# Deprecated API

## Contents

- Interfaces
- Classes
- Fields
- Methods
- Constructors
- Enum Constants

Deprecated Interfaces
Interface
Description
htsjdk.samtools.util.Lazy.LazyInitializer
since 1/2017 use a `Supplier` instead

Deprecated Classes
Class
Description
htsjdk.samtools.apps.TimeChannel
This is deprecated with no replacement. 1/19
htsjdk.samtools.apps.TimeRandomAccessFile
This is deprecated with no replacement. 1/19
htsjdk.samtools.filter.FilteringIterator
use `FilteringSamIterator` instead
htsjdk.samtools.filter.NotPrimaryAlignmentFilter
use `SecondaryAlignmentFilter` instead.
htsjdk.samtools.NotPrimarySkippingIterator
use `SecondaryAlignmentSkippingIterator` instead.
htsjdk.samtools.SAMTagUtil
as of 11/2018, the functions in this class have been absorbed by the `SAMTag` enum.
htsjdk.samtools.SQTagUtil
since 11/2018. SQ is a reserved tag that shouldn't be used and this code untested.
htsjdk.samtools.util.CollectionUtil.Partitioner
use Collectors.groupingBy instead
htsjdk.samtools.util.StringLineReader
use `BufferedLineReader.fromString(String)`.
htsjdk.variant.variantcontext.filter.FilteringIterator
since 2/29/16 use `FilteringVariantContextIterator` instead
htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
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

Deprecated Fields
Field
Description
htsjdk.samtools.BamFileIoUtils.BAM_FILE_EXTENSION
since June 2019 Use `FileExtensions.BAM` instead.
htsjdk.samtools.BAMIndex.BAI_INDEX_SUFFIX
since June 2019 Use `FileExtensions.BAI_INDEX` instead.
htsjdk.samtools.BAMIndex.BAMIndexSuffix
since June 2019 Use `FileExtensions.BAI_INDEX` instead.
htsjdk.samtools.BAMIndex.CSI_INDEX_SUFFIX
since June 2019 Use `FileExtensions.CSI` instead.
htsjdk.samtools.cram.build.CramIO.CRAM_FILE_EXTENSION
since June 2019 Use `FileExtensions.CRAM` instead.
htsjdk.samtools.cram.CRAIIndex.CRAI_INDEX_SUFFIX
since June 2019 Use `FileExtensions.CRAM_INDEX` instead.
htsjdk.samtools.reference.ReferenceSequenceFileFactory.FASTA_EXTENSIONS
since June 2019 Use `FileExtensions.FASTA` instead.
htsjdk.samtools.reference.ReferenceSequenceFileFactory.FASTA_INDEX_EXTENSION
since June 2019 Use `FileExtensions.FASTA_INDEX` instead.
htsjdk.samtools.SAMSequenceRecord.RESERVED_MRNM_SEQUENCE_NAME
htsjdk.samtools.SAMTagUtil.AM
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.AS
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.BC
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.BQ
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.BZ
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CB
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CC
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CG
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CM
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CO
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CP
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CQ
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CR
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CS
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CT
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.CY
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.E2
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.FI
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.FS
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.FT
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.FZ
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.GC
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.GQ
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.GS
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.H0
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.H1
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.H2
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.HI
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.IH
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.LB
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.MC
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.MD
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.MF
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.MI
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.MQ
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.NH
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.NM
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.OC
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.OF
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.OP
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.OQ
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.OR
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.OX
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.PG
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.PQ
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.PT
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.PU
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.Q2
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.QT
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.QX
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.R2
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.RG
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.RT
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.RX
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.S2
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.SA
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.SM
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.SQ
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.TC
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.U2
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SAMTagUtil.UQ
use `SAMTag.getBinaryTag()` instead.
htsjdk.samtools.SBIIndex.FILE_EXTENSION
since June 2019 Use `FileExtensions.SBI` instead.
htsjdk.samtools.util.GZIIndex.DEFAULT_EXTENSION
since June 2019 Use `FileExtensions.GZI` instead.
htsjdk.samtools.util.IntervalList.INTERVAL_LIST_FILE_EXTENSION
since June 2019 Use `FileExtensions.INTERVAL_LIST` instead.
htsjdk.samtools.util.IOUtil.BCF_FILE_EXTENSION
since June 2019 Use `FileExtensions.BCF` instead.
htsjdk.samtools.util.IOUtil.BLOCK_COMPRESSED_EXTENSIONS
Use since June 2019 `FileExtensions.BLOCK_COMPRESSED` instead.
