDictionary() - Method in class htsjdk.variant.vcf.VCFFormatHeaderLine
shouldBeAddedToDictionary() - Method in class htsjdk.variant.vcf.VCFHeaderLine
  By default the header lines won't be added to the dictionary, unless this method will be override (for example in FORMAT, INFO or FILTER header lines)
shouldBeAddedToDictionary() - Method in class htsjdk.variant.vcf.VCFInfoHeaderLine
shouldEmitContainer(int, int, int) - Method in class htsjdk.samtools.cram.build.ContainerFactory
  Determine if a Container should be emitted based on the current reference context and the reference context for the next record to be processed, and the encoding strategy parameters.
showDialog() - Method in interface htsjdk.samtools.seekablestream.UserPasswordInput
SignatureStream - Class in htsjdk.beta.io.bundle
  An input stream over the first `signaturePrefixLength` bytes of another input stream, used to allow multiple codecs to probe those bytes for a file format/version signature.
SignatureStream(int, byte[]) - Constructor for class htsjdk.beta.io.bundle.SignatureStream
  Create a signature probe stream containing the first signaturePrefixLength bytes of an input stream that can be probed for a signature.
SILENT - Enum constant in enum class htsjdk.samtools.ValidationStringency
  Like LENIENT, only don't emit warning messages.
SimpleAllele - Class in htsjdk.variant.variantcontext
  An implementation of `Allele` which includes a byte[] of the bases in the allele or the symbolic name.
SimpleAllele(byte[], boolean) - Constructor for class htsjdk.variant.variantcontext.SimpleAllele
SimpleAllele(SimpleAllele, boolean) - Constructor for class htsjdk.variant.variantcontext.SimpleAllele
  Creates a new allele based on the provided one.
SimpleAllele(String, boolean) - Constructor for class htsjdk.variant.variantcontext.SimpleAllele
SimpleBEDFeature - Class in htsjdk.tribble.bed
  Feature from a BED file without exon blocks.
SimpleBEDFeature(int, int, String) - Constructor for class htsjdk.tribble.bed.SimpleBEDFeature
SimpleFeature - Class in htsjdk.tribble
  A simple concrete Feature.
SimpleFeature(String, int, int) - Constructor for class htsjdk.tribble.SimpleFeature
SINGLE_BREAKEND_INDICATOR - Static variable in interface htsjdk.variant.variantcontext.Allele
  Non ref allele representations
SINGLE_REFERENCE_TYPE - Enum constant in enum class htsjdk.samtools.cram.ref.ReferenceContextType
SINGULAR - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Singular Genomics
site(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenericSiteWriter
site(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.SiteWriter
sitesOnlyVariantContext(VariantContext) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Returns a newly allocated VC that is the same as VC, but without genotypes
sitesOnlyVariantContexts(Collection) - Static method in class htsjdk.variant.variantcontext.VariantContextUtils
  Returns a newly allocated list of VC, where each VC is the same as the input VCs, but without genotypes
SiteWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.SiteWriter
size() - Method in class htsjdk.samtools.CoordinateSortedPairInfoMap
size() - Method in class htsjdk.samtools.cram.io.CRAMByteWriter
  Return the number of bytes written so far.
size() - Method in class htsjdk.samtools.DuplicateSet
  Returns the number of records in this set.
size() - Method in class htsjdk.samtools.LinearIndex
size() - Method in class htsjdk.samtools.reference.FastaSequenceIndex
  Returns the number of elements in the index.
size() - Method in class htsjdk.samtools.SAMRecordSetBuilder
size() - Method in class htsjdk.samtools.SAMSequenceDictionary
size() - Method in class htsjdk.samtools.SBIIndex
  Returns number of entries in the index.
size() - Method in class htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel
size() - Method in class htsjdk.samtools.util.AbstractLocusInfo
size() - Method in class htsjdk.samtools.util.DiskBackedQueue
  Return the total number of elements in the queue, both in memory and on disk
size() - Method in class htsjdk.samtools.util.Histogram
  Returns the size of this histogram.
size() - Method in class htsjdk.samtools.util.IntervalList
  Returns the count of intervals in the list.
size() - Method in class htsjdk.samtools.util.IntervalTree
  Return the number of intervals in the tree.
size() - Method in class htsjdk.samtools.util.IntervalTreeMap
size() - Method in class htsjdk.samtools.util.SamLocusIterator.LocusInfo
size() - Method in class htsjdk.samtools.util.SamRecordTrackingBuffer
  Return the total number of elements in the queue, both in memory and on disk
size() - Method in class htsjdk.tribble.index.interval.IntervalTree
size() - Method in class htsjdk.variant.variantcontext.GenotypesContext
size() - Method in class htsjdk.variant.variantcontext.LazyGenotypesContext
size(String) - Method in class htsjdk.samtools.util.ftp.FTPClient
  Return the size of the remote file
sizeInRam() - Method in class htsjdk.samtools.CoordinateSortedPairInfoMap
sizeIsOverflow(byte) - Static method in class htsjdk.variant.bcf2.BCF2Utils
SIZEOF - Static variable in class htsjdk.samtools.util.SortingLongCollection
SIZEOF_BCF_HEADER - Static variable in class htsjdk.variant.bcf2.BCF2Codec
  sizeof a BCF header (+ min/max version).
sizeOfTree(File) - Static method in class htsjdk.samtools.util.IOUtil
  Returns the size (in bytes) of the file or directory and all it's children.
skip(long) - Method in class htsjdk.samtools.cram.io.CountingInputStream
skip(long) - Method in class htsjdk.samtools.cram.io.CRC32InputStream
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekableBufferedStream
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekableFileStream
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStream
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekableHTTPStream
skip(long) - Method in class htsjdk.samtools.seekablestream.SeekablePathStream
skip(long) - Method in class htsjdk.samtools.util.Md5CalculatingInputStream
skip(long) - Method in class htsjdk.tribble.readers.LongLineBufferedReader
  Skips characters.
skip(long) - Method in interface htsjdk.tribble.readers.Positional
  Skip the next nBytes in the stream.
skip(long) - Method in class htsjdk.tribble.readers.PositionalBufferedStream
skipBytes(int) - Method in class htsjdk.samtools.AbstractBAMFileIndex
skipFully(InputStream, long) - Static method in class htsjdk.samtools.cram.io.InputStreamUtils
  Skip the specified number of bytes from the `InputStream`.
skipHeaderBytes() - Method in class htsjdk.tribble.FeatureCodecHeader
skipNewlines() - Method in class htsjdk.samtools.util.FastLineReader
  Advance over any EOLN chars (CR or LF)
skipNextBlock(int, InputStream) - Method in class htsjdk.variant.bcf2.BCF2Decoder
  Skips the next record from input stream, invalidating current block data
SKIPPED_REGION - Static variable in enum class htsjdk.samtools.CigarOperator
skipToSequence(int) - Method in class htsjdk.samtools.AbstractBAMFileIndex
skipToSequence(int) - Method in class htsjdk.samtools.CSIIndex
slice(ByteBuffer) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Create a little-endian slice of the given ByteBuffer (from position to limit).
Slice - Class in htsjdk.samtools.cram.structure
  A CRAM slice is a logical construct that is just a subset of the blocks in a Slice.
Slice(CRAMVersion, CompressionHeader, InputStream, long) - Constructor for class htsjdk.samtools.cram.structure.Slice
  Create a slice by reading a serialized Slice from an input stream.
Slice(List, CompressionHeader, long, long) - Constructor for class htsjdk.samtools.cram.structure.Slice
  Create a single Slice from CRAM Compression Records and a Compression Header.
SliceBlocks - Class in htsjdk.samtools.cram.structure
  Manage the (logical) set of blocks that constitute a `Slice`, not including the Slice header block, which is managed by `Slice`.
SliceBlocks(CRAMVersion, int, InputStream) - Constructor for class htsjdk.samtools.cram.structure.SliceBlocks
  Read the set of blocks that make up a slice from a CRAM stream.
SliceBlocks(Block, List) - Constructor for class htsjdk.samtools.cram.structure.SliceBlocks
  Create a new SliceBlocks object from a core block and one or more external blocks.
SliceBlocksReadStreams - Class in htsjdk.samtools.cram.structure
  Provides a layer over a `SliceBlocks` object and acts as a bridge between the DataSeries codecs and their underlying blocks when reading a CRAM stream by presenting a bit (core) or byte (external) stream for each block.
SliceBlocksReadStreams(SliceBlocks, CompressorCache) - Constructor for class htsjdk.samtools.cram.structure.SliceBlocksReadStreams
SliceBlocksWriteStreams - Class in htsjdk.samtools.cram.structure
  Provides a layer over a `SliceBlocks` object and acts as a bridge between the DataSeries codecs and their underlying blocks when writing a CRAM stream by presenting a bit (core) or byte (external) stream for each block.
SliceBlocksWriteStreams(CompressionHeader) - Constructor for class htsjdk.samtools.cram.structure.SliceBlocksWriteStreams
SliceFactory - Class in htsjdk.samtools.cram.build
  Factory for creating `Slice`s when writing a CRAM stream.
SliceFactory(CRAMEncodingStrategy, CRAMReferenceSource, SAMFileHeader, long) - Constructor for class htsjdk.samtools.cram.build.SliceFactory
slurp(File) - Static method in class htsjdk.samtools.util.IOUtil
  Convenience overload for `IOUtil.slurp(java.io.InputStream, java.nio.charset.Charset)` using the default charset `Charset.defaultCharset()`.
slurp(InputStream) - Static method in class htsjdk.samtools.util.IOUtil
  Convenience overload for `IOUtil.slurp(java.io.InputStream, java.nio.charset.Charset)` using the default charset `Charset.defaultCharset()`.
slurp(InputStream, Charset) - Static method in class htsjdk.samtools.util.IOUtil
  Reads all of the stream into a String, decoding with the provided `Charset` then closes the stream quietly.
slurp(Iterable) - Static method in class htsjdk.samtools.util.Iterables
slurp(Iterator) - Static method in class htsjdk.samtools.util.Iterables
slurpLines(File) - Static method in class htsjdk.samtools.util.IOUtil
  Returns all of the untrimmed lines in the provided file.
slurpLines(InputStream) - Static method in class htsjdk.samtools.util.IOUtil
SM - Enum constant in enum class htsjdk.samtools.SAMTag
SM - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
SMALL - Enum constant in enum class htsjdk.samtools.cram.structure.CRAMCompressionProfile
  Size-optimized profile.
smartMergeHeaders(Collection, boolean) - Static method in class htsjdk.variant.vcf.VCFUtils
SnappyLoader - Class in htsjdk.samtools.util
  Checks if Snappy is available, and provides methods for wrapping InputStreams and OutputStreams with Snappy if it is.
SnappyLoader() - Constructor for class htsjdk.samtools.util.SnappyLoader
SNP - Enum constant in enum class htsjdk.variant.variantcontext.VariantContext.Type
SnpFilter - Class in htsjdk.variant.variantcontext.filter
  A Predicate on VariantContexts that returns true at sites that are SNPs
SnpFilter() - Constructor for class htsjdk.variant.variantcontext.filter.SnpFilter
SOFT_CLIP - Static variable in enum class htsjdk.samtools.CigarOperator
SoftClip - Class in htsjdk.samtools.cram.encoding.readfeatures
  A read feature representing a soft clip similar to `CigarOperator.S`.
SoftClip(int, byte[]) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
softClip3PrimeEndOfRead(SAMRecord, int) - Static method in class htsjdk.samtools.util.CigarUtil
  Adjust the cigar of `rec` based on adapter clipping using soft-clipping
softClipEndOfRead(int, List) - Static method in class htsjdk.samtools.util.CigarUtil
  Adjust the cigar based on adapter clipping
Solexa - Enum constant in enum class htsjdk.samtools.util.FastqQualityFormat
  Early Solexa/Illumina (pre pipeline 1.3) style scores which encode Solexa qualities using an ASCII offset of 64
SOLEXA_ADDEND - Static variable in class htsjdk.samtools.util.SolexaQualityConverter
  This value is added to a Solexa quality score to make it printable ASCII
solexaCharToPhredBinary(byte) - Method in class htsjdk.samtools.util.SolexaQualityConverter
  Convert a solexa quality ASCII character into a phred score.
SolexaNoiseFilter - Class in htsjdk.samtools.filter
  Filter to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact.
SolexaNoiseFilter() - Constructor for class htsjdk.samtools.filter.SolexaNoiseFilter
SolexaQualityConverter - Class in htsjdk.samtools.util
  Optimized method for converting Solexa ASCII qualities into Phred scores.
SOLID - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Life Technologies
SOMATIC_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
Some example data - Section in class htsjdk.variant.variantcontext.VariantContext
sort() - Method in class htsjdk.samtools.util.IntervalList
  Deprecated.
  use `IntervalList.sorted()` instead.
SORT_ORDER_TAG - Static variable in class htsjdk.samtools.SAMFileHeader
sorted() - Method in class htsjdk.samtools.util.IntervalList
  returns an independent sorted IntervalList
sortedString(Map) - Static method in class htsjdk.tribble.util.ParsingUtils
sortedString(Map) - Static method in class htsjdk.variant.variantcontext.Genotype
  a utility method for generating sorted strings from a map key set.
SortingCollection<T> - Class in htsjdk.samtools.util
  Collection to which many records can be added.
SortingCollection.Codec<T> - Interface in htsjdk.samtools.util
  Client must implement this class, which defines the way in which records are written to and read from file.
SortingLongCollection - Class in htsjdk.samtools.util
  Accumulate a list of longs that can then be sorted in natural order and iterated over.
SortingLongCollection(int, File...) - Constructor for class htsjdk.samtools.util.SortingLongCollection
  Prepare to accumulate values to be sorted
SortingLongCollection(int, Path...) - Constructor for class htsjdk.samtools.util.SortingLongCollection
  Prepare to accumulate values to be sorted
SortingVariantContextWriter - Class in htsjdk.variant.variantcontext.writer
  Deprecated.
  9/2017, this class is completely untested and unsupported, there is no replacement at this time if you use this class please file an issue on github or it will be removed at some point in the future
SortingVariantContextWriter(VariantContextWriter, int) - Constructor for class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
SortingVariantContextWriter(VariantContextWriter, int, boolean) - Constructor for class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
  create a local-sorting VCF writer, given an inner VCF writer to write to
sortList(Collection) - Static method in class htsjdk.tribble.util.ParsingUtils
  a small utility function for sorting a list
source(String) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells us that the resulting VariantContext should have source field set to source
SOURCE_KEY - Static variable in class htsjdk.variant.vcf.VCFHeader
sourceLikeBam(SeekableStream) - Static method in class htsjdk.samtools.SamStreams
sourceLikeCram(SeekableStream) - Static method in class htsjdk.samtools.SamStreams
SPAN_DEL - Static variable in interface htsjdk.variant.variantcontext.Allele
SPAN_DEL_STRING - Static variable in interface htsjdk.variant.variantcontext.Allele
  A generic static SPAN_DEL allele for use
SPANNING_DELETION_ALLELE - Static variable in class htsjdk.variant.vcf.VCFConstants
SPECIES_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
spillToDisk() - Method in class htsjdk.samtools.util.SortingCollection
  Sort the records in memory, write them to a file, and clear the buffer of records in memory.
split(long) - Method in class htsjdk.samtools.SBIIndex
  Split the data file for this index into non-overlapping chunks of roughly the given size that cover the whole file and that can be read independently of one another.
split(String, char) - Static method in class htsjdk.tribble.util.ParsingUtils
  Split the string into tokens separated by the given delimiter.
split(String, String[], char) - Static method in class htsjdk.samtools.util.StringUtil
  Split the string into tokens separated by the given delimiter.
split(String, String[], char) - Static method in class htsjdk.tribble.util.ParsingUtils
  Split the string into tokesn separated by the given delimiter.
split(String, String[], char, boolean) - Static method in class htsjdk.tribble.util.ParsingUtils
  Split the string into tokens separated by the given delimiter.
splitConcatenateExcessTokens(String, String[], char) - Static method in class htsjdk.samtools.util.StringUtil
  Split the string into tokens separated by the given delimiter.
splitWhitespace(String, String[]) - Static method in class htsjdk.tribble.util.ParsingUtils
  Split the string into tokens separated by tab or space(s).
