A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes All Packages

## A

A - picard.analysis.artifacts.Transition.Base
A - picard.illumina.parser.IntensityChannel
aa - picard.fingerprint.DiploidHaplotype
Aa - picard.fingerprint.DiploidHaplotype
AA - picard.arrays.illumina.IlluminaGenotype
AA - picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
AA - picard.fingerprint.DiploidGenotype
AA - picard.fingerprint.DiploidHaplotype
AA_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
AB - picard.arrays.illumina.IlluminaGenotype
AB - picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
AB_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
AB_FILTER - Static variable in class picard.vcf.filter.AlleleBalanceFilter
  The filter string used for sites that fail the allele balance filter.
AbstractAlignmentMerger - Class in picard.sam
  Abstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean) - Constructor for class picard.sam.AbstractAlignmentMerger
  constructor with a default setting for unmappingReadsStrategy.
AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, AbstractAlignmentMerger.UnmappingReadStrategy) - Constructor for class picard.sam.AbstractAlignmentMerger
  Constructor
AbstractAlignmentMerger.UnmappingReadStrategy - Enum in picard.sam
AbstractIlluminaPositionFileReader - Class in picard.illumina.parser.readers
  The position files of Illumina are nearly the same form: Pos files consist of text based tabbed x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary x-y float pairs.
AbstractIlluminaPositionFileReader(File) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
AbstractIlluminaPositionFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
  Use this ctor if lane and tile are not discernible from file name.
AbstractIlluminaPositionFileReader.PositionInfo - Class in picard.illumina.parser.readers
AbstractInputParser - Class in picard.util
  Class for parsing text files where each line consists of fields separated by whitespace.
AbstractInputParser() - Constructor for class picard.util.AbstractInputParser
AbstractMarkDuplicatesCommandLineProgram - Class in picard.sam.markduplicates.util
  Abstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM/CRAM files.
AbstractMarkDuplicatesCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator - Class in picard.sam.markduplicates.util
  Little class used to package up a header and an iterable/iterator.
AbstractOpticalDuplicateFinderCommandLineProgram - Class in picard.sam.markduplicates.util
  Abstract class that holds parameters and methods common to classes that optical duplicate detection.
AbstractOpticalDuplicateFinderCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
AbstractWgsMetricsCollector<T extends htsjdk.samtools.util.AbstractRecordAndOffset> - Class in picard.analysis
  Class for collecting data on reference coverage, base qualities and excluded bases from one AbstractLocusInfo object for CollectWgsMetrics.
AC - picard.fingerprint.DiploidGenotype
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectBaseDistributionByCycle
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectGcBiasMetrics
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectInsertSizeMetrics
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectQualityYieldMetrics
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectRnaSeqMetrics
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.MeanQualityByCycle
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.QualityScoreDistribution
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.SinglePassSamProgram
  Should be implemented by subclasses to accept SAMRecords one at a time.
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
acceptRecord(ARGTYPE) - Method in interface picard.metrics.PerUnitMetricCollector
  Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
acceptRecord(SAMRecord) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
acceptRecord(SAMRecord) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
  Adds information about an individual SAMRecord to the statistics.
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
  Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record
acceptRecord(InsertSizeCollectorArgs) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
acceptRecord(GcBiasCollectorArgs) - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
acceptRecord(SAMRecordAndReference) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
acceptRecord(SAMRecordAndReference) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
accumulate(VariantContext) - Method in class picard.vcf.CallingMetricAccumulator
  Incorporates the provided variant's data into the metric analysis.
accumulate(VariantContext) - Method in class picard.vcf.GvcfMetricAccumulator
accumulate(VariantContext) - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
AccumulateQualityYieldMetrics - Class in picard.util
  Combines multiple Picard QualityYieldMetrics files into a single file.
AccumulateQualityYieldMetrics() - Constructor for class picard.util.AccumulateQualityYieldMetrics
AccumulateVariantCallingMetrics - Class in picard.vcf
  Combines multiple Variant Calling Metrics files into a single file.
AccumulateVariantCallingMetrics() - Constructor for class picard.vcf.AccumulateVariantCallingMetrics
ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasDetailMetrics
ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasSummaryMetrics
accumulators() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
  Returns the `VariantProcessor.Accumulator`s associated with this executor.
accumulators() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
ACCURACY - Variable in class picard.sam.DownsampleSam
ACGT_CODES - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
ACTION - Variable in class picard.util.IntervalListTools
ADAPTER_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
ADAPTER_TRUNCATION_LENGTH - Variable in class picard.illumina.MarkIlluminaAdapters
AdapterMarker - Class in picard.util
  Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
AdapterMarker(int, AdapterPair...) - Constructor for class picard.util.AdapterMarker
AdapterMarker(AdapterPair...) - Constructor for class picard.util.AdapterMarker
  Truncates adapters to DEFAULT_ADAPTER_LENGTH
AdapterPair - Interface in picard.util
ADAPTERS - Variable in class picard.illumina.MarkIlluminaAdapters
ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToFastq
ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToSam
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord) - Method in class picard.util.AdapterMarker
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double) - Method in class picard.util.AdapterMarker
  Overrides defaults for minMatchBases and maxErrorRate
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
  Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads.
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
  Deprecated.
  Use the varargs version. This no longer returns a warning string..
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
  Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
  Deprecated.