htsjdk.samtools.util.IOUtil.COMPRESSED_VCF_FILE_EXTENSION
since June 2019 Use `FileExtensions.COMPRESSED_VCF` instead.
htsjdk.samtools.util.IOUtil.COMPRESSED_VCF_INDEX_EXTENSION
since June 2019 Use `FileExtensions.COMPRESSED_VCF_INDEX` instead.
htsjdk.samtools.util.IOUtil.DICT_FILE_EXTENSION
since June 2019 Use `FileExtensions.DICT` instead.
htsjdk.samtools.util.IOUtil.INTERVAL_LIST_FILE_EXTENSION
since June 2019 Use `FileExtensions.INTERVAL_LIST` instead.
htsjdk.samtools.util.IOUtil.SAM_FILE_EXTENSION
since June 2019 Use `FileExtensions.SAM` instead.
htsjdk.samtools.util.IOUtil.STANDARD_BUFFER_SIZE
Use `Defaults.NON_ZERO_BUFFER_SIZE` instead.
htsjdk.samtools.util.IOUtil.VCF_EXTENSIONS
since June 2019 Use `FileExtensions.VCF_LIST` instead.
htsjdk.samtools.util.IOUtil.VCF_EXTENSIONS_LIST
since June 2019 Use `FileExtensions.VCF_LIST` instead.
htsjdk.samtools.util.IOUtil.VCF_FILE_EXTENSION
since June 2019 Use `FileExtensions.VCF` instead.
htsjdk.samtools.util.IOUtil.VCF_INDEX_EXTENSION
since June 2019 Use `FileExtensions.VCF_INDEX` instead.
htsjdk.tribble.AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS
since June 2019 use `FileExtensions.BLOCK_COMPRESSED` instead.
htsjdk.tribble.bed.BEDCodec.BED_EXTENSION
since June 2019 Use `FileExtensions.BED` instead.
htsjdk.tribble.Tribble.STANDARD_INDEX_EXTENSION
since June 2019 Use `FileExtensions.TRIBBLE_INDEX` instead.
htsjdk.tribble.util.TabixUtils.STANDARD_INDEX_EXTENSION
Use since June 2019 `FileExtensions.TABIX_INDEX` instead.
htsjdk.variant.vcf.VCFConstants.GENOTYPE_LIKELIHOODS_KEY

Deprecated Methods
Method
Description
htsjdk.samtools.AbstractBAMFileIndex.optimizeChunkList(List<Chunk>, long)
Invoke `Chunk.optimizeChunkList(List, long)` directly.
htsjdk.samtools.AbstractBAMFileIndex.regionToBins(int, int)
Use `GenomicIndexUtil.regionToBins(int, int)` instead. Get candidate bins for the specified region
htsjdk.samtools.AbstractSAMHeaderRecord.setAttribute(String, Object)
Use `AbstractSAMHeaderRecord.setAttribute(String, String)` instead
htsjdk.samtools.DuplicateSetIterator.setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy)
htsjdk.samtools.fastq.FastqRecord.getReadHeader()
since 02/2017. Use `FastqRecord.getReadName()` instead
htsjdk.samtools.fastq.FastqRecord.length()
since 02/2017. Use `FastqRecord.getReadLength()` instead
htsjdk.samtools.reference.IndexedFastaSequenceFile.canCreateIndexedFastaReader(File)
use `ReferenceSequenceFileFactory.canCreateIndexedFastaReader(Path)` instead.
htsjdk.samtools.reference.IndexedFastaSequenceFile.canCreateIndexedFastaReader(Path)
use `ReferenceSequenceFileFactory.canCreateIndexedFastaReader(Path)` instead.
htsjdk.samtools.SAMFileHeader.getTextHeader()
since May 1st 2019 - text version of header is no longer stored.
htsjdk.samtools.SAMFileHeader.setAttribute(String, Object)
Use `SAMFileHeader.setAttribute(String, String)` instead
htsjdk.samtools.SAMFileHeader.setTextHeader(String)
since May 1st 2019 - text version of header is no longer stored.