SQ - Enum constant in enum class htsjdk.samtools.SAMTag
  Deprecated.
  for backwards compatibility only
SQ - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
SQ_A - Enum constant in enum class htsjdk.samtools.SQTagUtil.SQBase
  Deprecated.
SQ_C - Enum constant in enum class htsjdk.samtools.SQTagUtil.SQBase
  Deprecated.
SQ_G - Enum constant in enum class htsjdk.samtools.SQTagUtil.SQBase
  Deprecated.
SQ_T - Enum constant in enum class htsjdk.samtools.SQTagUtil.SQBase
  Deprecated.
sqScaledProbabilityRatio(double, double) - Static method in class htsjdk.samtools.SQTagUtil
  Deprecated.
  Convert a pair of likelihoods into a value suitable for passing to baseAndProbDiffToSqValue.
SQTagUtil - Class in htsjdk.samtools
  Deprecated.
  since 11/2018. SQ is a reserved tag that shouldn't be used and this code untested.
SQTagUtil() - Constructor for class htsjdk.samtools.SQTagUtil
  Deprecated.
SQTagUtil.SQBase - Enum Class in htsjdk.samtools
  Deprecated.
  The ordinals of these are stored in the high-order 2 bits of each byte of the SQ tag.
sqValueToBase(byte) - Static method in class htsjdk.samtools.SQTagUtil
  Deprecated.
  Retrieve the 2nd-best base call from SQ value.
sqValueToBaseOrdinal(byte) - Static method in class htsjdk.samtools.SQTagUtil
  Deprecated.
  Retrieve the 2nd-best base call from SQ value.
sqValueToProbRatio(byte) - Static method in class htsjdk.samtools.SQTagUtil
  Deprecated.
  Retrieve SQ-scaled probability ratio from SQ value.
Standard - Enum constant in enum class htsjdk.samtools.util.FastqQualityFormat
  Sanger style FASTQ files which encode PHRED qualities using an ASCII offset of 33
STANDARD_BUFFER_SIZE - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  Use `Defaults.NON_ZERO_BUFFER_SIZE` instead.
STANDARD_INDEX_EXTENSION - Static variable in class htsjdk.tribble.Tribble
  Deprecated.
  since June 2019 Use `FileExtensions.TRIBBLE_INDEX` instead.
STANDARD_INDEX_EXTENSION - Static variable in class htsjdk.tribble.util.TabixUtils
  Deprecated.
  Use since June 2019 `FileExtensions.TABIX_INDEX` instead.
STANDARD_TAGS - Static variable in class htsjdk.samtools.SAMFileHeader
  These tags are of known type, so don't need a type field in the text representation.
STANDARD_TAGS - Static variable in class htsjdk.samtools.SAMProgramRecord
STANDARD_TAGS - Static variable in class htsjdk.samtools.SAMReadGroupRecord
STANDARD_TAGS - Static variable in class htsjdk.samtools.SAMSequenceRecord
  The standard tags are stored in text header without type information, because the type of these tags is known.
standardDeviation() - Method in class htsjdk.tribble.util.MathUtils.RunningStat
start - Variable in class htsjdk.samtools.QueryInterval
  1-based, inclusive
start - Variable in class htsjdk.tribble.bed.SimpleBEDFeature
start - Variable in class htsjdk.tribble.MutableFeature
start - Variable in class htsjdk.variant.variantcontext.VariantContext
start() - Method in class htsjdk.samtools.util.StopWatch
start(long) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells us that the resulting VariantContext should have the specified contig start
start(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenotypesWriter
start(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GTWriter
start(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IGFGenotypesWriter
start(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IntegerTypeGenotypesWriter
start(BCF2Encoder, VariantContext) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
startPositionColumn - Variable in class htsjdk.tribble.index.tabix.TabixFormat
  One-based index of the column in the file being indexed containing the start position.
startSequence(String) - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Starts the input of the bases of a new sequence.
startSequence(String, int) - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Starts the input of the bases of a new sequence.
startSequence(String, String) - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Starts the input of the bases of a new sequence.
startSequence(String, String, int) - Method in class htsjdk.samtools.reference.FastaReferenceWriter
  Starts the input of the bases of a new sequence.
startWithInsertion(Cigar) - Static method in class htsjdk.samtools.util.AbstractLocusIterator
  Check if cigar start with an insertion, ignoring other operators that do not consume references bases
StaticallyTypeGenotypesWriter(VCFHeader, BCF2FieldEncoder) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.StaticallyTypeGenotypesWriter
statsSummary() - Method in class htsjdk.tribble.index.AbstractIndex
stderr - Variable in class htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput
  May be null if interleaved
stdout - Variable in class htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput
STEP - Static variable in class htsjdk.samtools.cram.compression.range.Constants
stop - Variable in class htsjdk.variant.variantcontext.VariantContext
stop() - Method in class htsjdk.samtools.util.StopWatch
stop(long) - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells us that the resulting VariantContext should have the specified contig stop
StopWatch - Class in htsjdk.samtools.util
  Utility to help in performance testing.
StopWatch() - Constructor for class htsjdk.samtools.util.StopWatch
storeArray(ByteBuffer, int[], int) - Static method in class htsjdk.samtools.cram.compression.fqzcomp.FQZCompEncode
  Serialize an array using the two-level run-length encoding used by FQZComp for tables.
strand - Variable in class htsjdk.tribble.bed.SimpleBEDFeature
Strand - Enum Class in htsjdk.tribble.annotation
  Enum for strand, which can be encoded as a string
STRAND_BIAS_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
stream() - Method in interface htsjdk.samtools.util.CloseableIterator
  Returns a Stream that will consume from the underlying iterator.
STREAM_TYPES - Static variable in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
StreamBasedTabixIndexCreator - Class in htsjdk.tribble.index.tabix
  A `TabixIndexCreator` that can write to an output stream.
StreamBasedTabixIndexCreator(SAMSequenceDictionary, TabixFormat, OutputStream) - Constructor for class htsjdk.tribble.index.tabix.StreamBasedTabixIndexCreator
STRICT - Enum constant in enum class htsjdk.samtools.ValidationStringency
  Do the right thing, throw an exception if something looks wrong.
String - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderLineType
STRING - Enum constant in enum class htsjdk.samtools.SamFlagField
stringCache - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
StringHeader - Class in htsjdk.samtools.metrics
  A simple header who's data type is a single String.
StringHeader() - Constructor for class htsjdk.samtools.metrics.StringHeader
  Default constructor.
StringHeader(String) - Constructor for class htsjdk.samtools.metrics.StringHeader
  Constructor that uses the supplied value as the value of the header.
StringLineReader - Class in htsjdk.samtools.util
  Deprecated.
  use `BufferedLineReader.fromString(String)`.
StringLineReader(String) - Constructor for class htsjdk.samtools.util.StringLineReader
  Deprecated.
StringOrCharacter(VCFCompoundHeaderLine, Map) - Constructor for class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
stringToBytes(String) - Static method in class htsjdk.samtools.util.StringUtil
stringToBytes(String, int, int) - Static method in class htsjdk.samtools.util.StringUtil
StringUtil - Class in htsjdk.samtools.util
  Grab-bag of stateless String-oriented utilities.
StringUtil() - Constructor for class htsjdk.samtools.util.StringUtil
STRIPE_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.range.RangeParams
STRIPE_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
stripeTranspose(ByteBuffer, int[]) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Transpose (de-interleave) input data into N=4 separate streams using round-robin byte distribution.
StructuralVariantType - Enum Class in htsjdk.variant.variantcontext
  Type of Structural Variant as defined in the VCF spec 4.2
subContextFromSample(String) - Method in class htsjdk.variant.variantcontext.VariantContext
subContextFromSamples(Set) - Method in class htsjdk.variant.variantcontext.VariantContext
subContextFromSamples(Set, boolean) - Method in class htsjdk.variant.variantcontext.VariantContext
  This method subsets down to a set of samples.
subcontexts - Section in class htsjdk.variant.variantcontext.VariantContext
SUBEXPONENTIAL - Enum constant in enum class htsjdk.samtools.cram.structure.EncodingID
  Subexponential codes.
SubexponentialIntegerEncoding - Class in htsjdk.samtools.cram.encoding.core
subList(int, int) - Method in class htsjdk.variant.variantcontext.GenotypesContext
subsetToSamples(Set) - Method in class htsjdk.variant.variantcontext.GenotypesContext
  Return a freshly allocated subcontext of this context containing only the samples listed in samples.
Substitution - Class in htsjdk.samtools.cram.encoding.readfeatures
  A substitution event captured in read coordinates.
Substitution(int, byte) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Substitution
Substitution(int, byte, byte) - Constructor for class htsjdk.samtools.cram.encoding.readfeatures.Substitution
SubstitutionMatrix - Class in htsjdk.samtools.cram.structure
  Substitution matrix, used to represent base substitutions for reference-based CRAM compression.
SubstitutionMatrix(byte[]) - Constructor for class htsjdk.samtools.cram.structure.SubstitutionMatrix
  Create a SubstitutionMatrix from a serialized byte array
SubstitutionMatrix(List) - Constructor for class htsjdk.samtools.cram.structure.SubstitutionMatrix
  Create a SubstitutionMatrix given a list of CramCompressionRecord
subtract(IntervalList, IntervalList) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for subtracting one IntervalLists from another.
subtract(Collection, Collection) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for subtracting a collection of IntervalLists from another.
SUM_OF_BASE_QUALITIES - Enum constant in enum class htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy
sumOfErrorProbabilities(SAMRecord) - Static method in class htsjdk.samtools.util.QualityUtil
  Calculates the sum of error probabilities for all read bases in the SAM record.
sumQualitiesOfMismatches(SAMRecord, byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the sum of qualities for mismatched bases in the read.
sumQualitiesOfMismatches(SAMRecord, byte[], int) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the sum of qualities for mismatched bases in the read.
sumQualitiesOfMismatches(SAMRecord, byte[], int, boolean) - Static method in class htsjdk.samtools.util.SequenceUtil
  Calculates the sum of qualities for mismatched bases in the read.
SUPPLEMENTARY_ALIGNMENT - Enum constant in enum class htsjdk.samtools.SAMFlag
Supported Types - Section in enum class htsjdk.variant.variantcontext.VariantContext.Type
SV_SIMPLE_CNV - Static variable in interface htsjdk.variant.variantcontext.Allele
SV_SIMPLE_DEL - Static variable in interface htsjdk.variant.variantcontext.Allele
SV_SIMPLE_DUP - Static variable in interface htsjdk.variant.variantcontext.Allele
SV_SIMPLE_INS - Static variable in interface htsjdk.variant.variantcontext.Allele
SV_SIMPLE_INV - Static variable in interface htsjdk.variant.variantcontext.Allele
SVTYPE - Static variable in class htsjdk.variant.vcf.VCFConstants
  INFO Type of structural variant
SYMBOLIC - Enum constant in enum class htsjdk.variant.variantcontext.VariantContext.Type
SYMBOLIC_ALLELE_END - Static variable in interface htsjdk.variant.variantcontext.Allele
SYMBOLIC_ALLELE_START - Static variable in interface htsjdk.variant.variantcontext.Allele
SynchronousLineReader - Class in htsjdk.tribble.readers
  Implementation of `LineReader` that reads lines directly from the underlying stream or reader.
SynchronousLineReader(InputStream) - Constructor for class htsjdk.tribble.readers.SynchronousLineReader
SynchronousLineReader(Reader) - Constructor for class htsjdk.tribble.readers.SynchronousLineReader
synchronouslyClose() - Method in class htsjdk.samtools.fastq.AsyncFastqWriter
synchronouslyClose() - Method in class htsjdk.samtools.util.AbstractAsyncWriter
synchronouslyClose() - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
synchronouslyWrite(FastqRecord) - Method in class htsjdk.samtools.fastq.AsyncFastqWriter
synchronouslyWrite(VariantContext) - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
synchronouslyWrite(T) - Method in class htsjdk.samtools.util.AbstractAsyncWriter

## T

t - Static variable in class htsjdk.samtools.util.SequenceUtil
  Byte typed variables for all normal bases.
T - Static variable in class htsjdk.samtools.util.SequenceUtil
  Byte typed variables for all normal bases.
TABIX - Enum constant in enum class htsjdk.tribble.index.IndexFactory.IndexType
TABIX_INDEX - Static variable in class htsjdk.samtools.util.FileExtensions
TabixFeatureReader<T,SOURCE> - Class in htsjdk.tribble
TabixFeatureReader(String, AsciiFeatureCodec) - Constructor for class htsjdk.tribble.TabixFeatureReader
TabixFeatureReader(String, String, AsciiFeatureCodec) - Constructor for class htsjdk.tribble.TabixFeatureReader
TabixFeatureReader(String, String, AsciiFeatureCodec, Function, Function) - Constructor for class htsjdk.tribble.TabixFeatureReader
TabixFormat - Class in htsjdk.tribble.index.tabix
  The values in a Tabix header that define the format of the file being indexed, e.g.
TabixFormat() - Constructor for class htsjdk.tribble.index.tabix.TabixFormat
TabixFormat(int, int, int, int, char, int) - Constructor for class htsjdk.tribble.index.tabix.TabixFormat
TabixIndex - Class in htsjdk.tribble.index.tabix
  This class represent a Tabix index that has been built in memory or read from a file.
TabixIndex(TabixFormat, List, BinningIndexContent[]) - Constructor for class htsjdk.tribble.index.tabix.TabixIndex
TabixIndex(File) - Constructor for class htsjdk.tribble.index.tabix.TabixIndex
  Convenient ctor that opens the file, wraps with with BGZF reader, and closes after reading index.
TabixIndex(InputStream) - Constructor for class htsjdk.tribble.index.tabix.TabixIndex
TabixIndex(Path) - Constructor for class htsjdk.tribble.index.tabix.TabixIndex
  Convenient ctor that opens the path, wraps with with BGZF reader, and closes after reading index.
TabixIndexCreator - Class in htsjdk.tribble.index.tabix
  IndexCreator for Tabix.
TabixIndexCreator(SAMSequenceDictionary, TabixFormat) - Constructor for class htsjdk.tribble.index.tabix.TabixIndexCreator
TabixIndexCreator(TabixFormat) - Constructor for class htsjdk.tribble.index.tabix.TabixIndexCreator
tabixIndexFile(File) - Static method in class htsjdk.tribble.Tribble
  Return the File of the tabix index file for the provided `file` Does not actually create an index
tabixIndexFile(String) - Static method in class htsjdk.tribble.Tribble
  Return the name of the tabix index file for the provided `filename` Does not actually create an index
TabixIndexMerger - Class in htsjdk.tribble.index.tabix
  Merges tabix files for parts of a VCF file that have been concatenated.
TabixIndexMerger(OutputStream, long) - Constructor for class htsjdk.tribble.index.tabix.TabixIndexMerger
tabixIndexPath(Path) - Static method in class htsjdk.tribble.Tribble
  Return the name of the tabix index file for the provided `path` Does not actually create an index
TabixIteratorLineReader - Class in htsjdk.tribble.readers
TabixIteratorLineReader(TabixReader.Iterator) - Constructor for class htsjdk.tribble.readers.TabixIteratorLineReader
TabixReader - Class in htsjdk.tribble.readers
TabixReader(String) - Constructor for class htsjdk.tribble.readers.TabixReader
TabixReader(String, SeekableStream) - Constructor for class htsjdk.tribble.readers.TabixReader
TabixReader(String, String) - Constructor for class htsjdk.tribble.readers.TabixReader
TabixReader(String, String, SeekableStream) - Constructor for class htsjdk.tribble.readers.TabixReader
TabixReader(String, String, SeekableStream, Function) - Constructor for class htsjdk.tribble.readers.TabixReader
TabixReader(String, String, Function, Function) - Constructor for class htsjdk.tribble.readers.TabixReader
TabixReader.Iterator - Interface in htsjdk.tribble.readers
TabixReader.TIndex - Class in htsjdk.tribble.readers
TabixReader.TPair64 - Class in htsjdk.tribble.readers
TabixReaderFailure(String, String) - Constructor for exception class htsjdk.tribble.TribbleException.TabixReaderFailure
TabixReaderFailure(String, String, Exception) - Constructor for exception class htsjdk.tribble.TribbleException.TabixReaderFailure
TabixUtils - Class in htsjdk.tribble.util
  classes that have anything to do with tabix
TabixUtils() - Constructor for class htsjdk.tribble.util.TabixUtils
TabixUtils.TIndex - Class in htsjdk.tribble.util
TabixUtils.TIntv - Class in htsjdk.tribble.util
TabixUtils.TPair64 - Class in htsjdk.tribble.util
tag - Variable in class htsjdk.samtools.SAMBinaryTagAndValue
tag - Variable in class htsjdk.samtools.SAMRecord.SAMTagAndValue
TAG_VALUE_TOO_LARGE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Unsigned integer tag value is deprecated in BAM.