  Use the varargs version. This no longer returns a warning string..
adapterTrimIlluminaSingleRead(SAMRecord) - Method in class picard.util.AdapterMarker
adapterTrimIlluminaSingleRead(SAMRecord, int, double) - Method in class picard.util.AdapterMarker
  Overrides defaults for minMatchBases and maxErrorRate
adapterTrimIlluminaSingleRead(SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
  Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
  Deprecated.
  Use the varargs version. This no longer returns a warning string..
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
  Invokes adapterTrimIlluminRead with default parameters for a single read.
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
  Deprecated.
  Use the varargs version. This no longer returns a warning string..
AdapterUtility - Class in picard.analysis
  A utility class for matching reads to adapters.
AdapterUtility(List<String>) - Constructor for class picard.analysis.AdapterUtility
add(HaplotypeProbabilities) - Method in class picard.fingerprint.Fingerprint
add(PedFile.PedTrio) - Method in class picard.pedigree.PedFile
  Adds a trio to the PedFile keyed by the individual id.
add(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
  Adds the end to this set, if not already added based on physical location
add(ReadEndsForMateCigar, SamRecordTrackingBuffer, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.MarkQueue
  Add a record to the mark queue.
ADD_MATE_CIGAR - Variable in class picard.sam.FixMateInformation
ADD_MATE_CIGAR - Variable in class picard.sam.MergeBamAlignment
ADD_PG_TAG_TO_READS - Variable in class picard.sam.util.PGTagArgumentCollection
addAllLevelsToFile(MetricsFile<METRIC_TYPE, Histogram_KEY>) - Method in class picard.metrics.MultiLevelCollector
  Add all metrics to the given file in the following MetricAccumulationLevel order ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
addBase(int) - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
  Adds a single point of depth at the desired offset into the coverage array.
addBase(int, int) - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
  Adds some depth at the desired offset into the coverage array.
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in interface picard.sam.SamErrorMetric.BaseCalculator
  The function by which new loci are "shown" to the calculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.BaseErrorCalculator
  the function by which new loci are "shown" to the calculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
  The function by which new loci are "shown" to the calculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
  The function by which new loci are "shown" to the calculator
addBaseQHistogram(MetricsFile<WgsMetrics, Integer>) - Method in class picard.analysis.AbstractWgsMetricsCollector
AddCommentsToBam - Class in picard.sam
  A tool to add comments to a BAM file header.
AddCommentsToBam() - Constructor for class picard.sam.AddCommentsToBam
addCoverageCounts(int, int, int[]) - Method in class picard.annotation.Gene.Transcript
addCustomBindings(DocWorkUnit) - Method in class picard.util.help.PicardHelpDocWorkUnitHandler
  Add any custom freemarker bindings discovered via custom javadoc tags.
addData(ClusterData, BarcodeData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
addData(ClusterData, PfData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
addData(ClusterData, PositionalData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
addDuplicateReadToMetrics(SAMRecord, DuplicationMetrics) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
addEdge(Node, Node) - Method in class picard.util.GraphUtils.Graph
addExon(int, int) - Method in class picard.annotation.Gene.Transcript
addHaplotype(HaplotypeBlock) - Method in class picard.fingerprint.HaplotypeMap
  Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
addInfo(AbstractLocusInfo<EdgingRecordAndOffset>, ReferenceSequence, boolean) - Method in class picard.analysis.FastWgsMetricsCollector
addInfo(AbstractLocusInfo<SamLocusIterator.RecordAndOffset>, ReferenceSequence, boolean) - Method in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
addInfo(AbstractLocusInfo<T>, ReferenceSequence, boolean) - Method in class picard.analysis.AbstractWgsMetricsCollector
  Accumulates the data from AbstractLocusInfo in inner structures
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BciFileFaker
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BclFileFaker
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BclIndexFaker
addLeadingZeros() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
addLeadingZeros() - Method in class picard.illumina.parser.fakers.FileFaker
addLeadingZeros() - Method in class picard.illumina.parser.fakers.FilterFileFaker
addLeadingZeros() - Method in class picard.illumina.parser.fakers.LocsFileFaker
addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
addLeadingZeros() - Method in class picard.illumina.parser.fakers.PosFileFaker
addLocationInformation(String, PhysicalLocation) - Method in class picard.sam.util.ReadNameParser
addMetricsByLibrary(String, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
addMetricsToFile(MetricsFile<BEAN, HKEY>) - Method in interface picard.metrics.PerUnitMetricCollector
  Any metrics collected will be added to the metric file provided.
addMetricsToFile(MetricsFile<METRIC_TYPE, Integer>) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
addMetricsToFile(MetricsFile<AlignmentSummaryMetrics, Integer>) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
addMetricsToFile(MetricsFile<AlignmentSummaryMetrics, Integer>) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
addMetricsToFile(MetricsFile<CollectQualityYieldMetrics.QualityYieldMetrics, Integer>) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
addMetricsToFile(MetricsFile<InsertSizeMetrics, Integer>) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
addMetricsToFile(MetricsFile<RnaSeqMetrics, Integer>) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
addMetricsToFile(MetricsFile<GcBiasMetrics, Integer>) - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
addMissingTruthAndMissingCallStates(double, long, GenotypeConcordanceCounts) - Static method in class picard.vcf.GenotypeConcordance
  Method to add missing sites that are KNOWN to be HOM_REF in the case of the NIST truth data set.
addNode(Node) - Method in class picard.util.GraphUtils.Graph
AddOATag - Class in picard.sam
AddOATag() - Constructor for class picard.sam.AddOATag
AddOrReplaceReadGroups - Class in picard.sam
  Assigns all the reads in a file to a single new read-group.