htsjdk.samtools.SAMFileHeader.SortOrder.getComparator()
since 7/2018, use `SAMFileHeader.SortOrder.getComparatorInstance()` with `Object.getClass()` instead
htsjdk.samtools.SamFileHeaderMerger.getMergedSequenceIndex(SamReader, Integer)
replaced by `SamFileHeaderMerger.getMergedSequenceIndex(SAMFileHeader, Integer)`
htsjdk.samtools.SamFileHeaderMerger.getProgramGroupId(SamReader, String)
replaced by `SamFileHeaderMerger.getProgramGroupId(SAMFileHeader, String)`
htsjdk.samtools.SamFileHeaderMerger.getReaders()
replaced by `SamFileHeaderMerger.getHeaders()`
htsjdk.samtools.SamFileHeaderMerger.getReadGroupId(SamReader, String)
replaced by `SamFileHeaderMerger.getReadGroupId(SAMFileHeader, String)`
htsjdk.samtools.SamFileValidator.setValidateIndex(boolean)
use `SamFileValidator.setIndexValidationStringency(BamIndexValidator.IndexValidationStringency)` instead
htsjdk.samtools.SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader, boolean, Path, File)
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
htsjdk.samtools.SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader, Path, File)
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
htsjdk.samtools.SAMFileWriterFactory.makeWriter(SAMFileHeader, boolean, Path, File)
since 6/18, use `SAMFileWriterFactory.makeWriter(SAMFileHeader, boolean, Path, Path)` instead
htsjdk.samtools.SAMFileWriterImpl.writeHeader(String)
since 06/2018. `SAMFileWriterImpl.writeHeader(SAMFileHeader)` is preferred for avoid String construction if not need it.
htsjdk.samtools.SamPairUtil.setMateInfo(SAMRecord, SAMRecord, SAMFileHeader)
use `SamPairUtil.setMateInfo(SAMRecord, SAMRecord)` instead
htsjdk.samtools.SamPairUtil.setMateInfo(SAMRecord, SAMRecord, SAMFileHeader, boolean)
use `SamPairUtil.setMateInfo(SAMRecord, SAMRecord, boolean)` instead
htsjdk.samtools.SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, SAMFileHeader, List<SamPairUtil.PairOrientation>)
use `SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, List)` instead
htsjdk.samtools.SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, SAMFileHeader, List<SamPairUtil.PairOrientation>, boolean)
use `SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, List, boolean)`
htsjdk.samtools.SAMRecord.computeIndexingBinIfAbsent(SAMRecord)
Use computeIndexingBin() if accessible or GenomicIndexUtil.regionToBin() otherwise.
htsjdk.samtools.SAMRecord.getNotPrimaryAlignmentFlag()
use `SAMRecord.isSecondaryAlignment()` instead.
htsjdk.samtools.SAMRecord.isAllowedAttributeValue(Object)
The attribute type and value checks have been moved directly into `SAMBinaryTagAndValue`.
htsjdk.samtools.SAMRecord.setNotPrimaryAlignmentFlag(boolean)
use `SAMRecord.setSecondaryAlignment(boolean)` instead.
htsjdk.samtools.SAMRecord.setReadUmappedFlag(boolean)
htsjdk.samtools.SamStreams.isGzippedSAMFile(InputStream)
use `IOUtil.isGZIPInputStream(InputStream)` instead
htsjdk.samtools.SAMTagUtil.getSingleton()
use the static methods in `SAMTag` instead
htsjdk.samtools.SAMTagUtil.makeBinaryTag(String)
use `instead`
htsjdk.samtools.SAMTagUtil.makeStringTag(short)
use `SAMTag.makeStringTag(short)` instead
htsjdk.samtools.SAMUtils.isReferenceSequenceCompatibleWithBAI(SAMSequenceRecord)
because the method does the exact opposite of what it says. Use the correctly named isReferenceSequenceIncompatibleWithBAI() instead.
htsjdk.samtools.seekablestream.SeekableStreamFactory.isFilePath(String)
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)`
htsjdk.samtools.util.AbstractLocusInfo.getRecordAndPositions()
since name of the method can be confusing, new implementation should be used `getRecordAndOffsets()`
htsjdk.samtools.util.BlockCompressedInputStream.assertNonDefectiveFile(File)
htsjdk.samtools.util.CollectionUtil.partition(Collection<V>, CollectionUtil.Partitioner<V, K>)
use java8 .stream().collect(Collectors.groupingBy(()-> function)) instead
htsjdk.samtools.util.Interval.getSequence()
use getContig() instead
htsjdk.samtools.util.IntervalList.getUniqueIntervals()
use `IntervalList.uniqued()`.`IntervalList.getIntervals()` instead.