TagFilter - Class in htsjdk.samtools.filter
  Filter class for matching tag attributes in SAMRecords $Id$
TagFilter(String, Object) - Constructor for class htsjdk.samtools.filter.TagFilter
  Constructor for a single value
TagFilter(String, Object, Boolean) - Constructor for class htsjdk.samtools.filter.TagFilter
  Constructor for a single value
TagFilter(String, List) - Constructor for class htsjdk.samtools.filter.TagFilter
  Constructor for multiple values
TagFilter(String, List, Boolean) - Constructor for class htsjdk.samtools.filter.TagFilter
  Constructor for multiple values
TagKeyCache - Class in htsjdk.samtools.cram.structure
  Caches the per-tag-ID metadata that is invariant across all records in a slice.
TagKeyCache(byte[][][]) - Constructor for class htsjdk.samtools.cram.structure.TagKeyCache
  Creates a TagKeyCache from a tag ID dictionary.
TagKeyCache.TagKeyInfo - Class in htsjdk.samtools.cram.structure
  Pre-computed metadata for a single tag ID.
tags - Variable in class htsjdk.samtools.util.htsget.HtsgetRequest
TAGS_TO_REVERSE - Static variable in class htsjdk.samtools.SAMRecord
  Tags that are known to need the reverse if the read is reverse complemented.
TAGS_TO_REVERSE_COMPLEMENT - Static variable in class htsjdk.samtools.SAMRecord
  Tags that are known to need the reverse complement if the read is reverse complemented.
TagValueAndUnsignedArrayFlag - Class in htsjdk.samtools
  CVO to use as a method return value.
TagValueAndUnsignedArrayFlag(Object, boolean) - Constructor for class htsjdk.samtools.TagValueAndUnsignedArrayFlag
TANDEM - Enum constant in enum class htsjdk.samtools.SamPairUtil.PairOrientation
TC - Enum constant in enum class htsjdk.samtools.SAMTag
TC - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
TC_TagCount - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
TempStreamFactory - Class in htsjdk.samtools.util
  Factory class for wrapping input and output streams for temporary files.
TempStreamFactory() - Constructor for class htsjdk.samtools.util.TempStreamFactory
TerminatorlessBlockCompressedOutputStream - Class in htsjdk.samtools.util
  An extension of `BlockCompressedOutputStream` that doesn't write an empty BGZF block at the end of the stream.
TerminatorlessBlockCompressedOutputStream(OutputStream) - Constructor for class htsjdk.samtools.util.TerminatorlessBlockCompressedOutputStream
test(SAMBinaryTagAndValue) - Method in class htsjdk.samtools.cram.digest.ContentDigests
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.CompoundFilter
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.GenotypeQualityFilter
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.HeterozygosityFilter
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.JavascriptVariantFilter
  Determines whether a VariantContext matches this filter
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.PassingVariantFilter
test(VariantContext) - Method in class htsjdk.variant.variantcontext.filter.SnpFilter
TestUtil - Class in htsjdk.samtools.util
TestUtil() - Constructor for class htsjdk.samtools.util.TestUtil
TextCigarCodec - Class in htsjdk.samtools
  Convert between String and Cigar class representations of CIGAR.
TextCigarCodec() - Constructor for class htsjdk.samtools.TextCigarCodec
TextTagCodec - Class in htsjdk.samtools
  Converter between SAM text representation of a tag, and in-memory Object representation.
TextTagCodec() - Constructor for class htsjdk.samtools.TextTagCodec
THOUSAND_GENOMES_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
THROW - Enum constant in enum class htsjdk.variant.variantcontext.JexlMissingValueTreatment
  Treat expressions with a missing value as an error and throw an `IllegalArgumentException`
tid - Variable in class htsjdk.tribble.util.TabixUtils.TIntv
TimeChannel - Class in htsjdk.samtools.apps
  Deprecated.
  This is deprecated with no replacement. 1/19
TimeChannel() - Constructor for class htsjdk.samtools.apps.TimeChannel
  Deprecated.
TimeRandomAccessFile - Class in htsjdk.samtools.apps
  Deprecated.
  This is deprecated with no replacement. 1/19
TimeRandomAccessFile() - Constructor for class htsjdk.samtools.apps.TimeRandomAccessFile
  Deprecated.
TIndex() - Constructor for class htsjdk.tribble.readers.TabixReader.TIndex
TIndex() - Constructor for class htsjdk.tribble.util.TabixUtils.TIndex
TIntv() - Constructor for class htsjdk.tribble.util.TabixUtils.TIntv
TL_TagIdList - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
TLEN - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
TM_TestMark - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
TN_TagNameAndType - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
toArray() - Method in class htsjdk.samtools.util.DiskBackedQueue
  Not supported at this time
toArray() - Method in class htsjdk.variant.variantcontext.GenotypesContext
toArray(T[]) - Method in class htsjdk.variant.variantcontext.GenotypesContext
toArray(T1[]) - Method in class htsjdk.samtools.util.DiskBackedQueue
  Not supported at this time
toBamReadBasesInPlace(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
  Update and return the given array of bases by upper casing and then replacing all non-BAM read bases with N
toBriefString() - Method in class htsjdk.variant.variantcontext.Genotype
toBufferedStream(InputStream) - Static method in class htsjdk.samtools.util.IOUtil
  Wrap the given stream in a BufferedInputStream, if it isn't already wrapper
toBundle(String) - Static method in class htsjdk.beta.io.bundle.BundleJSON
  Create a Bundle from a jsonString.
toBundle(String, Function) - Static method in class htsjdk.beta.io.bundle.BundleJSON
  Create a Bundle from jsonString using a custom class that implements `IOPath` for all resources.
toBundleList(String) - Static method in class htsjdk.beta.io.bundle.BundleJSON
  Create a List<Bundle> from a jsonString.
toBundleList(String, Function) - Static method in class htsjdk.beta.io.bundle.BundleJSON
  Create a List<Bundle> from a jsonString, using a custom class that implements `IOPath` for all resources.
toByteArray() - Method in class htsjdk.samtools.cram.io.CRAMByteWriter
  Return a copy of the bytes written so far.
toByteArray(ByteBuffer) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Return a byte array with contents matching the ByteBuffer from position 0 to limit.
toChunkList(long[]) - Static method in class htsjdk.samtools.BAMFileSpan
  The list of chunks is often represented as an array of longs where every even-numbered index is a start coordinate and every odd-numbered index is a stop coordinate.
toClassName(String) - Method in class htsjdk.utils.ClassFinder
  Convert a filename to a class name by removing '.class' and converting '/'s to '.'s.
toCoordinateArray() - Method in class htsjdk.samtools.BAMFileSpan
  Convert the chunk list to an array of offsets, paired in [start,end) format.
toDirective(String) - Static method in enum class htsjdk.tribble.gff.Gff3Codec.Gff3Directive
toEncodingDescriptor() - Method in class htsjdk.samtools.cram.encoding.CRAMEncoding
toFastQString() - Method in class htsjdk.samtools.fastq.FastqRecord
  Returns the record as the String FASTQ format.
toHeaderVersion(String) - Static method in enum class htsjdk.variant.vcf.VCFHeaderVersion
  get the header version
toHexDigit(int) - Static method in class htsjdk.samtools.util.StringUtil
toHtsPath(Path) - Static method in class htsjdk.beta.plugin.IOUtils
  Convert Path to GATKPath, returning null if input was null.
toIntegerSafe(long) - Static method in class htsjdk.beta.plugin.interval.HtsIntervalUtils
  Convert a long coordinate to an integer, for use with interconverting between old style integer coordinates and new style long coordinates.
toIntervalList() - Method in class htsjdk.variant.vcf.VCFFileReader
  Converts the underlying VCFFileReader to an IntervalList.
toIntervalList(boolean) - Method in class htsjdk.variant.vcf.VCFFileReader
toIntervalList(VCFFileReader) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Converts a vcf to an IntervalList.
toIntervalList(VCFFileReader, boolean) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Converts a `VCFFileReader` to an IntervalList.
toIntervalList(Path) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Parse a VCF file and convert to an IntervalList The name field of the IntervalList is taken from the ID field of the variant, if it exists.
toIntervalList(Path, boolean) - Static method in class htsjdk.variant.vcf.VCFFileReader
toIntervals(VCFFileReader, boolean) - Static method in class htsjdk.variant.vcf.VCFFileReader
  Converts a `VCFFileReader` to an `Iterator<Interval>` The name field of the Interval is taken from the ID field of the variant, if it exists.
toJSON(Bundle) - Static method in class htsjdk.beta.io.bundle.BundleJSON
  Serialize a bundle to a JSON string representation.
toJSON(List) - Static method in class htsjdk.beta.io.bundle.BundleJSON
  Convert a (non-empty) List of Bundles to a JSON array string representation.
TOKEN_CHAR - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_DELTA - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_DELTA0 - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_DIFF - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_DIGITS - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_DIGITS0 - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_DUP - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_DZLEN - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_END - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_MATCH - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_NOP - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_STRING - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TOKEN_TYPE - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
TokenStreams - Class in htsjdk.samtools.cram.compression.nametokenisation
  Token streams for the CRAM 3.1 name tokeniser.
TokenStreams(ByteBuffer, int, int) - Constructor for class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
  The outer index corresponds to the (column) position in a name (starting at index 0).
TokenStreams(ByteBuffer, int, int, RANSNx16Decode) - Constructor for class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
toList() - Method in interface htsjdk.samtools.util.CloseableIterator
  Consumes the contents of the iterator and returns it as a List.
toList(Class, Object) - Static method in class htsjdk.variant.bcf2.BCF2Utils
  Helper function that takes an object and returns a list representation of it: o == null => [] o is a list => o else => [o]
toLocatable(HtsInterval) - Static method in class htsjdk.beta.plugin.interval.HtsIntervalUtils
  Convert an HtsInterval to a `Locatable`
toLocatableList(List) - Static method in class htsjdk.beta.plugin.interval.HtsIntervalUtils
  Convert a List of `HtsInterval` to a list of `Locatable`.
toLowerCase(byte) - Static method in class htsjdk.samtools.util.StringUtil
toPath() - Method in class htsjdk.io.HtsPath
  Resolve the URI to a `Path` object.
toPath() - Method in interface htsjdk.io.IOPath
  Resolve this `IOPath` to an NIO `java.nio.file.Path`.
toPath(File) - Static method in class htsjdk.samtools.util.IOUtil
toQueryInterval(HtsInterval, SAMSequenceDictionary) - Static method in class htsjdk.beta.plugin.interval.HtsIntervalUtils
  Convert an HtsInterval to a QueryInterval
toQueryIntervalArray(List, SAMSequenceDictionary) - Static method in class htsjdk.beta.plugin.interval.HtsIntervalUtils
  Convert a list of `HtsInterval` to an array of `QueryInterval`
toSAMRecord(SAMFileHeader) - Method in class htsjdk.samtools.cram.structure.CRAMCompressionRecord
  Create a SAMRecord from the CRAMRecord.
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.core.BetaIntegerEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanByteEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanIntegerEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.core.experimental.GolombIntegerEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.core.GammaIntegerEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.core.SubexponentialIntegerEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.CRAMEncoding
  Serialize encoding parameters to an ITF8-encoded byte array.
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.external.ByteArrayStopEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.external.ExternalByteArrayEncoding
toSerializedEncodingParams() - Method in class htsjdk.samtools.cram.encoding.external.ExternalEncoding
toStrand(String) - Static method in enum class htsjdk.tribble.annotation.Strand
  Deprecated.
  please use `Strand.decode(char)` instead.
toStrategy() - Method in enum class htsjdk.samtools.cram.structure.CRAMCompressionProfile
  Create a new `CRAMEncodingStrategy` configured with this profile's settings.
toString() - Method in class htsjdk.beta.io.bundle.Bundle
toString() - Method in class htsjdk.beta.io.bundle.BundleResourceBase
toString() - Method in class htsjdk.beta.io.bundle.InputStreamResource
toString() - Method in class htsjdk.beta.io.bundle.OutputStreamResource
toString() - Method in class htsjdk.beta.io.bundle.SeekableStreamResource
toString() - Method in class htsjdk.beta.plugin.HtsVersion
toString() - Method in class htsjdk.io.HtsPath
toString() - Method in class htsjdk.samtools.AbstractSAMHeaderRecord
  Simple to String that outputs the concrete class name and the set of attributes stored.
toString() - Method in class htsjdk.samtools.BAMFileSpan
  Creates a string representation of this chunk list.
toString() - Method in class htsjdk.samtools.Chunk
toString() - Method in class htsjdk.samtools.Cigar
toString() - Method in class htsjdk.samtools.CigarElement
toString() - Method in enum class htsjdk.samtools.CigarOperator
  Returns the cigar operator as it would be seen in a SAM file.
toString() - Method in class htsjdk.samtools.cram.common.CRAMVersion
toString() - Method in class htsjdk.samtools.cram.compression.ExternalCompressor
toString() - Method in class htsjdk.samtools.cram.compression.GZIPExternalCompressor
toString() - Method in class htsjdk.samtools.cram.compression.range.RangeExternalCompressor
toString() - Method in class htsjdk.samtools.cram.compression.range.RangeParams
toString() - Method in class htsjdk.samtools.cram.compression.rans.RANS4x8Params
toString() - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Params
toString() - Method in class htsjdk.samtools.cram.compression.RANS4x8ExternalCompressor
toString() - Method in class htsjdk.samtools.cram.compression.RANSNx16ExternalCompressor
toString() - Method in class htsjdk.samtools.cram.CRAIEntry
toString() - Method in class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.core.BetaIntegerEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanByteEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.core.CanonicalHuffmanIntegerEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.core.experimental.GolombIntegerEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.core.GammaIntegerEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanBitCode
toString() - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParams
toString() - Method in class htsjdk.samtools.cram.encoding.core.SubexponentialIntegerEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.external.ByteArrayStopEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.external.ExternalByteArrayEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.external.ExternalEncoding
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Bases
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Deletion
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.HardClip
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.InsertBase
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Insertion
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Padding
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.ReadBase
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.RefSkip
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Scores
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.SoftClip
toString() - Method in class htsjdk.samtools.cram.encoding.readfeatures.Substitution
toString() - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
toString() - Method in class htsjdk.samtools.cram.ref.ReferenceContext
toString() - Method in class htsjdk.samtools.cram.structure.AlignmentContext
toString() - Method in class htsjdk.samtools.cram.structure.block.Block
toString() - Method in record class htsjdk.samtools.cram.structure.CompressorDescriptor
  Returns a string representation of this record class.
toString() - Method in class htsjdk.samtools.cram.structure.Container
toString() - Method in class htsjdk.samtools.cram.structure.ContainerHeader
toString() - Method in class htsjdk.samtools.cram.structure.CRAMEncodingStrategy
toString() - Method in class htsjdk.samtools.cram.structure.EncodingDescriptor
toString() - Method in class htsjdk.samtools.cram.structure.Slice
toString() - Method in class htsjdk.samtools.cram.structure.SubstitutionMatrix
toString() - Method in enum class htsjdk.samtools.fastq.FastqReader.LineType
toString() - Method in class htsjdk.samtools.fastq.FastqReader
toString() - Method in class htsjdk.samtools.fastq.FastqRecord
  Returns `FastqRecord.toFastQString()`.
toString() - Method in class htsjdk.samtools.liftover.LiftOver.PartialLiftover
toString() - Method in interface htsjdk.samtools.metrics.Header
  Converts the header to a String for persisting to a file.
toString() - Method in class htsjdk.samtools.metrics.MetricBase
  Converts the metric class to a human readable string.
toString() - Method in class htsjdk.samtools.metrics.StringHeader
toString() - Method in class htsjdk.samtools.metrics.VersionHeader
toString() - Method in class htsjdk.samtools.QueryInterval
toString() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  Returns the full path to the reference file, or the source if no path was specified.