AddOrReplaceReadGroups() - Constructor for class picard.sam.AddOrReplaceReadGroups
addReadData(ClusterData, int, BaseData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
addReadData(ClusterData, int, CbclData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
addReadData(ClusterData, int, QualityData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
addReadToLibraryMetrics(SAMRecord, SAMFileHeader, LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
ADDRESS_A_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
ADDRESS_B_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
addResults(MatchResults) - Method in class picard.fingerprint.FingerprintResults
addRow(GenotypeConcordanceStates.CallState, GenotypeConcordanceStates.ContingencyState[]...) - Method in class picard.vcf.GenotypeConcordanceScheme
  Adds a row to the scheme
addSingletonToCount(LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
addSnp(Snp) - Method in class picard.fingerprint.HaplotypeBlock
  Adds a SNP to the haplotype.
addToLogLikelihoods(Snp, List<Allele>, double[]) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
  Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.AbstractWgsMetricsCollector
  Adds collected metrics and depth histogram to file
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in interface picard.analysis.WgsMetricsProcessor
  Adds result metric's data to input file
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.WgsMetricsProcessorImpl
addToProbs(Snp, byte, byte) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
  Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
addToProbs(Snp, byte, byte) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
  Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
addTranscript(String, int, int, int, int, int) - Method in class picard.annotation.Gene
addUmiObservation(String, String) - Method in class picard.sam.markduplicates.UmiMetrics
  Add an observation of a UMI to the metrics
addUmiObservationN() - Method in class picard.sam.markduplicates.UmiMetrics
  Add an observation of a UMI containing at least one N to the metrics
advance() - Method in class picard.util.AbstractInputParser
advanceFile() - Method in class picard.util.BasicInputParser
afterExecute(Runnable, Throwable) - Method in class picard.util.ThreadPoolExecutorWithExceptions
AG - picard.fingerprint.DiploidGenotype
Aligned - picard.sam.ViewSam.AlignmentStatus
ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
ALIGNED_READS - Variable in class picard.analysis.GcBiasSummaryMetrics
  The total number of aligned reads used to compute the gc bias metrics.
ALIGNED_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
ALIGNED_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
ALIGNED_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
ALIGNED_READS_ONLY - Variable in class picard.sam.MergeBamAlignment
ALIGNER_PROPER_PAIR_FLAGS - Variable in class picard.sam.MergeBamAlignment
ALIGNMENT_STATUS - Variable in class picard.sam.ViewSam
AlignmentSummaryMetrics - Class in picard.analysis
  High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
AlignmentSummaryMetrics() - Constructor for class picard.analysis.AlignmentSummaryMetrics
AlignmentSummaryMetrics.Category - Enum in picard.analysis
AlignmentSummaryMetricsCollector - Class in picard.analysis
AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, boolean, List<String>, int, Set<SamPairUtil.PairOrientation>, boolean) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector
AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector - Class in picard.analysis
AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector - Class in picard.analysis
  Class that counts reads that match various conditions
All - picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
All - picard.sam.ViewSam.AlignmentStatus
All - picard.sam.ViewSam.PfStatus
ALL - picard.sam.markduplicates.CheckDuplicateMarking.Mode
ALL_GTS_FILTERED - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
  Filter string that is used to filter a Variant when all variant genotypes are filtered out.
ALL_READS - picard.analysis.MetricAccumulationLevel
allAlleles - Variable in class picard.vcf.GenotypeConcordance.Alleles
ALLELE_A - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ALLELE_A_PROBE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
ALLELE_B - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ALLELE_B_PROBE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
ALLELE_FRACTION - Variable in class picard.analysis.CollectWgsMetrics
ALLELE_FRACTION - Variable in class picard.analysis.directed.CollectTargetedMetrics
ALLELE_FRACTION - Variable in class picard.analysis.TheoreticalSensitivityMetrics
  The allele fraction which theoretical sensitivity is calculated for.
AlleleBalanceFilter - Class in picard.vcf.filter
  Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
AlleleBalanceFilter(double) - Constructor for class picard.vcf.filter.AlleleBalanceFilter
Alleles(OrderedSet<String>, String, String, String, String) - Constructor for class picard.vcf.GenotypeConcordance.Alleles
allelesToStringList(List<Allele>) - Static method in class picard.util.LiftoverUtils
  This is a utility method that will convert a list of alleles into a list of base strings.
AlleleSubsettingUtils - Class in picard.util
  Utilities class containing methods for restricting `VariantContext` and `GenotypesContext` objects to a reduced set of alleles, as well as for choosing the best set of alleles to keep and for cleaning up annotations and genotypes after subsetting.
AlleleSubsettingUtils() - Constructor for class picard.util.AlleleSubsettingUtils
ALLOW_AND_IGNORE_EMPTY_LINES - Variable in class picard.sam.FastqToSam
ALLOW_CONTIG_LENGTH_DISCORDANCE - Variable in class picard.sam.ReorderSam
ALLOW_DUPLICATE_READS - Variable in class picard.fingerprint.CrosscheckFingerprints
ALLOW_INCOMPLETE_DICT_CONCORDANCE - Variable in class picard.sam.ReorderSam
ALLOW_MISSING_FIELDS_IN_HEADER - Variable in class picard.vcf.LiftoverVcf
ALLOW_MISSING_UMIS - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS - Variable in class picard.sam.PositionBasedDownsampleSam
allVisitedAlignmentsEqual() - Method in class picard.sam.SamComparisonMetric
ALSO_IGNORE_DUPLICATES - Variable in class picard.analysis.CollectGcBiasMetrics
ALT_BASE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
  The alternative base (or it's complement).