htsjdk.samtools.util.IntervalList.getUniqueIntervals(boolean)
use `IntervalList.uniqued(boolean)`.`IntervalList.getIntervals()` or `IntervalList.getUniqueIntervals(IntervalList, boolean)` instead.
htsjdk.samtools.util.IntervalList.sort()
use `IntervalList.sorted()` instead.
htsjdk.samtools.util.IntervalList.unique()
use `IntervalList.uniqued()` instead.
htsjdk.samtools.util.IntervalList.unique(boolean)
use `IntervalList.uniqued(boolean)` instead.
htsjdk.samtools.util.IOUtil.createTempDir(String, String)
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.
htsjdk.samtools.util.RelativeIso8601Date.getDate()
htsjdk.samtools.util.RelativeIso8601Date.getDay()
htsjdk.samtools.util.RelativeIso8601Date.getHours()
htsjdk.samtools.util.RelativeIso8601Date.getMinutes()
htsjdk.samtools.util.RelativeIso8601Date.getMonth()
htsjdk.samtools.util.RelativeIso8601Date.getSeconds()
htsjdk.samtools.util.RelativeIso8601Date.getTimezoneOffset()
htsjdk.samtools.util.RelativeIso8601Date.getYear()
htsjdk.samtools.util.RelativeIso8601Date.setDate(int)
htsjdk.samtools.util.RelativeIso8601Date.setHours(int)
htsjdk.samtools.util.RelativeIso8601Date.setMinutes(int)
htsjdk.samtools.util.RelativeIso8601Date.setMonth(int)
htsjdk.samtools.util.RelativeIso8601Date.setSeconds(int)
htsjdk.samtools.util.RelativeIso8601Date.setTime(long)
htsjdk.samtools.util.RelativeIso8601Date.setYear(int)
htsjdk.samtools.util.SortingCollection.newInstance(Class<T>, SortingCollection.Codec<T>, Comparator<T>, int, File...)
since 2017-09. Use `SortingCollection.newInstance(Class, Codec, Comparator, int, Path...)` instead
htsjdk.samtools.util.SortingCollection.newInstance(Class<T>, SortingCollection.Codec<T>, Comparator<T>, int, Collection<File>)
since 2017-09. Use `SortingCollection.newInstanceFromPaths(Class, Codec, Comparator, int, Collection)` instead
htsjdk.samtools.util.TestUtil.getTempDirecory(String, String)
Use properly spelled method. `TestUtil.getTempDirectory(String, String)`
htsjdk.samtools.util.TestUtil.recursiveDelete(File)
Since 3/19, prefer `IOUtil.recursiveDelete(Path)`
htsjdk.tribble.AbstractFeatureReader.hasBlockCompressedExtension(File)
use `IOUtil.hasBlockCompressedExtension(File)`.
htsjdk.tribble.AbstractFeatureReader.hasBlockCompressedExtension(String)
use `IOUtil.hasBlockCompressedExtension(String)`.
htsjdk.tribble.AbstractFeatureReader.hasBlockCompressedExtension(URI)
use `IOUtil.hasBlockCompressedExtension(URI)`.
htsjdk.tribble.annotation.Strand.toStrand(String)
please use `Strand.decode(char)` instead.
htsjdk.tribble.Feature.getChr()
on 03/2015. Use getContig() instead.
htsjdk.tribble.index.AbstractIndex.getIndexedFile()
on 03/2017. Use `AbstractIndex.getIndexedPath()` instead.