toString() - Method in class htsjdk.samtools.reference.FastaSequenceFile
  Returns the full path to the reference file, or the source if no path was specified.
toString() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
  Returns the full path to the reference file, or the source if no path was specified.
toString() - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
  For debugging.
toString() - Method in class htsjdk.samtools.reference.ReferenceSequence
toString() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
toString() - Method in class htsjdk.samtools.SAMFileWriterFactory
toString() - Method in class htsjdk.samtools.SamInputResource
toString() - Method in class htsjdk.samtools.SAMRecord
  Returns this record formatted as it would appear in a SAM file.
toString() - Method in class htsjdk.samtools.SAMSequenceDictionary
toString() - Method in class htsjdk.samtools.SAMSequenceRecord
toString() - Method in class htsjdk.samtools.SAMValidationError
toString() - Method in class htsjdk.samtools.SBIIndex.Header
toString() - Method in class htsjdk.samtools.SBIIndex
toString() - Method in class htsjdk.samtools.util.AbstractLocusInfo
toString() - Method in class htsjdk.samtools.util.GZIIndex.IndexEntry
toString() - Method in class htsjdk.samtools.util.GZIIndex
toString() - Method in class htsjdk.samtools.util.Histogram.Bin
  Returns the String format for the value in the bin.
toString() - Method in class htsjdk.samtools.util.Histogram
toString() - Method in class htsjdk.samtools.util.Interval
toString() - Method in class htsjdk.samtools.util.IntervalTree.Node
toString() - Method in class htsjdk.samtools.util.Iso8601Date
toString() - Method in class htsjdk.samtools.util.RelativeIso8601Date
  Returns a `String` representation of this date.
toString() - Method in class htsjdk.samtools.util.Tuple
toString() - Method in enum class htsjdk.tribble.annotation.Strand
toString() - Method in class htsjdk.tribble.index.interval.Interval
toString() - Method in class htsjdk.tribble.index.interval.IntervalTree
toString() - Method in class htsjdk.tribble.readers.AsciiLineReader
toString() - Method in class htsjdk.tribble.readers.LineIteratorImpl
toString() - Method in class htsjdk.tribble.readers.SynchronousLineReader
toString() - Method in class htsjdk.tribble.readers.TabixIteratorLineReader
toString() - Method in class htsjdk.tribble.readers.TabixReader
toString() - Method in class htsjdk.variant.bcf2.BCF2Codec.SitesInfoForDecoding
toString() - Method in class htsjdk.variant.bcf2.BCFVersion
toString() - Method in interface htsjdk.variant.variantcontext.Allele
toString() - Method in class htsjdk.variant.variantcontext.Genotype
toString() - Method in class htsjdk.variant.variantcontext.GenotypeLikelihoods
toString() - Method in class htsjdk.variant.variantcontext.GenotypesContext
toString() - Method in class htsjdk.variant.variantcontext.SimpleAllele
toString() - Method in class htsjdk.variant.variantcontext.VariantContext
toString() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
toString() - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldWriter
toString() - Method in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
  Gets a string representation of this object.
toString() - Method in class htsjdk.variant.vcf.VCFHeader
toString() - Method in class htsjdk.variant.vcf.VCFHeaderLine
toStringDecodeGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContext
toStringEncoding() - Method in class htsjdk.variant.vcf.VCFCompoundHeaderLine
  make a string representation of this header line
toStringEncoding() - Method in class htsjdk.variant.vcf.VCFHeaderLine
  Should be overloaded in sub classes to do subclass specific
toStringEncoding() - Method in class htsjdk.variant.vcf.VCFSimpleHeaderLine
toStringEncoding(Map) - Static method in class htsjdk.variant.vcf.VCFHeaderLine
  create a string of a mapping pair for the target VCF version
toStringIfExists(String, int) - Static method in class htsjdk.variant.variantcontext.Genotype
  Returns a display name for field name with value v if this isn't -1.
toStringIfExists(String, int[]) - Static method in class htsjdk.variant.variantcontext.Genotype
  Returns a display name for field name with values vs if this isn't null.
toStringIfExists(String, String) - Static method in class htsjdk.variant.variantcontext.Genotype
  Returns a display name for field name with String value v if this isn't null.
toStringWithoutGenotypes() - Method in class htsjdk.variant.variantcontext.VariantContext
TOTAL_FREQ - Static variable in class htsjdk.samtools.cram.compression.rans.Constants
TOTAL_FREQ_SHIFT - Static variable in class htsjdk.samtools.cram.compression.rans.Constants
TOTAL_MAPPED_REFERENCE_LENGTH - Enum constant in enum class htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy
TOTAL_TOKEN_TYPES - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
totalFrequency - Variable in class htsjdk.samtools.cram.compression.range.ByteModel
toUpperCase(byte) - Static method in class htsjdk.samtools.util.StringUtil
toUpperCase(byte[]) - Static method in class htsjdk.samtools.util.StringUtil
  Converts in place all lower case letters to upper case in the byte array provided.
toURI() - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
toURI() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
  Convert request to a URI which can be used to make http request for data blocks
TPair64(long, long) - Constructor for class htsjdk.tribble.readers.TabixReader.TPair64
TPair64(long, long) - Constructor for class htsjdk.tribble.util.TabixUtils.TPair64
TPair64(TabixReader.TPair64) - Constructor for class htsjdk.tribble.readers.TabixReader.TPair64
TPair64(TabixUtils.TPair64) - Constructor for class htsjdk.tribble.util.TabixUtils.TPair64
transferByStream(InputStream, OutputStream, long) - Static method in class htsjdk.samtools.util.IOUtil
  Transfers from the input stream to the output stream using stream operations and a buffer.
TREAT_AS_MATCH - Enum constant in enum class htsjdk.variant.variantcontext.JexlMissingValueTreatment
  Treat expressions with a missing value as a match and evaluate to true
TREAT_AS_MISMATCH - Enum constant in enum class htsjdk.variant.variantcontext.JexlMissingValueTreatment
  Treat expressions with a missing value as a mismatch and evaluate to false
TrialCompressor - Class in htsjdk.samtools.cram.compression
  An `ExternalCompressor` that tries multiple candidate compressors and selects the one that produces the smallest output.
TrialCompressor(List) - Constructor for class htsjdk.samtools.cram.compression.TrialCompressor
  Create a trial compressor with the given candidate compressors.
Tribble - Class in htsjdk.tribble
  Common, tribble wide constants and static functions
TRIBBLE_INDEX - Static variable in class htsjdk.samtools.util.FileExtensions
TribbleException - Exception Class in htsjdk.tribble
TribbleException(String) - Constructor for exception class htsjdk.tribble.TribbleException
TribbleException(String, Throwable) - Constructor for exception class htsjdk.tribble.TribbleException
TribbleException.CorruptedIndexFile - Exception Class in htsjdk.tribble
TribbleException.FeatureFileDoesntExist - Exception Class in htsjdk.tribble
TribbleException.InternalCodecException - Exception Class in htsjdk.tribble
TribbleException.InvalidDecodeLine - Exception Class in htsjdk.tribble
TribbleException.InvalidHeader - Exception Class in htsjdk.tribble
TribbleException.MalformedFeatureFile - Exception Class in htsjdk.tribble
TribbleException.TabixReaderFailure - Exception Class in htsjdk.tribble
TribbleException.UnableToCreateCorrectIndexType - Exception Class in htsjdk.tribble
TribbleException.UnableToReadIndexFile - Exception Class in htsjdk.tribble
TribbleIndexCreator - Class in htsjdk.tribble.index
  Base class for Tribble-specific index creators.
TribbleIndexCreator() - Constructor for class htsjdk.tribble.index.TribbleIndexCreator
TribbleIndexedFeatureReader<T,SOURCE> - Class in htsjdk.tribble
  A reader for text feature files (i.e.
TribbleIndexedFeatureReader(String, FeatureCodec, boolean) - Constructor for class htsjdk.tribble.TribbleIndexedFeatureReader
TribbleIndexedFeatureReader(String, FeatureCodec, boolean, Function, Function) - Constructor for class htsjdk.tribble.TribbleIndexedFeatureReader
TribbleIndexedFeatureReader(String, FeatureCodec, Index) - Constructor for class htsjdk.tribble.TribbleIndexedFeatureReader
TribbleIndexedFeatureReader(String, String, FeatureCodec, boolean) - Constructor for class htsjdk.tribble.TribbleIndexedFeatureReader
TribbleIndexedFeatureReader(String, String, FeatureCodec, boolean, Function, Function) - Constructor for class htsjdk.tribble.TribbleIndexedFeatureReader
trim(String, char) - Static method in class htsjdk.tribble.util.ParsingUtils
trimByTailLimit(int) - Method in class htsjdk.samtools.util.Histogram
  Trims the histogram when the bins in the tail of the distribution contain fewer than mode/tailLimit items
trimByWidth(int) - Method in class htsjdk.samtools.util.Histogram
  Trims the histogram so that only bins `<=` width are kept.
TrimmingUtil - Class in htsjdk.samtools.util
  Utility code for performing quality trimming.
TrimmingUtil() - Constructor for class htsjdk.samtools.util.TrimmingUtil
truncate(long) - Method in class htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel
TRUNCATED_FILE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
truncateSequenceName(String) - Static method in class htsjdk.samtools.SAMSequenceRecord
  Truncate sequence name at first whitespace.
tryReadBCFVersion(BufferedInputStream) - Static method in class htsjdk.variant.bcf2.BCF2Codec
  try to read a BCFVersion from an uncompressed BufferedInputStream.
TS_InsertSize - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
Tuple<A,B> - Class in htsjdk.samtools.util
  A simple tuple class.
Tuple(A, B) - Constructor for class htsjdk.samtools.util.Tuple
TV_TestMark - Enum constant in enum class htsjdk.samtools.cram.structure.DataSeries
TWO_GBS - Static variable in class htsjdk.samtools.util.IOUtil
type - Variable in class htsjdk.samtools.cram.structure.TagKeyCache.TagKeyInfo
  The single-character type code, e.g.
type - Variable in class htsjdk.variant.variantcontext.VariantContext
  The type (cached for performance reasons) of this context
type() - Method in class htsjdk.samtools.BAMFileReader
type() - Method in class htsjdk.samtools.CRAMFileReader
type() - Method in class htsjdk.samtools.HtsgetBAMFileReader
type() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
type() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
type() - Method in interface htsjdk.samtools.SamReader
Type() - Constructor for class htsjdk.samtools.SamReader.Type
TYPE_TOKEN_FLAG_MASK - Static variable in class htsjdk.samtools.cram.compression.nametokenisation.TokenStreams
typeIgnoringNonRef - Variable in class htsjdk.variant.variantcontext.VariantContext
  The type of this context, cached separately if ignoreNonRef is true

## U

u - Variable in class htsjdk.tribble.util.TabixUtils.TPair64
U2 - Enum constant in enum class htsjdk.samtools.SAMTag
U2 - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
UCSC_FLAGS - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
ULTIMA - Enum constant in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Ultima Genomics
UnableToCreateCorrectIndexType(String) - Constructor for exception class htsjdk.tribble.TribbleException.UnableToCreateCorrectIndexType
UnableToCreateCorrectIndexType(String, Exception) - Constructor for exception class htsjdk.tribble.TribbleException.UnableToCreateCorrectIndexType
UnableToReadIndexFile(String, String, Exception) - Constructor for exception class htsjdk.tribble.TribbleException.UnableToReadIndexFile
UNAVAILABLE - Enum constant in enum class htsjdk.variant.variantcontext.GenotypeType
  There is no allele data availble for this sample (alleles.isEmpty)
UNAVAILABLE_SEQUENCE_INDEX - Static variable in class htsjdk.samtools.SAMSequenceRecord
UNBOUND_DESCRIPTION - Static variable in class htsjdk.variant.vcf.VCFHeaderLine
UNBOUNDED - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderLineCount
UNBOUNDED_ENCODING_v3 - Static variable in class htsjdk.variant.vcf.VCFConstants
UNBOUNDED_ENCODING_v4 - Static variable in class htsjdk.variant.vcf.VCFConstants
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.BZIP2ExternalCompressor
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.ExternalCompressor
  Decompress the data.
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.fqzcomp.FQZCompExternalCompressor
  Decompress the data.
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.GZIPExternalCompressor
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.LZMAExternalCompressor
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.nametokenisation.NameTokeniserExternalCompressor
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.range.RangeExternalCompressor
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.rans.RANS4x8Decode
  Uncompress a rANS 4x8 encoded byte stream.
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.rans.RANSDecode
  Uncompress a rANS-encoded byte stream.
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.rans.RANSNx16Decode
  Uncompress a rANS Nx16 encoded byte stream.
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.RANS4x8ExternalCompressor
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.RANSNx16ExternalCompressor
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.RAWExternalCompressor
uncompress(byte[]) - Method in class htsjdk.samtools.cram.compression.TrialCompressor
  Decompress data.
uncompress(ByteBuffer) - Static method in class htsjdk.samtools.cram.compression.fqzcomp.FQZCompDecode
  Decompress a FQZComp-compressed quality score block.
uncompress(ByteBuffer) - Method in class htsjdk.samtools.cram.compression.range.RangeDecode
  Decompress data that was compressed with the CRAM 3.1 arithmetic (range) codec.
uncompress(ByteBuffer, byte) - Method in class htsjdk.samtools.cram.compression.nametokenisation.NameTokenisationDecode
  Uncompress the compressed name data in the input buffer.
UNDEFINED_FIELD_VALUE - Static variable in class htsjdk.tribble.gff.Gff3Constants
underlyingReader() - Method in class htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
  Access the underlying `SamReader.PrimitiveSamReader` used by this adapter.
UNEXPECTED_BLOCK_LENGTH_MSG - Static variable in class htsjdk.samtools.util.BlockCompressedInputStream
unfiltered() - Method in class htsjdk.variant.variantcontext.GenotypeBuilder
  This genotype is unfiltered
unfiltered() - Method in class htsjdk.variant.variantcontext.VariantContextBuilder
  Tells this builder that the resulting VariantContext be unfiltered
UNFILTERED - Static variable in class htsjdk.variant.vcf.VCFConstants
UNINITIALIZED_INDEXING_PARAMETER - Static variable in class htsjdk.samtools.cram.structure.Slice
UNINITIALIZED_LENGTH - Static variable in class htsjdk.samtools.cram.build.CRAMReferenceRegion
UNINITIALIZED_REFERENCE_ID - Static variable in class htsjdk.samtools.cram.ref.ReferenceContext
UNINITIALIZED_START - Static variable in class htsjdk.samtools.cram.build.CRAMReferenceRegion
union(IntervalList, IntervalList) - Static method in class htsjdk.samtools.util.IntervalList
union(Collection) - Static method in class htsjdk.samtools.util.IntervalList
  A utility function for finding the union of a list of IntervalLists, checks for equal dictionaries.
unique() - Method in class htsjdk.samtools.util.IntervalList
  Deprecated.
  use `IntervalList.uniqued()` instead.
unique(boolean) - Method in class htsjdk.samtools.util.IntervalList
  Deprecated.
  use `IntervalList.uniqued(boolean)` instead.
uniqued() - Method in class htsjdk.samtools.util.IntervalList
  Returned an independent IntervalList that is sorted and uniquified.
uniqued(boolean) - Method in class htsjdk.samtools.util.IntervalList
  Returned an independent IntervalList that is sorted and uniquified.
unknown - Enum constant in enum class htsjdk.samtools.SAMFileHeader.SortOrder
UNKNOWN_LIBRARY_STRING - Static variable in class htsjdk.samtools.SAMRecordDuplicateComparator
UNKNOWN_MAPPING_QUALITY - Static variable in class htsjdk.samtools.SAMRecord
  Alignment score for a good alignment, but where computing a Phred-score is not feasible.
UNKNOWN_SEQUENCE_LENGTH - Static variable in class htsjdk.samtools.SAMSequenceRecord
  If one sequence has this length, and another sequence had a different length, isSameSequence will not complain that they are different sequences.