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The (upper-case) alternative base that is called as a result of DNA damage.
ALT_COUNT - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
  The number of alt bases observed.
ALT_NAMES - Variable in class picard.sam.CreateSequenceDictionary
ALT_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause
ALT_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage.
ALTERNATIVE_SINGLE_END - picard.util.IlluminaUtil.IlluminaAdapterPair
altValues() - Static method in enum picard.analysis.artifacts.Transition
  Like values(), but ignores the ref:ref "transitions".
AMPLICON_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
AMPLICON_TERRITORY - Variable in class picard.analysis.directed.TargetedPcrMetrics
  The number of unique bases covered by the intervals of all amplicons in the amplicon set
ANALYSIS_DIR - Variable in class picard.fastq.BamToBfq
ANALYSIS_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The version number of the analysis run
ANALYSIS_VERSION_NUMBER - Variable in class picard.arrays.GtcToVcf
ANALYSIS_VERSION_NUMBER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
AnnotationException - Exception in picard.annotation
  Exception thrown when loading gene annotations.
AnnotationException(String) - Constructor for exception picard.annotation.AnnotationException
AnnotationException(String, Throwable) - Constructor for exception picard.annotation.AnnotationException
APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToSam
ARE_EQUAL - Variable in class picard.sam.SamComparisonMetric
  Whether or not to consider the two input files equal.
areEqual() - Method in class picard.sam.util.SamComparison
areHistogramsEmpty() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
ARRAY_TYPE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ArraysControlCodesSummaryMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
ArraysControlInfo - Class in picard.arrays.illumina
  A simple class to store names and counts for the the Control Information fields that are stored in an Illumina GTC file.
ArraysControlInfo(String, String, int, int) - Constructor for class picard.arrays.illumina.ArraysControlInfo
ArraysVariantCallingDetailMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
ArraysVariantCallingSummaryMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  A "nickname" of this artifact, if it is a known error mode.
ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  A "nickname" of this artifact, if it is a known error mode.
asList() - Method in class picard.vcf.GenotypeConcordance.Alleles
assertMinimumQualities() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
  Reviews the qualities observed thus far and throws an exception if any are below the minimum quality threshold.
assertPairedMates(SAMRecord, SAMRecord) - Static method in class picard.sam.SamToFastq
assertProperFileStructure(File) - Method in class picard.illumina.parser.readers.BclReader
assertSorted(SAMFileHeader.SortOrder) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
  Establishes that records returned by this iterator are expected to be in the specified sort order.
assignLocusFunctionForRange(int, LocusFunction[]) - Method in class picard.annotation.Gene.Transcript
  Write into locusFunctions the function of each position from start to start + locusFunctions.length relative to this transcript.
ASSUME_SORT_ORDER - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
ASSUME_SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
ASSUME_SORTED - Variable in class picard.analysis.CollectMultipleMetrics
ASSUME_SORTED - Variable in class picard.analysis.CollectRrbsMetrics
ASSUME_SORTED - Variable in class picard.analysis.SinglePassSamProgram
ASSUME_SORTED - Variable in class picard.sam.FixMateInformation
ASSUME_SORTED - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
  Deprecated.
ASSUME_SORTED - Variable in class picard.sam.MergeSamFiles
ASSUME_SORTED_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
asVcf(ReferenceSequenceFile) - Method in class picard.fingerprint.HaplotypeMap
AsyncIterator<T> - Class in picard.util
  Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be efficient.
AsyncIterator(CloseableIterator<T>, int, String) - Constructor for class picard.util.AsyncIterator
AT - picard.fingerprint.DiploidGenotype
AT_DROPOUT - Variable in class picard.analysis.directed.PanelMetricsBase
  A measure of how undercovered <= 50% GC regions are relative to the mean.
AT_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
  Illumina-style AT dropout metric.
AtoA - picard.analysis.artifacts.Transition
AtoC - picard.analysis.artifacts.Transition
AtoG - picard.analysis.artifacts.Transition
AtomicIterator<T> - Interface in picard.util
  Describes
atomicIteratorOf(Iterable<E>) - Static method in class picard.util.Iterators
atomicIteratorOf(Iterator<E>) - Static method in class picard.util.Iterators
AtoT - picard.analysis.artifacts.Transition
ATTEMPTED_ALLELES - Static variable in class picard.vcf.LiftoverVcf
  Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
ATTEMPTED_LOCUS - Static variable in class picard.vcf.LiftoverVcf
  Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
ATTRIBUTE_TO_CLEAR - Variable in class picard.sam.RevertSam
ATTRIBUTES_TO_REMOVE - Variable in class picard.sam.MergeBamAlignment
ATTRIBUTES_TO_RETAIN - Variable in class picard.sam.MergeBamAlignment
ATTRIBUTES_TO_REVERSE - Variable in class picard.sam.MergeBamAlignment
ATTRIBUTES_TO_REVERSE_COMPLEMENT - Variable in class picard.sam.MergeBamAlignment
AUTOCALL_CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The overall autocall call rate
AUTOCALL_DATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The date this sample was autocalled
AUTOCALL_DATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
AUTOCALL_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The sex, as determined by Autocall
AUTOCALL_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
AUTOCALL_PF - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  Whether the sample passes QC based on call rate threshold
AUTOCALL_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The version of autocall used for calling this sample
AUTOCALL_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
AVG_POS_3PRIME_SOFTCLIP_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
  The average length of the soft-clipped bases at the 3' end of reads.
awaitCompletion() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
  Blocks until the work is complete.
awaitCompletion() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
awaitThreadPoolTermination(String, ThreadPoolExecutor, Duration) - Static method in class picard.util.ThreadPoolExecutorUtil
awaitTileProcessingCompletion() - Method in class picard.illumina.SortedBasecallsConverter

## B

B - picard.illumina.parser.ReadType
BAD_ASSAYS_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
BAD_CYCLES - Variable in class picard.analysis.AlignmentSummaryMetrics
  The number of instrument cycles in which 80% or more of base calls were no-calls.