htsjdk.tribble.index.IndexFactory.writeIndex(Index, File)
use `Index.write(File)` instead
htsjdk.tribble.readers.AsciiLineReader.readLine(PositionalBufferedStream)
8/8/2017 use `AsciiLineReader.from(InputStream)` to create a new AsciiLineReader and `AsciiLineReader.readLine()`
htsjdk.variant.utils.SAMSequenceDictionaryExtractor.extractDictionary(File)
in favor of `SAMSequenceDictionaryExtractor.extractDictionary(Path)`
htsjdk.variant.variantcontext.Allele.wouldBeBreakpoint(byte[])
htsjdk.variant.variantcontext.Allele.wouldBeNoCallAllele(byte[])
htsjdk.variant.variantcontext.Allele.wouldBeNullAllele(byte[])
htsjdk.variant.variantcontext.Allele.wouldBeSingleBreakend(byte[])
htsjdk.variant.variantcontext.Allele.wouldBeStarAllele(byte[])
htsjdk.variant.variantcontext.Allele.wouldBeSymbolicAllele(byte[])
htsjdk.variant.variantcontext.Genotype.getAttributeAsDouble(String, double)
htsjdk.variant.variantcontext.Genotype.getAttributeAsInt(String, int)
htsjdk.variant.variantcontext.Genotype.getAttributeAsString(String, String)
htsjdk.variant.variantcontext.Genotype.getLog10PError()
htsjdk.variant.variantcontext.Genotype.getPhredScaledQual()
htsjdk.variant.variantcontext.Genotype.hasLog10PError()
htsjdk.variant.variantcontext.GenotypeLikelihoods.fromGLField(String)
htsjdk.variant.variantcontext.GenotypeLikelihoods.getAllelePairUsingDeprecatedOrdering(int)
since 2/5/13
htsjdk.variant.variantcontext.GenotypeLikelihoods.getLog10GQ(GenotypeType)
since 2/5/13 use `GenotypeLikelihoods.getLog10GQ(Genotype, VariantContext)` or `GenotypeLikelihoods.getLog10GQ(Genotype, List)`
htsjdk.variant.variantcontext.GenotypeLikelihoods.getPLIndecesOfAlleles(int, int)
7/18 use `GenotypeLikelihoods.getPLIndicesOfAlleles(int, int)` instead
htsjdk.variant.variantcontext.GenotypeLikelihoods.initializeAnyploidPLIndexToAlleleIndices(int, int)
as of sept 2020, this method is no longer necessary
htsjdk.variant.variantcontext.VariantContext.getGLIndecesOfAlternateAllele(Allele)
7/18 use `VariantContext.getGLIndicesOfAlternateAllele(Allele)` instead
htsjdk.variant.vcf.VCFEncoder.setAllowMissingFieldsInHeader(boolean)
since 10/24/13 use the constructor
htsjdk.variant.vcf.VCFEncoder.setVCFHeader(VCFHeader)
since 10/24/13 use the constructor
htsjdk.variant.vcf.VCFFileReader.fromVcf(VCFFileReader)
since July 2018 since use `VCFFileReader.toIntervalList(VCFFileReader)` instead
htsjdk.variant.vcf.VCFFileReader.fromVcf(VCFFileReader, boolean)
since July 2018 since use `VCFFileReader.toIntervalList(VCFFileReader, boolean)` instead
htsjdk.variant.vcf.VCFFileReader.fromVcf(File)
since July 2018 use `VCFFileReader.toIntervalList(Path)` instead
htsjdk.variant.vcf.VCFFileReader.fromVcf(File, boolean)
since July 2018 use `VCFFileReader.toIntervalList(Path, boolean)` instead

Deprecated Constructors
Constructor
Description
htsjdk.samtools.MergingSamRecordIterator(SamFileHeaderMerger, boolean)
replaced by `MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean)`
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder)
replaced by `SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)`
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder, boolean)
replaced by `SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)`
htsjdk.samtools.SAMRecordDuplicateComparator(List<SAMFileHeader>)
htsjdk.samtools.SAMSequenceRecord(String)
Use `SAMSequenceRecord(String, int)` instead. sequenceLength is required for the object to be considered valid.
htsjdk.tribble.readers.AsciiLineReader(PositionalBufferedStream)
8/8/2017 use `AsciiLineReader.from(InputStream)`
htsjdk.tribble.readers.AsciiLineReader(InputStream)
8/8/2017 use `AsciiLineReader.from(InputStream)`

Deprecated Enum Constants
Enum Constant
Description
htsjdk.samtools.SAMFlag.NOT_PRIMARY_ALIGNMENT
use `SAMFlag.SECONDARY_ALIGNMENT` instead.
htsjdk.samtools.SAMReadGroupRecord.PlatformValue.BGI
Use SAMReadGroupRecord.PlatformValue.DNBSEQ instead.
htsjdk.samtools.SAMReadGroupRecord.PlatformValue.OTHER
OTHER is not an official value. It is recommended to omit PL if it is not in this list or is unknown.
htsjdk.samtools.SAMTag.GC
for backwards compatibility only
htsjdk.samtools.SAMTag.GQ
for backwards compatibility only
htsjdk.samtools.SAMTag.GS
for backwards compatibility only
htsjdk.samtools.SAMTag.MF
for backwards compatibility only
htsjdk.samtools.SAMTag.RT
use BC instead, for backwards compatibilty only
htsjdk.samtools.SAMTag.S2
for backwards compatibility only
htsjdk.samtools.SAMTag.SQ
for backwards compatibility only