UNMAPPED_UNPLACED_CONTEXT - Static variable in class htsjdk.samtools.cram.ref.ReferenceContext
UNMAPPED_UNPLACED_CONTEXT - Static variable in class htsjdk.samtools.cram.structure.AlignmentContext
UNMAPPED_UNPLACED_ID - Static variable in class htsjdk.samtools.cram.ref.ReferenceContext
UNMAPPED_UNPLACED_INTERVAL - Static variable in class htsjdk.samtools.util.htsget.HtsgetRequest
UNMAPPED_UNPLACED_TYPE - Enum constant in enum class htsjdk.samtools.cram.ref.ReferenceContextType
UNPHASED - Static variable in class htsjdk.variant.vcf.VCFConstants
UNPHASED_ALLELE_SEPARATOR - Static variable in class htsjdk.variant.variantcontext.Genotype
UNRECOGNIZED_HEADER_TYPE - Enum constant in enum class htsjdk.samtools.SAMValidationError.Type
  Header record is not one of the standard types
unrollFiles(Collection, String...) - Static method in class htsjdk.samtools.util.IOUtil
  Go through the files provided and if they have one of the provided file extensions pass the file into the output otherwise assume that file is a list of filenames and unfold it into the output.
unrollPaths(Collection, String...) - Static method in class htsjdk.samtools.util.IOUtil
  Go through the files provided and if they have one of the provided file extensions pass the file to the output otherwise assume that file is a list of filenames and unfold it into the output (recursively).
UNSET_GENOMIC_LOCATION - Static variable in class htsjdk.samtools.GenomicIndexUtil
  E.g.
unsetBuffering() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Do not use buffering in the next `VariantContextWriter` created by this builder.
unsetCreateMD5() - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Don't create an MD5 digest file for the next `VariantContextWriter` created by this builder.
unsetDefaultOption(Options) - Static method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Remove an option from the set of default `Options` that will be used as the initial set of options for all VariantContextWriterBuilders created after this call.
unsetOption(Options) - Method in class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Remove one option from the set of `Options` for the `VariantContextWriterBuilder`, if it's present.
unsorted - Enum constant in enum class htsjdk.samtools.SAMFileHeader.SortOrder
UnsortedFileException - Exception Class in htsjdk.tribble.exception
  an exception for when we've discovered that an input file is unsorted; sorted files are required by Tribble
UnsortedFileException() - Constructor for exception class htsjdk.tribble.exception.UnsortedFileException
UnsortedFileException(String) - Constructor for exception class htsjdk.tribble.exception.UnsortedFileException
UnsortedFileException(String, Throwable) - Constructor for exception class htsjdk.tribble.exception.UnsortedFileException
UnsortedFileException(Throwable) - Constructor for exception class htsjdk.tribble.exception.UnsortedFileException
UNSPECIFIED - Enum constant in enum class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType
UNSPECIFIED_ALTERNATE_ALLELE - Static variable in interface htsjdk.variant.variantcontext.Allele
UNSPECIFIED_ALTERNATE_ALLELE_STRING - Static variable in interface htsjdk.variant.variantcontext.Allele
unzipBlock(byte[], byte[], int) - Method in class htsjdk.samtools.util.BlockGunzipper
  Decompress GZIP-compressed data
unzipBlock(byte[], int, byte[], int, int) - Method in class htsjdk.samtools.util.BlockGunzipper
  Decompress GZIP-compressed data
updateLongestFeature(int) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
Upgradeable - Interface in htsjdk.beta.plugin
  Placeholder interface for methods for upgrading one version of a format to a newer version.
upperCase(byte) - Static method in class htsjdk.samtools.util.SequenceUtil
upperCase(byte[]) - Static method in class htsjdk.samtools.util.SequenceUtil
UQ - Enum constant in enum class htsjdk.samtools.SAMTag
UQ - Variable in class htsjdk.samtools.SAMTagUtil
  Deprecated.
  use `SAMTag.getBinaryTag()` instead.
URI_TAG - Static variable in class htsjdk.samtools.SAMSequenceRecord
URLHelper - Interface in htsjdk.tribble.util
  Interface defining a helper class for dealing with URL resources.
URLHelperFactory - Interface in htsjdk.tribble.util
  A factory for creating `URLHelper` instances.
USE_ASYNC_IO - Enum constant in enum class htsjdk.variant.variantcontext.writer.Options
USE_ASYNC_IO_READ_FOR_SAMTOOLS - Static variable in class htsjdk.samtools.Defaults
  Should asynchronous read I/O be used where supported by the samtools package (one thread per file).
USE_ASYNC_IO_WRITE_FOR_SAMTOOLS - Static variable in class htsjdk.samtools.Defaults
  Should asynchronous write I/O be used where supported by the samtools package (one thread per file).
USE_ASYNC_IO_WRITE_FOR_TRIBBLE - Static variable in class htsjdk.samtools.Defaults
  Should asynchronous write I/O be used where supported by the tribble package (one thread per file).
USE_CRAM_REF_DOWNLOAD - Static variable in class htsjdk.samtools.Defaults
  Boolean describing whether downloading a reference file is allowed (for CRAM files), in case the reference file is not specified by the user Enabling this is not necessarily a good idea, since this process often fails.
USE_LIBDEFLATE - Static variable in class htsjdk.samtools.Defaults
  Whether to attempt to use jlibdeflate (libdeflate via JNI) for DEFLATE compression and decompression.
UserPasswordInput - Interface in htsjdk.samtools.seekablestream
Utils - Class in htsjdk.samtools.cram.build
Utils - Class in htsjdk.samtools.cram.compression.rans
  Utility methods for rANS encoding and decoding: cumulative frequency lookup, state renormalization, and frequency table normalization.
Utils() - Constructor for class htsjdk.samtools.cram.compression.rans.Utils

## V

v - Variable in class htsjdk.tribble.util.TabixUtils.TPair64
VALID_BASES_LOWER - Static variable in class htsjdk.samtools.util.SequenceUtil
VALID_BASES_UPPER - Static variable in class htsjdk.samtools.util.SequenceUtil
VALID_FILTER - Static variable in class htsjdk.variant.variantcontext.VariantContext
validate - Static variable in class htsjdk.variant.vcf.AbstractVCFCodec
VALIDATE_CRC_CHECKSUMS - Enum constant in enum class htsjdk.samtools.SamReaderFactory.Option
  For `SamReader`s backed by block-compressed streams, enable CRC validation of those streams.
validateAlignmentContext(boolean, ReferenceContext, int, int) - Static method in class htsjdk.samtools.cram.structure.AlignmentContext
  Determine if the provided values would result in a valid alignment context.
validateAlternateAlleles() - Method in class htsjdk.variant.variantcontext.VariantContext
validateArg(boolean, String) - Static method in class htsjdk.utils.ValidationUtils
validateArg(boolean, Supplier) - Static method in class htsjdk.utils.ValidationUtils
validateBamFileTermination(File) - Method in class htsjdk.samtools.SamFileValidator
validateBamFileTermination(Path) - Method in class htsjdk.samtools.SamFileValidator
validateChromosomeCounts() - Method in class htsjdk.variant.variantcontext.VariantContext
validateCigar(long) - Method in class htsjdk.samtools.SAMRecord
  Run all validations of CIGAR.
validateCigar(SAMRecord, Cigar, Integer, List, long, String) - Static method in class htsjdk.samtools.SAMUtils
  Run all validations of the mate's CIGAR.
VALIDATED_KEY - Static variable in class htsjdk.variant.vcf.VCFConstants
validateIndexHeader(int, LittleEndianInputStream) - Method in class htsjdk.tribble.index.AbstractIndex
validateMateCigar(SAMRecord, long) - Static method in class htsjdk.samtools.SAMUtils
  Run all validations of the mate's CIGAR.
validateOffset(int, byte[]) - Method in class htsjdk.samtools.util.AbstractRecordAndOffset
validateReferenceBases(Allele, Allele) - Method in class htsjdk.variant.variantcontext.VariantContext
validateRequest() - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
validateRequest() - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
  Validates that the user query obeys htsget spec
validateRSIDs(Set) - Method in class htsjdk.variant.variantcontext.VariantContext
validateSamFileSummary(SamReader, ReferenceSequenceFile) - Method in class htsjdk.samtools.SamFileValidator
  Outputs validation summary report to out.
validateSamFileVerbose(SamReader, ReferenceSequenceFile) - Method in class htsjdk.samtools.SamFileValidator
  Outputs validation error details to out.
validateSequenceName(String) - Static method in class htsjdk.samtools.SAMSequenceRecord
  Throw an exception if the sequence name is not valid.
validateToSequences(SAMSequenceDictionary) - Method in class htsjdk.samtools.liftover.LiftOver
  Throw an exception if all the "to" sequence names in the chains are not found in the given sequence dictionary.
validateVersionCompatibility(BCFVersion, BCFVersion) - Method in class htsjdk.variant.bcf2.BCF2Codec
  Validate the actual version against the supported version to determine compatibility.
validateVersionTransition(VCFHeaderVersion, VCFHeaderVersion) - Static method in class htsjdk.variant.vcf.VCFHeader
  Throw if `fromVersion` is not compatible with a `toVersion`.
ValidationMetrics() - Constructor for class htsjdk.samtools.SamFileValidator.ValidationMetrics
validationStringency - Variable in class htsjdk.samtools.cram.encoding.reader.CramRecordReader
validationStringency() - Method in class htsjdk.samtools.SamReaderFactory
validationStringency(ValidationStringency) - Method in class htsjdk.samtools.SamReaderFactory
  Set this factory's `ValidationStringency` to the provided one, then returns itself.
ValidationStringency - Enum Class in htsjdk.samtools
  How strict to be when reading a SAM or BAM, beyond bare minimum validation.
ValidationUtils - Class in htsjdk.utils
  Simple functions that streamline the checking of values.
ValidationUtils() - Constructor for class htsjdk.utils.ValidationUtils
value - Variable in class htsjdk.samtools.cram.common.MutableInt
value - Variable in class htsjdk.samtools.SAMBinaryTagAndValue
value - Variable in class htsjdk.samtools.SAMRecord.SAMTagAndValue
value - Variable in class htsjdk.samtools.TagValueAndUnsignedArrayFlag
value() - Method in enum class htsjdk.tribble.bed.BEDCodec.StartOffset
VALUE_DELIMITER - Static variable in class htsjdk.tribble.gff.Gff3Constants
valueOf(int) - Static method in enum class htsjdk.samtools.SAMFlag
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.beta.plugin.HtsContentType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.beta.plugin.interval.HtsQueryRule
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.BamIndexValidator.IndexValidationStringency
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.CigarOperator
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.cram.compression.range.RangeParams.ORDER
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.cram.compression.rans.RANSParams.ORDER
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.cram.ref.ReferenceContextType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.cram.structure.block.BlockContentType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.cram.structure.CRAMCompressionProfile
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.cram.structure.DataSeries
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.cram.structure.DataSeriesType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.cram.structure.EncodingID
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.DownsamplingIteratorFactory.Strategy
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.fastq.FastqConstants.FastqExtensions
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.fastq.FastqReader.LineType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SAMFileHeader.GroupOrder
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SAMFileHeader.SortOrder
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SAMFlag
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SamFlagField
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SamIndexes
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SamPairUtil.PairOrientation
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SamReaderFactory.Option
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SAMTag
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SAMValidationError.Severity
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SAMValidationError.Type
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.SQTagUtil.SQBase
  Deprecated.
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.util.AbstractRecordAndOffset.AlignmentType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.util.BlockCompressedInputStream.FileTermination
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.util.EdgingRecordAndOffset.Type
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.util.FastqQualityFormat
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.util.GzipCodec.Format
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.util.htsget.HtsgetClass
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.util.htsget.HtsgetFormat
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.util.Log.LogLevel
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.util.QualityEncodingDetector.FileContext
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.samtools.ValidationStringency
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.tribble.annotation.Strand
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.tribble.bed.BEDCodec.StartOffset
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.tribble.gff.Gff3Codec.DecodeDepth
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.tribble.gff.Gff3Codec.Gff3Directive
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.tribble.index.AbstractIndex.IndexType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.tribble.index.IndexFactory.IndexBalanceApproach
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.tribble.index.IndexFactory.IndexType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.bcf2.BCF2Type
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.variantcontext.GenotypeType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.variantcontext.JexlMissingValueTreatment
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.variantcontext.StructuralVariantType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.variantcontext.VariantContext.Type
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.variantcontext.VariantContext.Validation
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.variantcontext.writer.Options
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.vcf.VCFCompoundHeaderLine.SupportedHeaderLineType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.vcf.VCFHeaderLineCount
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.vcf.VCFHeaderLineType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class htsjdk.variant.vcf.VCFHeaderVersion
  Returns the enum constant of this class with the specified name.
valueOfCaseInsensitive(String) - Static method in enum class htsjdk.samtools.cram.structure.CRAMCompressionProfile
  Look up a profile by name, ignoring case.
values() - Static method in enum class htsjdk.beta.plugin.HtsContentType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.beta.plugin.interval.HtsQueryRule
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.BamIndexValidator.IndexValidationStringency
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.CigarOperator
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.cram.compression.range.RangeParams.ORDER
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.cram.compression.rans.RANSParams.ORDER
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.cram.ref.ReferenceContextType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.cram.structure.block.BlockCompressionMethod
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.cram.structure.block.BlockContentType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.cram.structure.CRAMCompressionProfile
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.cram.structure.DataSeries
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.cram.structure.DataSeriesType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.cram.structure.EncodingID
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.DownsamplingIteratorFactory.Strategy
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.fastq.FastqConstants.FastqExtensions
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.fastq.FastqReader.LineType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SAMFileHeader.GroupOrder
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SAMFileHeader.SortOrder
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SAMFlag
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SamFlagField
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SamIndexes
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SamPairUtil.PairOrientation
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SamReaderFactory.Option
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SAMReadGroupRecord.PlatformValue
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SAMTag
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SAMValidationError.Severity
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SAMValidationError.Type
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.SQTagUtil.SQBase
  Deprecated.
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.util.AbstractRecordAndOffset.AlignmentType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.util.BlockCompressedInputStream.FileTermination
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.util.EdgingRecordAndOffset.Type
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.util.FastqQualityFormat
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.util.GzipCodec.Format
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Method in class htsjdk.samtools.util.Histogram
  Returns a `Collection` view of the values contained in this histogram.
values() - Static method in enum class htsjdk.samtools.util.htsget.HtsgetClass
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.util.htsget.HtsgetFormat
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.util.htsget.HtsgetRequestField
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.util.Log.LogLevel
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.util.QualityEncodingDetector.FileContext
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.samtools.ValidationStringency
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.tribble.annotation.Strand
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.tribble.bed.BEDCodec.StartOffset
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.tribble.gff.Gff3Codec.DecodeDepth
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.tribble.gff.Gff3Codec.Gff3Directive
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.tribble.index.AbstractIndex.IndexType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.tribble.index.IndexFactory.IndexBalanceApproach
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.tribble.index.IndexFactory.IndexType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.bcf2.BCF2Type
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.variantcontext.GenotypeType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.variantcontext.JexlMissingValueTreatment
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.variantcontext.StructuralVariantType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.variantcontext.VariantContext.Type
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.variantcontext.VariantContext.Validation
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.variantcontext.writer.Options
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.vcf.VCFCompoundHeaderLine.SupportedHeaderLineType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.vcf.VCFHeaderLineCount
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.vcf.VCFHeaderLineType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class htsjdk.variant.vcf.VCFHeaderVersion
  Returns an array containing the constants of this enum class, in the order they are declared.
ValuesIterator(Iterator) - Constructor for class htsjdk.samtools.util.IntervalTree.ValuesIterator
variance() - Method in class htsjdk.tribble.util.MathUtils.RunningStat
VARIANT_CONTEXTS - Enum constant in enum class htsjdk.beta.plugin.HtsContentType
  Haploid reference content type (see `VariantsFormats` for related formats)
VariantContext - Class in htsjdk.variant.variantcontext
  High-level overview
VariantContext(VariantContext) - Constructor for class htsjdk.variant.variantcontext.VariantContext
  Copy constructor
VariantContext(String, String, String, long, long, Collection, GenotypesContext, double, Set, Map, boolean, EnumSet) - Constructor for class htsjdk.variant.variantcontext.VariantContext
  the actual constructor.
VariantContext.Type - Enum Class in htsjdk.variant.variantcontext
VariantContext.Validation - Enum Class in htsjdk.variant.variantcontext
VariantContextBuilder - Class in htsjdk.variant.variantcontext
  Builder class for `VariantContext`.