BAF - Static variable in class picard.arrays.illumina.InfiniumVcfFields
BafRegressMetrics - Class in picard.arrays
BafRegressMetrics() - Constructor for class picard.arrays.BafRegressMetrics
BAIT_BIAS_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
BAIT_BIAS_IN - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
BAIT_BIAS_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
BAIT_DESIGN_EFFICIENCY - Variable in class picard.analysis.directed.HsMetrics
  The ratio of TARGET_TERRITORY/BAIT_TERRITORY.
BAIT_INTERVALS - Variable in class picard.analysis.directed.CollectHsMetrics
BAIT_OFFSET - Variable in class picard.util.BaitDesigner
BAIT_SET - Variable in class picard.analysis.directed.HsMetrics
  The name of the bait set used in the hybrid selection.
BAIT_SET_NAME - Variable in class picard.analysis.directed.CollectHsMetrics
BAIT_SIZE - Variable in class picard.util.BaitDesigner
BAIT_TERRITORY - Variable in class picard.analysis.directed.HsMetrics
  The number of bases which are localized to one or more baits.
BaitBiasDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
BaitBiasSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
BaitDesigner - Class in picard.util
  Designs baits for hybrid selection!
BaitDesigner() - Constructor for class picard.util.BaitDesigner
BaitDesigner.DesignStrategy - Enum in picard.util
  Set of possible design strategies for bait design.
BALANCING_WITHOUT_INTERVAL_SUBDIVISION - picard.util.IntervalList.IntervalListScatterMode
  A scatter approach that differs from `IntervalListScatterMode.INTERVAL_SUBDIVISION` in a few ways.
BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW - picard.util.IntervalList.IntervalListScatterMode
  A scatter approach that differs from `IntervalListScatterMode.BALANCING_WITHOUT_INTERVAL_SUBDIVISION`.
bAlleleFreq - Variable in class picard.arrays.illumina.InfiniumGTCRecord
bam - picard.sam.RevertSam.FileType
BamIndexStats - Class in picard.sam
  Command line program to print statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate.
BamIndexStats() - Constructor for class picard.sam.BamIndexStats
BamToBfq - Class in picard.fastq
  Converts a BAM file into a BFQ (binary fastq formatted) file.
BamToBfq() - Constructor for class picard.fastq.BamToBfq
BamToBfqWriter - Class in picard.fastq
  Deprecated.
BamToBfqWriter(File, File, String, Integer, Integer, boolean, String, boolean, boolean, Integer) - Constructor for class picard.fastq.BamToBfqWriter
  Deprecated.
BamToBfqWriter(File, String, boolean, String, boolean) - Constructor for class picard.fastq.BamToBfqWriter
  Deprecated.
barcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
Barcode - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
Barcode - Static variable in enum picard.illumina.parser.ReadType
BARCODE - Variable in class picard.illumina.BarcodeMetric
  The barcode (from the set of expected barcodes) for which the following metrics apply.
BARCODE - Variable in class picard.illumina.ExtractIlluminaBarcodes
BARCODE_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
BARCODE_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
  Column header for the first barcode sequence (preferred).
BARCODE_DELIMITER - Static variable in class picard.util.IlluminaUtil
BARCODE_FILE - Variable in class picard.illumina.ExtractIlluminaBarcodes
BARCODE_NAME - Variable in class picard.illumina.BarcodeMetric
  The barcode name.
BARCODE_NAME_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
  Column header for the barcode name.
BARCODE_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToSam
BARCODE_POPULATION_STRATEGY - Variable in class picard.illumina.IlluminaBasecallsToSam
BARCODE_PREFIXES - Static variable in class picard.illumina.ExtractBarcodesProgram
BARCODE_SEQUENCE_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
BARCODE_TAG - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
BARCODE_WITHOUT_DELIMITER - Variable in class picard.illumina.BarcodeMetric
barcodeBytes - Variable in class picard.illumina.BarcodeMetric
barcodeBytes - Variable in class picard.util.BarcodeEditDistanceQuery
  list of barcodes (e.g.
BarcodeEditDistanceQuery - Class in picard.util
  A class for finding the distance between multiple (matched) barcodes and multiple barcode reads.
BarcodeEditDistanceQuery(byte[][], byte[][], byte[][], int, int) - Constructor for class picard.util.BarcodeEditDistanceQuery
barcodeExtractor - Variable in class picard.illumina.BasecallsConverter
BarcodeExtractor - Class in picard.illumina
  BarcodeExtractor is used to match barcodes and collect barcode match metrics.