VariantContextBuilder() - Constructor for class htsjdk.variant.variantcontext.VariantContextBuilder
  Create an empty VariantContextBuilder where all values adopt their default values.
VariantContextBuilder(VariantContext) - Constructor for class htsjdk.variant.variantcontext.VariantContextBuilder
  Returns a new builder based on parent -- the new VC will have all fields initialized to their corresponding values in parent.
VariantContextBuilder(VariantContextBuilder) - Constructor for class htsjdk.variant.variantcontext.VariantContextBuilder
VariantContextBuilder(String, String, long, long, Collection) - Constructor for class htsjdk.variant.variantcontext.VariantContextBuilder
  Create an empty VariantContextBuilder where all values adopt their default values, but the bare min.
VariantContextComparator - Class in htsjdk.variant.variantcontext
  A Comparator that orders VariantContexts by the ordering of the contigs/chromosomes in the List provided at construction time, then by start position with each contig/chromosome.
VariantContextComparator(SAMSequenceDictionary) - Constructor for class htsjdk.variant.variantcontext.VariantContextComparator
VariantContextComparator(Collection) - Constructor for class htsjdk.variant.variantcontext.VariantContextComparator
  Creates a VariantContextComparator from the given VCF contig header lines.
VariantContextComparator(List) - Constructor for class htsjdk.variant.variantcontext.VariantContextComparator
VariantContextFilter - Interface in htsjdk.variant.variantcontext.filter
  API for filtering VariantContexts.
VariantContextUtils - Class in htsjdk.variant.variantcontext
VariantContextUtils() - Constructor for class htsjdk.variant.variantcontext.VariantContextUtils
VariantContextUtils.JexlVCMatchExp - Class in htsjdk.variant.variantcontext
  A simple but common wrapper for matching `VariantContext` objects using JEXL expressions
VariantContextWriter - Interface in htsjdk.variant.variantcontext.writer
  this class writes VCF files
VariantContextWriterBuilder - Class in htsjdk.variant.variantcontext.writer
VariantContextWriterBuilder() - Constructor for class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  Default constructor.
VariantContextWriterBuilder.OutputType - Enum Class in htsjdk.variant.variantcontext.writer
VariantsBundle - Class in htsjdk.beta.plugin.variants
  A `Bundle` for variants and variants-related resources that are backed by on disk files.
VariantsBundle(IOPath) - Constructor for class htsjdk.beta.plugin.variants.VariantsBundle
  Create a `VariantsBundle` containing only a variants resource.
VariantsBundle(IOPath, IOPath) - Constructor for class htsjdk.beta.plugin.variants.VariantsBundle
  Create a `VariantsBundle` containing only variants and an index.
VariantsBundle(Collection) - Constructor for class htsjdk.beta.plugin.variants.VariantsBundle
  Create a `VariantsBundle` using the resources in an existing bundle.
VariantsCodec - Interface in htsjdk.beta.plugin.variants
  Base class for all `HtsContentType.VARIANT_CONTEXTS` codecs.
VariantsCodecUtils - Class in htsjdk.beta.codecs.variants.vcf
  Utilities for VCF codec implementations.
VariantsCodecUtils() - Constructor for class htsjdk.beta.codecs.variants.vcf.VariantsCodecUtils
VariantsDecoder - Interface in htsjdk.beta.plugin.variants
  Base class for all `HtsContentType.VARIANT_CONTEXTS` decoders.
VariantsDecoderOptions - Class in htsjdk.beta.plugin.variants
VariantsDecoderOptions() - Constructor for class htsjdk.beta.plugin.variants.VariantsDecoderOptions
VariantsEncoder - Interface in htsjdk.beta.plugin.variants
  Base class for all `HtsContentType.VARIANT_CONTEXTS` encoders.
VariantsEncoderOptions - Class in htsjdk.beta.plugin.variants
VariantsEncoderOptions() - Constructor for class htsjdk.beta.plugin.variants.VariantsEncoderOptions
VariantsFormats - Class in htsjdk.beta.plugin.variants
  Class with string constants representing known formats supported by variants codecs.
VariantsFormats() - Constructor for class htsjdk.beta.plugin.variants.VariantsFormats
VariantsResolver - Class in htsjdk.beta.plugin.registry
  Class with methods for resolving inputs and outputs to variants encoders and decoders.
VariantsResolver() - Constructor for class htsjdk.beta.plugin.registry.VariantsResolver
  Create a VariantsResolver.
VCF - Enum constant in enum class htsjdk.samtools.util.htsget.HtsgetFormat
VCF - Enum constant in enum class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType
VCF - Static variable in class htsjdk.beta.plugin.variants.VariantsFormats
  VCF format.
VCF - Static variable in class htsjdk.samtools.util.FileExtensions
  extensions for VCF files and related formats.
VCF - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
VCF_CHARSET - Static variable in class htsjdk.variant.vcf.VCFEncoder
  The encoding used for VCF files: ISO-8859-1.
VCF_ENCODING_EPSILON - Static variable in class htsjdk.variant.vcf.VCFConstants
VCF_EXTENSIONS - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  since June 2019 Use `FileExtensions.VCF_LIST` instead.
VCF_EXTENSIONS_LIST - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  since June 2019 Use `FileExtensions.VCF_LIST` instead.
VCF_FILE_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  since June 2019 Use `FileExtensions.VCF` instead.
VCF_FLAGS - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
VCF_INDEX - Static variable in class htsjdk.samtools.util.FileExtensions
VCF_INDEX_EXTENSION - Static variable in class htsjdk.samtools.util.IOUtil
  Deprecated.
  since June 2019 Use `FileExtensions.VCF_INDEX` instead.
VCF_LIST - Static variable in class htsjdk.samtools.util.FileExtensions
VCF_LOCALE - Static variable in class htsjdk.variant.vcf.VCFConstants
VCF_STREAM - Enum constant in enum class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType
VCF_V32_VERSION - Static variable in class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFCodecV3_2
VCF_V33_VERSION - Static variable in class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFCodecV3_3
VCF_V40_VERSION - Static variable in class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFCodecV4_0
VCF_V41_VERSION - Static variable in class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFCodecV4_1
VCF_V42_VERSION - Static variable in class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFCodecV4_2
VCF_V43_VERSION - Static variable in class htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFCodecV4_3
VCF3_2 - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderVersion
VCF3_3 - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderVersion
VCF3_MAGIC_HEADER - Static variable in class htsjdk.variant.vcf.VCF3Codec
VCF3Codec - Class in htsjdk.variant.vcf
  A feature codec for the VCF3 specification, to read older VCF files.
VCF3Codec() - Constructor for class htsjdk.variant.vcf.VCF3Codec
VCF4_0 - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderVersion
VCF4_1 - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderVersion
VCF4_2 - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderVersion
VCF4_3 - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderVersion
VCF4_4 - Enum constant in enum class htsjdk.variant.vcf.VCFHeaderVersion
VCF4_MAGIC_HEADER - Static variable in class htsjdk.variant.vcf.VCFCodec
VCFAltHeaderLine - Class in htsjdk.variant.vcf
  A class representing ALT fields in the VCF header
VCFAltHeaderLine(String, VCFHeaderVersion) - Constructor for class htsjdk.variant.vcf.VCFAltHeaderLine
VCFCodec - Class in htsjdk.beta.codecs.variants.vcf
  InternalAPI Base class for concrete implementations of `HtsContentType.VARIANT_CONTEXTS` codecs.
VCFCodec - Class in htsjdk.variant.vcf
  A feature codec for the VCF 4 specification
VCFCodec() - Constructor for class htsjdk.beta.codecs.variants.vcf.VCFCodec
VCFCodec() - Constructor for class htsjdk.variant.vcf.VCFCodec
VCFCodecV3_2 - Class in htsjdk.beta.codecs.variants.vcf.vcfv3_2
  VCF V3.2 codec.
VCFCodecV3_2() - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFCodecV3_2
VCFCodecV3_3 - Class in htsjdk.beta.codecs.variants.vcf.vcfv3_3
  VCF V3.3 codec.
VCFCodecV3_3() - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFCodecV3_3
VCFCodecV4_0 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_0
  VCF V4.0 codec.
VCFCodecV4_0() - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFCodecV4_0
VCFCodecV4_1 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_1
  VCF V4.1 codec.
VCFCodecV4_1() - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFCodecV4_1
VCFCodecV4_2 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_2
  VCF V4.2 codec.
VCFCodecV4_2() - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFCodecV4_2
VCFCodecV4_3 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_3
  VCF V4.3 codec.
VCFCodecV4_3() - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFCodecV4_3
VCFCompoundHeaderLine - Class in htsjdk.variant.vcf
  a base class for compound header lines, which include info lines and format lines (so far)
VCFCompoundHeaderLine(String, int, VCFHeaderLineType, String, VCFCompoundHeaderLine.SupportedHeaderLineType) - Constructor for class htsjdk.variant.vcf.VCFCompoundHeaderLine
  create a VCF format header line
VCFCompoundHeaderLine(String, int, VCFHeaderLineType, String, VCFCompoundHeaderLine.SupportedHeaderLineType, String, String) - Constructor for class htsjdk.variant.vcf.VCFCompoundHeaderLine
  create a VCF format header line
VCFCompoundHeaderLine(String, VCFHeaderLineCount, VCFHeaderLineType, String, VCFCompoundHeaderLine.SupportedHeaderLineType) - Constructor for class htsjdk.variant.vcf.VCFCompoundHeaderLine
  create a VCF format header line
VCFCompoundHeaderLine(String, VCFHeaderLineCount, VCFHeaderLineType, String, VCFCompoundHeaderLine.SupportedHeaderLineType, String, String) - Constructor for class htsjdk.variant.vcf.VCFCompoundHeaderLine
  create a VCF format header line
VCFCompoundHeaderLine(String, VCFHeaderVersion, VCFCompoundHeaderLine.SupportedHeaderLineType) - Constructor for class htsjdk.variant.vcf.VCFCompoundHeaderLine
  create a VCF format header line
VCFCompoundHeaderLine.SupportedHeaderLineType - Enum Class in htsjdk.variant.vcf
VCFConstants - Class in htsjdk.variant.vcf
VCFConstants() - Constructor for class htsjdk.variant.vcf.VCFConstants
VCFContigHeaderLine - Class in htsjdk.variant.vcf
  A special class representing a contig VCF header line.
VCFContigHeaderLine(String, VCFHeaderVersion, String, int) - Constructor for class htsjdk.variant.vcf.VCFContigHeaderLine
  create a VCF contig header line
VCFContigHeaderLine(Map, int) - Constructor for class htsjdk.variant.vcf.VCFContigHeaderLine
VCFDecoder - Class in htsjdk.beta.codecs.variants.vcf
  InternalAPII Base class for concrete implementations of `HtsContentType.VARIANT_CONTEXTS` decoders.
VCFDecoder(Bundle, AbstractVCFCodec, VariantsDecoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.VCFDecoder
  InternalAPI Create a new VCF decoder.
VCFDecoderV3_2 - Class in htsjdk.beta.codecs.variants.vcf.vcfv3_2
  VCF V3.2 decoder.
VCFDecoderV3_2(Bundle, VariantsDecoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFDecoderV3_2
  Create a new VCF V3.2 decoder.
VCFDecoderV3_3 - Class in htsjdk.beta.codecs.variants.vcf.vcfv3_3
  VCF V3.3 decoder.
VCFDecoderV3_3(Bundle, VariantsDecoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFDecoderV3_3
  Create a new VCF V3.3 decoder.
VCFDecoderV4_0 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_0
  VCF V4.0 decoder.
VCFDecoderV4_0(Bundle, VariantsDecoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFDecoderV4_0
  Create a new VCF V4.0 decoder.
VCFDecoderV4_1 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_1
  VCF V4.1 decoder.
VCFDecoderV4_1(Bundle, VariantsDecoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFDecoderV4_1
  Create a new VCF V4.1 decoder.
VCFDecoderV4_2 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_2
  VCF V4.2 decoder.
VCFDecoderV4_2(Bundle, VariantsDecoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFDecoderV4_2
  Create a new VCF V4.2 decoder.
VCFDecoderV4_3 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_3
  VCF V4.3 decoder.
VCFDecoderV4_3(Bundle, VariantsDecoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFDecoderV4_3
  Create a new VCF V4.3 decoder.
VCFEncoder - Class in htsjdk.beta.codecs.variants.vcf
  InternalAPI Base class for concrete implementations of `HtsContentType.VARIANT_CONTEXTS` encoders.
VCFEncoder - Class in htsjdk.variant.vcf
  Functions specific to encoding VCF records.
VCFEncoder(Bundle, VariantsEncoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.VCFEncoder
  InternalAPI Create a new VCF encoder from a `Bundle`.
VCFEncoder(VCFHeader, boolean, boolean) - Constructor for class htsjdk.variant.vcf.VCFEncoder
  Prepare a VCFEncoder that will encode records appropriate to the given VCF header, optionally allowing missing fields in the header.
VCFEncoderV3_2 - Class in htsjdk.beta.codecs.variants.vcf.vcfv3_2
  VCF V3.2 encoder.
VCFEncoderV3_2(Bundle, VariantsEncoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFEncoderV3_2
  Create a new VCF V3.2 encoder.
VCFEncoderV3_3 - Class in htsjdk.beta.codecs.variants.vcf.vcfv3_3
  VCF V3.3 encoder.
VCFEncoderV3_3(Bundle, VariantsEncoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFEncoderV3_3
  Create a new VCF V3.3 encoder.
VCFEncoderV4_0 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_0
  VCF V4.0 encoder.
VCFEncoderV4_0(Bundle, VariantsEncoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFEncoderV4_0
  Create a new VCF V4.0 encoder.
VCFEncoderV4_1 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_1
  VCF V4.1 encoder.
VCFEncoderV4_1(Bundle, VariantsEncoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFEncoderV4_1
  Create a new VCF V4.1 encoder.
VCFEncoderV4_2 - Class in htsjdk.beta.codecs.variants.vcf.vcfv4_2
  VCF V4.2 encoder.
VCFEncoderV4_2(Bundle, VariantsEncoderOptions) - Constructor for class htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFEncoderV4_2
  Create a new VCF V4.2 encoder.
VCFFileReader - Class in htsjdk.variant.vcf
  Simplified interface for reading from VCF/BCF files.
VCFFileReader(File) - Constructor for class htsjdk.variant.vcf.VCFFileReader
  Constructs a VCFFileReader that requires the index to be present.
VCFFileReader(File, boolean) - Constructor for class htsjdk.variant.vcf.VCFFileReader
  Allows construction of a VCFFileReader that will or will not assert the presence of an index as desired.
VCFFileReader(File, File) - Constructor for class htsjdk.variant.vcf.VCFFileReader
  Constructs a VCFFileReader with a specified index.
VCFFileReader(File, File, boolean) - Constructor for class htsjdk.variant.vcf.VCFFileReader
  Allows construction of a VCFFileReader with a specified index file.
VCFFileReader(Path) - Constructor for class htsjdk.variant.vcf.VCFFileReader
  Constructs a VCFFileReader that requires the index to be present.
VCFFileReader(Path, boolean) - Constructor for class htsjdk.variant.vcf.VCFFileReader
  Allows construction of a VCFFileReader that will or will not assert the presence of an index as desired.
VCFFileReader(Path, Path) - Constructor for class htsjdk.variant.vcf.VCFFileReader
  Constructs a VCFFileReader with a specified index.
VCFFileReader(Path, Path, boolean) - Constructor for class htsjdk.variant.vcf.VCFFileReader
  Allows construction of a VCFFileReader with a specified index path.
VCFFilterHeaderLine - Class in htsjdk.variant.vcf
VCFFilterHeaderLine(String) - Constructor for class htsjdk.variant.vcf.VCFFilterHeaderLine
  Convenience constructor for FILTER whose description is the name
VCFFilterHeaderLine(String, VCFHeaderVersion) - Constructor for class htsjdk.variant.vcf.VCFFilterHeaderLine
  create a VCF info header line
VCFFilterHeaderLine(String, String) - Constructor for class htsjdk.variant.vcf.VCFFilterHeaderLine
  create a VCF filter header line
VCFFormatHeaderLine - Class in htsjdk.variant.vcf
VCFFormatHeaderLine(String, int, VCFHeaderLineType, String) - Constructor for class htsjdk.variant.vcf.VCFFormatHeaderLine
VCFFormatHeaderLine(String, VCFHeaderLineCount, VCFHeaderLineType, String) - Constructor for class htsjdk.variant.vcf.VCFFormatHeaderLine
VCFFormatHeaderLine(String, VCFHeaderVersion) - Constructor for class htsjdk.variant.vcf.VCFFormatHeaderLine
VCFHeader - Class in htsjdk.variant.vcf
  A class to represent a VCF header
VCFHeader() - Constructor for class htsjdk.variant.vcf.VCFHeader
  Create an empty VCF header with no header lines and no samples
VCFHeader(VCFHeader) - Constructor for class htsjdk.variant.vcf.VCFHeader
  Creates a deep copy of the given VCFHeader, duplicating all its metadata and sample names.
VCFHeader(VCFHeaderVersion, Set, Set) - Constructor for class htsjdk.variant.vcf.VCFHeader
  create a VCF header, given a target version, a list of meta data and auxiliary tags
VCFHeader(Set) - Constructor for class htsjdk.variant.vcf.VCFHeader
  create a VCF header, given a list of meta data and auxiliary tags
VCFHeader(Set, List) - Constructor for class htsjdk.variant.vcf.VCFHeader
VCFHeader(Set, Set) - Constructor for class htsjdk.variant.vcf.VCFHeader
  create a VCF header, given a list of meta data and auxiliary tags
VCFHeader.HEADER_FIELDS - Enum Class in htsjdk.variant.vcf
VCFHeaderLine - Class in htsjdk.variant.vcf
VCFHeaderLine(String, String) - Constructor for class htsjdk.variant.vcf.VCFHeaderLine
  create a VCF header line
VCFHeaderLineCount - Enum Class in htsjdk.variant.vcf
  the count encodings we use for fields in VCF header lines
VCFHeaderLineTranslator - Class in htsjdk.variant.vcf
  A class for translating between vcf header versions
VCFHeaderLineTranslator() - Constructor for class htsjdk.variant.vcf.VCFHeaderLineTranslator
VCFHeaderLineType - Enum Class in htsjdk.variant.vcf
  the type encodings we use for fields in VCF header lines
VCFHeaderReader - Class in htsjdk.variant.utils
  Utility class to read a VCF header without being told beforehand whether the input is VCF or BCF.
VCFHeaderVersion - Enum Class in htsjdk.variant.vcf
  information that identifies each header version
VCFIDHeaderLine - Interface in htsjdk.variant.vcf
  an interface for ID-based header lines
VCFInfoHeaderLine - Class in htsjdk.variant.vcf
VCFInfoHeaderLine(String, int, VCFHeaderLineType, String) - Constructor for class htsjdk.variant.vcf.VCFInfoHeaderLine
VCFInfoHeaderLine(String, int, VCFHeaderLineType, String, String, String) - Constructor for class htsjdk.variant.vcf.VCFInfoHeaderLine
VCFInfoHeaderLine(String, VCFHeaderLineCount, VCFHeaderLineType, String) - Constructor for class htsjdk.variant.vcf.VCFInfoHeaderLine
VCFInfoHeaderLine(String, VCFHeaderLineCount, VCFHeaderLineType, String, String, String) - Constructor for class htsjdk.variant.vcf.VCFInfoHeaderLine
VCFInfoHeaderLine(String, VCFHeaderVersion) - Constructor for class htsjdk.variant.vcf.VCFInfoHeaderLine
VCFIterator - Interface in htsjdk.variant.vcf
  An iterator of `VariantContext`.
VCFIteratorBuilder - Class in htsjdk.variant.vcf
  A Class building `VCFIterator` Example:
VCFIteratorBuilder() - Constructor for class htsjdk.variant.vcf.VCFIteratorBuilder
VCFMetaHeaderLine - Class in htsjdk.variant.vcf
  A class representing META fields in the VCF header
VCFMetaHeaderLine(String, VCFHeaderVersion) - Constructor for class htsjdk.variant.vcf.VCFMetaHeaderLine
VCFPassThruTextTransformer - Class in htsjdk.variant.vcf
  A no-op implementation of VCFTextTransformer for pre-v43 VCFs, when such encodings are not supported and no transformation need be done.
VCFPassThruTextTransformer() - Constructor for class htsjdk.variant.vcf.VCFPassThruTextTransformer
VCFPedigreeHeaderLine - Class in htsjdk.variant.vcf
  A class representing PEDIGREE fields in the VCF header
VCFPedigreeHeaderLine(String, VCFHeaderVersion) - Constructor for class htsjdk.variant.vcf.VCFPedigreeHeaderLine
VCFPercentEncodedTextTransformer - Class in htsjdk.variant.vcf
  Text transformer for attribute values embedded in VCF.
VCFPercentEncodedTextTransformer() - Constructor for class htsjdk.variant.vcf.VCFPercentEncodedTextTransformer
VCFReader - Interface in htsjdk.variant.vcf
  Interface for reading VCF/BCF files.
VCFRecordCodec - Class in htsjdk.variant.vcf
  Writes VariantContext instances to an OutputStream without headers or metadata.
VCFRecordCodec(VCFHeader) - Constructor for class htsjdk.variant.vcf.VCFRecordCodec
VCFRecordCodec(VCFHeader, boolean) - Constructor for class htsjdk.variant.vcf.VCFRecordCodec
VCFSampleHeaderLine - Class in htsjdk.variant.vcf
  A class representing SAMPLE fields in the VCF header
VCFSampleHeaderLine(String, VCFHeaderVersion) - Constructor for class htsjdk.variant.vcf.VCFSampleHeaderLine
VCFSimpleHeaderLine - Class in htsjdk.variant.vcf
VCFSimpleHeaderLine(String, VCFHeaderVersion, String, List) - Constructor for class htsjdk.variant.vcf.VCFSimpleHeaderLine
  create a VCF info header line
VCFSimpleHeaderLine(String, VCFHeaderVersion, String, List, List) - Constructor for class htsjdk.variant.vcf.VCFSimpleHeaderLine
  create a VCF info header line
VCFSimpleHeaderLine(String, String, String) - Constructor for class htsjdk.variant.vcf.VCFSimpleHeaderLine
  create a VCF filter header line
VCFSimpleHeaderLine(String, Map) - Constructor for class htsjdk.variant.vcf.VCFSimpleHeaderLine
VCFStandardHeaderLines - Class in htsjdk.variant.vcf
  Manages header lines for standard VCF
VCFStandardHeaderLines() - Constructor for class htsjdk.variant.vcf.VCFStandardHeaderLines
VCFTextTransformer - Interface in htsjdk.variant.vcf
  Interface for transforming attribute values embedded in VCF.
VCFUtils - Class in htsjdk.variant.vcf
VCFUtils() - Constructor for class htsjdk.variant.vcf.VCFUtils
verifyIndexMagicNumber(String) - Method in class htsjdk.samtools.AbstractBAMFileIndex
verifyIndexMagicNumber(String) - Method in class htsjdk.samtools.CSIIndex
version - Variable in class htsjdk.tribble.index.AbstractIndex
version - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
VERSION - Static variable in class htsjdk.tribble.index.AbstractIndex
VERSION_1 - Static variable in class htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0
VERSION_1 - Static variable in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMCodecV1_0
VERSION_1 - Static variable in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMCodecV1_0
VERSION_2_1 - Static variable in class htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMCodecV2_1
VERSION_3_0 - Static variable in class htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMCodecV3_0
VERSION_3_1 - Static variable in class htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMCodecV3_1
VERSION_TAG - Static variable in class htsjdk.samtools.SAMFileHeader
VERSION3_DIRECTIVE - Enum constant in enum class htsjdk.tribble.gff.Gff3Codec.Gff3Directive
VersionHeader - Class in htsjdk.samtools.metrics
  Header that stores information about the version of some piece of software or data used to create the metrics file.
VersionHeader() - Constructor for class htsjdk.samtools.metrics.VersionHeader

## W

warn(Object...) - Method in class htsjdk.samtools.util.Log
  Logs one or more message parts at level warn.
warn(Throwable, Object...) - Method in class htsjdk.samtools.util.Log
  Logs a Throwable and optional message parts at level warn.
warn(Supplier) - Method in class htsjdk.samtools.util.Log
  Logs a message part at level warn.
warnedAboutNoEqualsForNonFlag - Variable in class htsjdk.variant.vcf.AbstractVCFCodec
WARNING - Enum constant in enum class htsjdk.samtools.SAMValidationError.Severity
WARNING - Enum constant in enum class htsjdk.samtools.util.Log.LogLevel
What are they? - Section in class htsjdk.variant.variantcontext.VariantContext
WholeGenomeReferenceSequenceMask - Class in htsjdk.samtools.util
  Implementation of ReferenceSequenceMask that indicates that all the loci in the sequence dictionary are of interest.
WholeGenomeReferenceSequenceMask(SAMFileHeader) - Constructor for class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
WholeReadClippedFilter - Class in htsjdk.samtools.filter
  Filter SAMRecords so that only those that have at least one un-clipped base are returned.
WholeReadClippedFilter() - Constructor for class htsjdk.samtools.filter.WholeReadClippedFilter
withDataClass(HtsgetClass) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
withDataClass(HtsgetClass) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
withField(HtsgetRequestField) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
withField(HtsgetRequestField) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
withFields(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
withFields(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
withFormat(HtsgetFormat) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
withFormat(HtsgetFormat) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
withinDistanceOf(Locatable, int) - Method in interface htsjdk.samtools.util.Locatable
  Determines whether this interval comes within `distance` of overlapping the provided locatable.
withinRange(long) - Method in enum class htsjdk.variant.bcf2.BCF2Type
  Can we encode value v in this type, according to its declared range.
withInterval(Locatable) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
withInterval(Locatable) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
withIntervals(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
withNotag(String) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
withNotag(String) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
withNotags(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
withNotags(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
withSamFlagField(SamFlagField) - Method in class htsjdk.samtools.SAMLineParser
  Sets the expected SAM flag type expected for all records.
withTag(String) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
withTag(String) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
withTags(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetPOSTRequest
withTags(Collection) - Method in class htsjdk.samtools.util.htsget.HtsgetRequest
withUpdatedContigs(VCFHeader, File, SAMSequenceDictionary) - Static method in class htsjdk.variant.vcf.VCFUtils
  Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary
withUpdatedContigsAsLines(Set, File, SAMSequenceDictionary) - Static method in class htsjdk.variant.vcf.VCFUtils
withUpdatedContigsAsLines(Set, File, SAMSequenceDictionary, boolean) - Static method in class htsjdk.variant.vcf.VCFUtils
wordWrap(String, int) - Static method in class htsjdk.samtools.util.StringUtil
  Return input string with newlines inserted to ensure that all lines have length `<=` maxLineLength.
wordWrapSingleLine(String, int) - Static method in class htsjdk.samtools.util.StringUtil
Working with genotypes - Section in class htsjdk.variant.variantcontext.VariantContext
Working with Variant Contexts - Section in class htsjdk.variant.variantcontext.VariantContext
wouldBeBreakpoint(byte[]) - Static method in interface htsjdk.variant.variantcontext.Allele
  Deprecated.
wouldBeNoCallAllele(byte[]) - Static method in interface htsjdk.variant.variantcontext.Allele
  Deprecated.
wouldBeNullAllele(byte[]) - Static method in interface htsjdk.variant.variantcontext.Allele
  Deprecated.
wouldBeSingleBreakend(byte[]) - Static method in interface htsjdk.variant.variantcontext.Allele
  Deprecated.
wouldBeStarAllele(byte[]) - Static method in interface htsjdk.variant.variantcontext.Allele
  Deprecated.
wouldBeSymbolicAllele(byte[]) - Static method in interface htsjdk.variant.variantcontext.Allele
  Deprecated.
wrap(byte[]) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Wrap a byte array in a little-endian ByteBuffer.
wrapInputStream(InputStream) - Method in class htsjdk.samtools.util.SnappyLoader
  Wrap an InputStream in a SnappyInputStream.
wrapOutputStream(OutputStream) - Method in class htsjdk.samtools.util.SnappyLoader
  Wrap an OutputStream in a SnappyOutputStream.
wrappedIterator - Variable in class htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator
  The wrapped iterator.
wrapTempInputStream(InputStream, int) - Method in class htsjdk.samtools.util.TempStreamFactory
  Wrap the given InputStream in a SnappyInputStream if available.
wrapTempOutputStream(OutputStream, int) - Method in class htsjdk.samtools.util.TempStreamFactory
  Wrap the given OutputStream in a SnappyOutputStream if available.
write(boolean) - Method in interface htsjdk.samtools.cram.io.BitOutputStream
  Write a single bit specified in the boolean argument.
write(boolean) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
write(boolean, long) - Method in interface htsjdk.samtools.cram.io.BitOutputStream
  Write a single bit specified in the boolean argument repeatedly.
write(boolean, long) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
write(byte) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
write(byte[]) - Method in class htsjdk.samtools.cram.encoding.external.ExternalByteArrayCodec
write(byte[]) - Method in class htsjdk.samtools.cram.io.CRAMByteWriter
  Write all bytes from the given array.
write(byte[]) - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
write(byte[]) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
write(byte[]) - Method in class htsjdk.samtools.util.BlockCompressedOutputStream
  Writes b.length bytes from the specified byte array to this output stream.
write(byte[]) - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
write(byte[]) - Method in class htsjdk.samtools.util.PositionalOutputStream
write(byte[], int, int) - Method in class htsjdk.samtools.cram.io.CRAMByteWriter
  Write `len` bytes from the given array starting at offset `off`.
write(byte[], int, int) - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
write(byte[], int, int) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
write(byte[], int, int) - Method in class htsjdk.samtools.util.BlockCompressedOutputStream
  Writes len bytes from the specified byte array starting at offset off to this output stream.
write(byte[], int, int) - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
write(byte[], int, int) - Method in class htsjdk.samtools.util.PositionalOutputStream
write(byte[], int, int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
write(byte, int) - Method in interface htsjdk.samtools.cram.io.BitOutputStream
  Write specified number of bits supplied in the byte value.
write(byte, int) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
write(char[], int, int) - Method in class htsjdk.samtools.util.AsciiWriter
  All other Writer methods vector through this, so this is the only one that must be overridden.
write(int) - Method in class htsjdk.samtools.cram.io.CRAMByteWriter
  Write a single byte.
write(int) - Method in class htsjdk.samtools.cram.io.CRC32OutputStream
write(int) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
write(int) - Method in class htsjdk.samtools.util.BlockCompressedOutputStream
write(int) - Method in class htsjdk.samtools.util.Md5CalculatingOutputStream
write(int) - Method in class htsjdk.samtools.util.PositionalOutputStream
write(int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
write(int[], OutputStream) - Static method in class htsjdk.samtools.cram.io.CramIntArray
  Write CRAM int array to a `OutputStream`.
write(int, int) - Method in interface htsjdk.samtools.cram.io.BitOutputStream
  Write specified number of bits supplied in the integer value.
write(int, int) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
write(int, OutputStream) - Method in enum class htsjdk.variant.bcf2.BCF2Type
write(long, int) - Method in interface htsjdk.samtools.cram.io.BitOutputStream
  Write specified number of bits supplied in the long value.
write(long, int) - Method in class htsjdk.samtools.cram.io.DefaultBitOutputStream
write(A) - Method in interface htsjdk.io.Writer
  Writes one item.
write(CRAMVersion, OutputStream) - Method in class htsjdk.samtools.cram.structure.block.Block
  Write the block out to the the specified `OutputStream`.
write(CRAMVersion, OutputStream) - Method in class htsjdk.samtools.cram.structure.CompressionHeader
  Write this CompressionHeader out to an internal OutputStream, wrap it in a Block, and write that Block out to the passed-in OutputStream.
write(CRAMVersion, OutputStream) - Method in class htsjdk.samtools.cram.structure.Container
  Writes a complete `Container` with it's header to a `OutputStream`.
write(CRAMVersion, OutputStream) - Method in class htsjdk.samtools.cram.structure.ContainerHeader
  Write CRAM `Container` (header only) out into the given `OutputStream`.