BarcodeExtractor(Map<String, BarcodeMetric>, BarcodeMetric, ReadStructure, int, int, int, int, DistanceMetric) - Constructor for class picard.illumina.BarcodeExtractor
BarcodeExtractor.BarcodeMatch - Class in picard.illumina
  Utility class to hang onto data about the best match for a given barcode
BarcodeFileFaker - Class in picard.illumina.parser.fakers
  Created by jcarey on 3/13/14.
BarcodeFileFaker() - Constructor for class picard.illumina.parser.fakers.BarcodeFileFaker
BarcodeFileReader - Class in picard.illumina.parser.readers
  Reads a single barcode file line by line and returns the barcode if there was a match or NULL otherwise.
BarcodeFileReader(File) - Constructor for class picard.illumina.parser.readers.BarcodeFileReader
BarcodeMatch() - Constructor for class picard.illumina.BarcodeExtractor.BarcodeMatch
BarcodeMetric - Class in picard.illumina
  Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
BarcodeMetric() - Constructor for class picard.illumina.BarcodeMetric
  This ctor is necessary for when reading metrics from file
BarcodeMetric(String, String, String, String[]) - Constructor for class picard.illumina.BarcodeMetric
barcodeRecordWriterMap - Variable in class picard.illumina.BasecallsConverter
Barcodes - picard.illumina.parser.IlluminaDataType
BARCODES_DIR - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
BARCODES_DIR - Variable in class picard.illumina.IlluminaBasecallsToFastq
BARCODES_DIR - Variable in class picard.illumina.IlluminaBasecallsToSam
barcodeSeqsToString(byte[][]) - Static method in class picard.util.IlluminaUtil
  Concatenates all the barcode sequences with BARCODE_DELIMITER
barcodeSeqsToString(String[]) - Static method in class picard.util.IlluminaUtil
  Concatenates all the barcode sequences with BARCODE_DELIMITER
barcodeSeqsToString(List<String>) - Static method in class picard.util.IlluminaUtil
  Concatenates all the barcode sequences with BARCODE_DELIMITER
barcodeToMetrics - Variable in class picard.illumina.ExtractBarcodesProgram
base - Variable in enum picard.analysis.artifacts.Transition.Base
base - Variable in class picard.illumina.parser.ParameterizedFileUtil
  If you think of the file system as a tree, this is the deepest directory(node) on the tree that still contains all of the files for this given type (e.g.
BaseBclReader - Class in picard.illumina.parser.readers
BaseBclReader.CycleData - Class in picard.illumina.parser.readers
BaseBclReader.TileData - Class in picard.illumina.parser.readers
BaseCalculator - Interface in picard.sam.SamErrorMetric
  An interface that can take a collection of bases (provided as `SamLocusIterator.RecordAndOffset` and `SamLocusAndReferenceIterator.SAMLocusAndReference`) and generates a `ErrorMetric` from them.
BaseCallingProgramGroup - Class in picard.cmdline.programgroups
  Tools that process sequencing machine data, e.g.
BaseCallingProgramGroup() - Constructor for class picard.cmdline.programgroups.BaseCallingProgramGroup
BaseCalls - picard.illumina.parser.IlluminaDataType
BASECALLS_DIR - Variable in class picard.illumina.CheckIlluminaDirectory
BASECALLS_DIR - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
BASECALLS_DIR - Variable in class picard.illumina.ExtractBarcodesProgram
BASECALLS_DIR - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
BasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
  BasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
BasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, Integer, Integer, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor) - Constructor for class picard.illumina.BasecallsConverter
  Constructs a new BasecallsConverter object.
BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD> - Interface in picard.illumina
  Interface that defines a converter that takes ClusterData and returns OUTPUT_RECORD type objects.
BasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD> - Interface in picard.illumina
  Interface that defines a writer that will write out OUTPUT_RECORD type objects.
BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
  BasecallsConverterBuilder creates and configures BasecallsConverter objects.
BasecallsConverterBuilder(File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>) - Constructor for class picard.illumina.BasecallsConverterBuilder
  Constructs a new builder used for creating BasecallsConverter objects.
baseCycleStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Get the one-based cycle number of the base, taking the direction of the read into account
BaseDistributionByCycleMetrics - Class in picard.analysis
BaseDistributionByCycleMetrics() - Constructor for class picard.analysis.BaseDistributionByCycleMetrics
BaseErrorAggregation<CALCULATOR extends BaseCalculator> - Class in picard.sam.SamErrorMetric
  An interface and implementations for classes that apply a `RecordAndOffsetStratifier` to put bases into various "bins" and then compute an `ErrorMetric` on these bases using a `BaseErrorCalculator`.
BaseErrorAggregation(Supplier<CALCULATOR>, ReadBaseStratification.RecordAndOffsetStratifier) - Constructor for class picard.sam.SamErrorMetric.BaseErrorAggregation
BaseErrorCalculator - Class in picard.sam.SamErrorMetric
BaseErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.BaseErrorCalculator
BaseErrorMetric - Class in picard.sam.SamErrorMetric
  An error metric for the errors in bases.
BaseErrorMetric() - Constructor for class picard.sam.SamErrorMetric.BaseErrorMetric
BaseErrorMetric(String, long, long) - Constructor for class picard.sam.SamErrorMetric.BaseErrorMetric
BaseIlluminaDataProvider - Class in picard.illumina.parser
  Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects.