write(CRAMVersion, OutputStream) - Method in class htsjdk.samtools.cram.structure.Slice
write(BitOutputStream, T) - Method in class htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanCanoncialCodeGenerator
write(FastqRecord) - Method in class htsjdk.samtools.fastq.BasicFastqWriter
write(FastqRecord) - Method in interface htsjdk.samtools.fastq.FastqWriter
write(SAMRecord) - Method in class htsjdk.beta.codecs.reads.bam.bamV1_0.BAMEncoderV1_0
write(SAMRecord) - Method in class htsjdk.beta.codecs.reads.cram.CRAMEncoder
write(SAMRecord) - Method in class htsjdk.beta.codecs.reads.sam.samV1_0.SAMEncoderV1_0
write(Interval) - Method in class htsjdk.samtools.util.IntervalListWriter
  Writes a single interval list.
write(LittleEndianOutputStream) - Method in class htsjdk.tribble.index.AbstractIndex
write(LittleEndianOutputStream) - Method in interface htsjdk.tribble.index.ChrIndex
write(LittleEndianOutputStream) - Method in interface htsjdk.tribble.index.Index
  all indexes are writable to disk
write(LittleEndianOutputStream) - Method in class htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex
write(LittleEndianOutputStream) - Method in class htsjdk.tribble.index.linear.LinearIndex.ChrIndex
write(LittleEndianOutputStream) - Method in class htsjdk.tribble.index.tabix.TabixIndex
write(VariantContext) - Method in class htsjdk.beta.codecs.variants.vcf.VCFEncoder
write(File) - Method in class htsjdk.samtools.metrics.MetricsFile
  Writes out the metrics file to the supplied file.
write(File) - Method in class htsjdk.samtools.util.IntervalList
  Writes out the list of intervals to the supplied file.
write(File) - Method in interface htsjdk.tribble.index.Index
  Writes the index into a file.
write(OutputStream) - Method in class htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  Write the encoding map out to a CRAM Stream
write(OutputStream) - Method in class htsjdk.variant.bcf2.BCFVersion
  Write out the BCF magic information indicating this is a BCF file with corresponding major and minor versions
write(Writer) - Method in class htsjdk.samtools.metrics.MetricsFile
  Writes out the metrics file to the supplied writer.
write(Appendable, FastqRecord) - Static method in class htsjdk.samtools.fastq.FastqEncoder
  Writes a FastqRecord into the Appendable output.
write(Appendable, VariantContext) - Method in class htsjdk.variant.vcf.VCFEncoder
  encodes a `VariantContext` context as VCF, and writes it directly to an `Appendable` This may be more efficient than calling `VCFEncoder.encode(VariantContext)` and then writing the result since it avoids creating an intermediate string.
write(Integer) - Method in class htsjdk.samtools.cram.encoding.core.BetaIntegerCodec
write(Iterable) - Method in interface htsjdk.io.Writer
  Writes out one or more items in order.
write(ByteBuffer) - Method in class htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel
write(Path) - Method in class htsjdk.samtools.reference.FastaSequenceIndex
  Writes this index to the specified path.
write(Path) - Method in class htsjdk.samtools.util.IntervalList
  Writes out the list of intervals to the supplied path.
write(Path) - Method in class htsjdk.tribble.index.AbstractIndex
write(Path) - Method in interface htsjdk.tribble.index.Index
  Writes the index into a path.
write(Path) - Method in class htsjdk.tribble.index.tabix.TabixIndex
  Writes the index with BGZF.
write(List, OutputStream) - Static method in class htsjdk.samtools.cram.io.CramIntArray
  Write CRAM int List to a `OutputStream`.
write(R) - Method in interface htsjdk.beta.plugin.HtsEncoder
  Write a single record to the underlying output.
write(T) - Method in interface htsjdk.samtools.cram.encoding.CRAMCodec
  Write an object to the stream
write(T) - Method in class htsjdk.samtools.util.AbstractAsyncWriter
  Public method for sub-classes or ultimately consumers to put an item into the queue to be written out.
WRITE_BUFFER_INITIAL_SIZE - Static variable in class htsjdk.variant.variantcontext.writer.BCF2Encoder
WRITE_FULL_FORMAT_FIELD - Enum constant in enum class htsjdk.variant.variantcontext.writer.Options
writeAlignment(SAMRecord) - Method in class htsjdk.samtools.BAMFileWriter
writeAlignment(SAMRecord) - Method in class htsjdk.samtools.BAMStreamWriter
writeAlignment(SAMRecord) - Method in class htsjdk.samtools.CRAMContainerStreamWriter
  Accumulate alignment records until we meet the threshold to flush a container.
writeAlignment(SAMRecord) - Method in class htsjdk.samtools.CRAMFileWriter
  Write an alignment record.
writeAlignment(SAMRecord) - Method in class htsjdk.samtools.SAMFileWriterImpl
  Writes the record to disk.
writeAlignment(SAMRecord) - Method in class htsjdk.samtools.SAMTextWriter
  Write the record.
writeBasedOnFeatureFile(File) - Method in interface htsjdk.tribble.index.Index
  Write an appropriately named and located Index file based on the name and location of the featureFile.
writeBasedOnFeaturePath(Path) - Method in class htsjdk.tribble.index.AbstractIndex
writeBasedOnFeaturePath(Path) - Method in interface htsjdk.tribble.index.Index
  Write an appropriately named and located Index file based on the name and location of the featureFile.
writeBasedOnFeaturePath(Path) - Method in class htsjdk.tribble.index.tabix.TabixIndex
  Writes to a path with appropriate name and directory based on feature path.
writeBlocks(CRAMVersion, OutputStream) - Method in class htsjdk.samtools.cram.structure.SliceBlocks
  Write the coreBlock and each external block out to a CRAM stream.
writeBoolean(boolean) - Method in class htsjdk.samtools.util.BinaryCodec
  Writes a boolean (1 byte) to the output buffer
writeBoolean(boolean) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
writeByte(byte) - Method in class htsjdk.samtools.util.BinaryCodec
  Writes a byte to the output buffer
writeByte(int) - Method in class htsjdk.samtools.util.BinaryCodec
writeByte(int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
writeBytes(byte[]) - Method in class htsjdk.samtools.util.BinaryCodec
  Writes a byte array to the output buffer
writeBytes(byte[], int, int) - Method in class htsjdk.samtools.util.BinaryCodec
writeBytes(String) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
writeChar(int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
writeContainer(Container) - Method in class htsjdk.samtools.CRAMContainerStreamWriter
writeCramEOF(CRAMVersion, OutputStream) - Static method in class htsjdk.samtools.cram.build.CramIO
  Write an end-of-file marker to the `OutputStream`.
writeCramHeader(CramHeader, OutputStream) - Static method in class htsjdk.samtools.cram.build.CramIO
  Writes CRAM header into the specified `OutputStream`.
writeDouble(double) - Method in class htsjdk.samtools.util.BinaryCodec
  Write a double (8 bytes) to the output stream
writeDouble(double) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
writeFieldKey(BCF2Encoder) - Method in class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
  Write the field key (dictionary offset and type) into the BCF2Encoder stream
writeFloat(float) - Method in class htsjdk.samtools.util.BinaryCodec
  Write a float (4 bytes) to the output stream
writeFloat(float) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
writeGtField(Map, Appendable, Genotype) - Static method in class htsjdk.variant.vcf.VCFEncoder
  write the encoded GT field for a Genotype
writeHeader() - Method in class htsjdk.samtools.CRAMContainerStreamWriter
  Write a CRAM file header and the previously provided SAM header to the stream.
writeHeader(SAMFileHeader) - Method in class htsjdk.samtools.BAMStreamWriter
writeHeader(SAMFileHeader) - Method in class htsjdk.samtools.CRAMContainerStreamWriter
  Write a CRAM file header and the provided SAM header to the stream.
writeHeader(SAMFileHeader) - Method in class htsjdk.samtools.CRAMFileWriter
writeHeader(SAMFileHeader) - Method in class htsjdk.samtools.SAMFileWriterImpl
  Write the header to disk.
writeHeader(SAMFileHeader) - Method in class htsjdk.samtools.SAMTextWriter
writeHeader(BinaryCodec, SAMFileHeader) - Static method in class htsjdk.samtools.BAMFileWriter
  Writes a header to a BAM file.
writeHeader(BinaryCodec, SAMFileHeader, String) - Static method in class htsjdk.samtools.BAMFileWriter
  Writes a header to a BAM file.
writeHeader(VCFHeader) - Method in class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
writeHeader(VCFHeader) - Method in class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  Deprecated.
writeHeader(VCFHeader) - Method in interface htsjdk.variant.variantcontext.writer.VariantContextWriter
  Writes the header
writeHeader(OutputStream, SAMFileHeader) - Static method in class htsjdk.samtools.BAMFileWriter
  Write a BAM file header to an output stream in block compressed BAM format.
writeHeader(String) - Method in class htsjdk.samtools.BAMFileWriter
writeHeader(String) - Method in class htsjdk.samtools.CRAMFileWriter
writeHeader(String) - Method in class htsjdk.samtools.SAMFileWriterImpl
  Deprecated.
  since 06/2018. `SAMFileWriterImpl.writeHeader(SAMFileHeader)` is preferred for avoid String construction if not need it.
writeHeader(String) - Method in class htsjdk.samtools.SAMTextWriter
  Write the header text.
writeIndex(SeekableStream, OutputStream) - Static method in class htsjdk.samtools.CRAMCRAIIndexer
  Generate and write a CRAI index to an output stream from a CRAM input stream
writeIndex(Index, File) - Static method in class htsjdk.tribble.index.IndexFactory
  Deprecated.
  use `Index.write(File)` instead
writeIndex(OutputStream) - Method in class htsjdk.samtools.cram.CRAIIndex
  Write out the index to an output stream;
writeIndex(OutputStream) - Method in class htsjdk.samtools.util.GZIIndex
  Writes this index into the requested path.
writeIndex(Path) - Method in class htsjdk.samtools.util.GZIIndex
  Writes this index into the requested path.
writeInt(int) - Method in class htsjdk.samtools.util.BinaryCodec
  Write a 32-bit int to the output stream
writeInt(int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
writeInt32(int) - Static method in class htsjdk.samtools.cram.io.CramInt
  Write int value to an array of bytes encoded as CRAM int data type.
writeInt32(int, OutputStream) - Static method in class htsjdk.samtools.cram.io.CramInt
  Write int value to `OutputStream` encoded as CRAM int data type.
writeLong(long) - Method in class htsjdk.samtools.util.BinaryCodec
  Write a 64-bit long to the output stream
writeLong(long) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
Writer<A> - Interface in htsjdk.io
writeRandomReference(SAMFileHeader, Path) - Static method in class htsjdk.samtools.SAMRecordSetBuilder
  Writes a random (but deterministic) reference file given a `SAMFileHeader` output file is expected to have a non-compressed fasta suffix.
writeRandomReference(Path) - Method in class htsjdk.samtools.SAMRecordSetBuilder
  Writes a random (but deterministic) reference file given a `SAMFileHeader` output file is expected to have a non-compressed fasta suffix.
writeSAMFileHeaderContainer(CRAMVersion, SAMFileHeader, OutputStream) - Static method in class htsjdk.samtools.cram.structure.Container
  Write a SAMFileHeader container to a CRAM stream.
writeShort(int) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
writeShort(short) - Method in class htsjdk.samtools.util.BinaryCodec
  Write a 16-bit short to output stream
writeSingleSequenceReference(Path, boolean, boolean, String, String, byte[]) - Static method in class htsjdk.samtools.reference.FastaReferenceWriter
  Convenient method to write a FASTA file with a single sequence.
writeSingleSequenceReference(Path, int, boolean, boolean, String, String, byte[]) - Static method in class htsjdk.samtools.reference.FastaReferenceWriter
  Convenient method to write a FASTA file with a single sequence.
writeSingleValue(byte, Object, boolean) - Static method in class htsjdk.samtools.cram.structure.ReadTag
  Serialize a single tag value to a byte array in BAM binary format.
writeString(String) - Method in class htsjdk.tribble.util.LittleEndianOutputStream
  Srite a string as a null terminated byte array.
writeString(String, boolean, boolean) - Method in class htsjdk.samtools.util.BinaryCodec
  Writes a string to the buffer as ASCII bytes
writeStringToPath(IOPath, String) - Static method in class htsjdk.beta.io.IOPathUtils
  Write a String to an IOPath.
writeStringToPath(IOPath, String, boolean) - Static method in class htsjdk.beta.plugin.IOUtils
  Write a String to an IOPath.
writeTable(PrintStream) - Method in class htsjdk.tribble.index.linear.LinearIndex
  Code to convert linear index to a text table for analysis
writeTag(short, Object, boolean) - Method in class htsjdk.samtools.BinaryTagCodec
  Write the given tag name and value to disk.
writeToSliceBlocks(CRAMCodecModelContext, List, int) - Method in class htsjdk.samtools.cram.encoding.writer.CramRecordWriter
  Writes a series of Cram Compression Records to the underlying `SliceBlocks`, using this class's Encodings
writeToStream(OutputStream) - Method in class htsjdk.samtools.cram.CRAIEntry
  Serialize the entry to a CRAI index stream.
writeUByte(short) - Method in class htsjdk.samtools.util.BinaryCodec
  Write an 8-bit unsigned byte.
writeUInt(long) - Method in class htsjdk.samtools.util.BinaryCodec
  Write a 32-bit unsigned int.
writeUint7(int, byte[], int[]) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Write uint7 into byte[] at posHolder[0], advancing posHolder[0].
writeUint7(int, ByteBuffer) - Static method in class htsjdk.samtools.cram.compression.CompressionUtils
  Write an unsigned integer using 7-bit variable-length encoding (uint7).
writeUnsignedITF8(int) - Static method in class htsjdk.samtools.cram.io.ITF8
  Writes an unsigned (32 bit) integer to a byte new array encoded as ITF8.
writeUnsignedITF8(int, CRAMByteWriter) - Static method in class htsjdk.samtools.cram.io.ITF8
  Writes an unsigned ITF8 integer to a `CRAMByteWriter`.
writeUnsignedITF8(int, OutputStream) - Static method in class htsjdk.samtools.cram.io.ITF8
  Writes an unsigned (32 bit) integer to an `OutputStream` encoded as ITF8.
writeUnsignedITF8(int, ByteBuffer) - Static method in class htsjdk.samtools.cram.io.ITF8
  Writes an unsigned (32 bit) integer to an `OutputStream` encoded as ITF8.
writeUnsignedLTF8(long, CRAMByteWriter) - Static method in class htsjdk.samtools.cram.io.LTF8
  Writes an unsigned LTF8 long to a `CRAMByteWriter`.
writeUnsignedLTF8(long, OutputStream) - Static method in class htsjdk.samtools.cram.io.LTF8
  Writes an unsigned long value to the output stream.
writeUShort(int) - Method in class htsjdk.samtools.util.BinaryCodec
  Write a 16-bit unsigned short.
written - Variable in class htsjdk.tribble.util.LittleEndianOutputStream

## X

X - Enum constant in enum class htsjdk.samtools.CigarOperator
  Mismatches the reference.
XF - Static variable in class htsjdk.samtools.ReservedTagConstants
  The Four54 edit string of 454 cafie and homopolymer corrections
XN - Static variable in class htsjdk.samtools.ReservedTagConstants
  Present and set to 1 if a read is a noise read.
XQ - Static variable in class htsjdk.samtools.ReservedTagConstants
  The sum of the mismatched qualities.
XS - Static variable in class htsjdk.samtools.ReservedTagConstants
  The original sequence before 454 cafie and homopolymer correction
XT - Static variable in class htsjdk.samtools.ReservedTagConstants
  The name of an attribute which stores the 1-based index of the start of sequence within a read (in original orientation) that should be clipped or trimmed before alignment and downstream use.

## Z

ZERO - Enum constant in enum class htsjdk.samtools.cram.compression.range.RangeParams.ORDER
ZERO - Enum constant in enum class htsjdk.samtools.cram.compression.rans.RANSParams.ORDER
ZERO - Enum constant in enum class htsjdk.tribble.bed.BEDCodec.StartOffset
ZERO_B_EOF_MARKER - Static variable in class htsjdk.samtools.cram.build.CramIO
  The 'zero-B' EOF marker as per CRAM specs v2.1.
ZERO_BASED - Static variable in class htsjdk.tribble.index.tabix.TabixFormat
ZERO_F_EOF_MARKER - Static variable in class htsjdk.samtools.cram.build.CramIO
  The zero-F EOF marker as per CRAM specs v3.0.

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