BaseIlluminaDataProvider(int, OutputMapping) - Constructor for class picard.illumina.parser.BaseIlluminaDataProvider
baseIndexMap - Static variable in enum picard.analysis.artifacts.Transition
baseQualityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies into the base-quality of the base under consideration
bases - Variable in class picard.illumina.parser.BclData
BASES_TO_WRITE - Variable in class picard.fastq.BamToBfq
BasicInputParser - Class in picard.util
  TextFileParser which reads a single text file.
BasicInputParser(boolean, int, File...) - Constructor for class picard.util.BasicInputParser
  Constructor.
BasicInputParser(boolean, int, InputStream...) - Constructor for class picard.util.BasicInputParser
BasicInputParser(boolean, File...) - Constructor for class picard.util.BasicInputParser
  Constructor.
BasicInputParser(boolean, InputStream...) - Constructor for class picard.util.BasicInputParser
  Constructor.
BB - picard.arrays.illumina.IlluminaGenotype
BB - picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
BB_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
bci - Variable in class picard.illumina.parser.MultiTileFileUtil
BciFileFaker - Class in picard.illumina.parser.fakers
  Created by jcarey on 3/14/14.
BciFileFaker() - Constructor for class picard.illumina.parser.fakers.BciFileFaker
Bcl - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
BclData - Class in picard.illumina.parser
  A class that implements the IlluminaData interfaces provided by this parser One BclData object is returned to IlluminaDataProvider per cluster and each first level array in bases and qualities represents a single read in that cluster
BclData(int[]) - Constructor for class picard.illumina.parser.BclData
BclFileFaker - Class in picard.illumina.parser.fakers
BclFileFaker() - Constructor for class picard.illumina.parser.fakers.BclFileFaker
BclIndexFaker - Class in picard.illumina.parser.fakers
BclIndexFaker() - Constructor for class picard.illumina.parser.fakers.BclIndexFaker
BclIndexReader - Class in picard.illumina.parser.readers
  Annoyingly, there are two different files with extension .bci in NextSeq output.
BclIndexReader(File) - Constructor for class picard.illumina.parser.readers.BclIndexReader
bclQualityEvaluationStrategy - Variable in class picard.illumina.ExtractBarcodesProgram
BclQualityEvaluationStrategy - Class in picard.illumina.parser.readers
  Describes a mechanism for revising and evaluating qualities read from a BCL file.
BclQualityEvaluationStrategy(int) - Constructor for class picard.illumina.parser.readers.BclQualityEvaluationStrategy
BclReader - Class in picard.illumina.parser.readers
  BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters.
BclReader(File, BclQualityEvaluationStrategy, boolean) - Constructor for class picard.illumina.parser.readers.BclReader
BclReader(List<File>, int[], BclQualityEvaluationStrategy, boolean) - Constructor for class picard.illumina.parser.readers.BclReader
BEAD_SET_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
BEADSET_ID - Static variable in class picard.arrays.illumina.InfiniumVcfFields
BedToIntervalList - Class in picard.util
BedToIntervalList() - Constructor for class picard.util.BedToIntervalList
beforeExecute(Thread, Runnable) - Method in class picard.util.ThreadPoolExecutorWithExceptions
BestEndMapqPrimaryAlignmentStrategy - Class in picard.sam
  For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary.
BestEndMapqPrimaryAlignmentStrategy() - Constructor for class picard.sam.BestEndMapqPrimaryAlignmentStrategy
BestMapqPrimaryAlignmentSelectionStrategy - Class in picard.sam
  This strategy was designed for TopHat output, but could be of general utility.
BestMapqPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
binnedHomopolymerStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies a base onto the make up (repeating base and following reference base) and length-scale of the homopolymer from whence it came.
binnedReadCycleStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies into quintiles of read cycle.
BinnedReadCycleStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
biSiteHeterogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  the rate of heterogeneity within doubleton sets.
biSiteHomogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  the rate of homogeneity within doubleton sets.
BLOCK_SIZE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
BOT - picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
BpmToNormalizationManifestCsv - Class in picard.arrays.illumina
  A simple program to convert an Illumina bpm (bead pool manifest file) into a normalization manifest (bpm.csv) file The normalization manifest (bpm.csv) is a simple text file generated by Illumina tools - it has a specific format and is used by ZCall .
BpmToNormalizationManifestCsv() - Constructor for class picard.arrays.illumina.BpmToNormalizationManifestCsv
BREAK_BANDS_AT_MULTIPLES_OF - Variable in class picard.util.IntervalListTools
BUFFER_SIZE - Variable in class picard.util.FifoBuffer
bufferSize() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
bufferSize() - Method in class picard.illumina.parser.fakers.BciFileFaker
bufferSize() - Method in class picard.illumina.parser.fakers.BclFileFaker
bufferSize() - Method in class picard.illumina.parser.fakers.BclIndexFaker
bufferSize() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
bufferSize() - Method in class picard.illumina.parser.fakers.FileFaker
bufferSize() - Method in class picard.illumina.parser.fakers.FilterFileFaker
bufferSize() - Method in class picard.illumina.parser.fakers.LocsFileFaker
bufferSize() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
bufferSize() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
bufferSize() - Method in class picard.illumina.parser.fakers.PosFileFaker
build() - Method in class picard.illumina.BasecallsConverterBuilder
  Builds a basecalls converter
build() - Method in interface picard.vcf.processor.VariantProcessor.AccumulatorGenerator
build() - Method in class picard.vcf.processor.VariantProcessor.Builder
BUILD_37 - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
Build37ExtendedIlluminaManifest - Class in picard.arrays.illumina
  A class to represent an 'Extended' Illumina Manifest file.
Build37ExtendedIlluminaManifest(File) - Constructor for class picard.arrays.illumina.Build37ExtendedIlluminaManifest
Build37ExtendedIlluminaManifestRecord - Class in picard.arrays.illumina
  A class to represent a record (line) from an Extended Illumina Manifest [Assay] entry
Build37ExtendedIlluminaManifestRecord.Flag - Enum in picard.arrays.illumina
Build37ExtendedIlluminaManifestRecordCreator - Class in picard.arrays.illumina
BuildBamIndex - Class in picard.sam
  Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
BuildBamIndex() - Constructor for class picard.sam.BuildBamIndex
byHundredMegabaseChunks(List<File>) - Static method in class picard.vcf.processor.VariantIteratorProducer
  Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(List<File>, IntervalList) - Static method in class picard.vcf.processor.VariantIteratorProducer
  Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached), that also performs on-the-fly filtering of `VariantContext`
ByIntervalListVariantContextIterator - Class in picard.vcf
  Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.
ByIntervalListVariantContextIterator(VCFFileReader, IntervalList) - Constructor for class picard.vcf.ByIntervalListVariantContextIterator
byteArrayToCharArray(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
byteArrayToFloat(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
  Utility method to convert a byte array to a float value.
byteArrayToInt(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
  Utility method to convert an unsigned short to an int.
byteArrayToString(byte[][], String) - Static method in class picard.util.IlluminaUtil
  Concatenates all the barcode sequences with BARCODE_DELIMITER
byWholeContigSubdividingWithWidth(long) - Static method in class picard.vcf.processor.VcfFileSegmentGenerator

## C

C - picard.analysis.artifacts.Transition.Base
C - picard.illumina.parser.IntensityChannel
C_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
C_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The number of alt (A/T) basecalls observed at sites where the genome reference == C.
C_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs.
C_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
C_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The number of ref basecalls observed at sites where the genome reference == C.
CALCULATE_BY - Variable in class picard.fingerprint.CalculateFingerprintMetrics
CALCULATE_TUMOR_AWARE_RESULTS - Variable in class picard.fingerprint.CrosscheckFingerprints
calculateAllGcs(byte[], int, int) - Static method in class picard.analysis.GcBiasUtils
calculateDerivedFields() - Method in class picard.analysis.artifacts.ErrorSummaryMetrics
calculateDerivedFields() - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
calculateDerivedFields() - Method in class picard.analysis.MergeableMetricBase
  Placeholder method that will calculate the derived fields from the other ones.
calculateDerivedFields() - Method in class picard.analysis.replicates.IndependentReplicateMetric
calculateDerivedFields() - Method in class picard.analysis.WgsMetrics
calculateDerivedFields() - Method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
calculateDerivedFields() - Method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
calculateDerivedFields() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
calculateDerivedFields() - Method in class picard.sam.DuplicationMetrics
  Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.
calculateDerivedFields() - Method in class picard.sam.markduplicates.UmiMetrics
calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.BaseErrorMetric
calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.IndelErrorMetric
calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.OverlappingErrorMetric
calculateDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
calculateDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
calculateDerivedFields() - Method in class picard.vcf.MendelianViolations.MendelianViolationMetrics
calculateDerivedMetrics() - Method in class picard.sam.DuplicationMetrics
  Deprecated.
calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  Calculate the error rate given the raw counts.
calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  Calculate the error rate given the raw counts.
CalculateFingerprintMetrics - Class in picard.fingerprint
  Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have.
CalculateFingerprintMetrics() - Constructor for class picard.fingerprint.CalculateFingerprintMetrics
calculateFromDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
calculateFromDerivedFields(long) - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
calculateGc(byte[], int, int, GcBiasUtils.CalculateGcState) - Static method in class picard.analysis.GcBiasUtils
calculateGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
  Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
calculateMatchResults(Fingerprint, Fingerprint) - Static method in class picard.fingerprint.FingerprintChecker
  Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.
calculateMatchResults(Fingerprint, Fingerprint, double, double) - Static method in class picard.fingerprint.FingerprintChecker
calculateMatchResults(Fingerprint, Fingerprint, double, double, boolean, boolean) - Static method in class picard.fingerprint.FingerprintChecker
  Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.
calculateNonRefGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
  Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
CalculateReadGroupChecksum - Class in picard.sam
CalculateReadGroupChecksum() - Constructor for class picard.sam.CalculateReadGroupChecksum
calculateRefWindowsByGc(int, File, int) - Static method in class picard.analysis.GcBiasUtils
calculateRoiHistogram() - Method in class picard.sam.DuplicationMetrics
  Calculates a histogram using the estimateRoi method to estimate the effective yield doing x sequencing for x=1..10.
calculateSensitivities(int, Histogram<Integer>, Histogram<Integer>, List<Double>) - Static method in class picard.analysis.TheoreticalSensitivity
  This is a utility function to calculate the metrics specific to running theoretical sensitivity over several different allele fractions.
calculateWordCount(byte[]) - Method in class picard.util.AbstractInputParser
  Calculates the number of delimiter-separated "words" in a line and sets the value of `wordCount`
call() - Method in enum picard.analysis.artifacts.Transition
  Gets the call for the transition.
CALL_RATE - Variable in class picard.arrays.BafRegressMetrics
  The call rate of the sample (number of non-missing genotypes)
CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The overall call rate
CALL_RATE_PF_THRESHOLD - Static variable in class picard.arrays.CollectArraysVariantCallingMetrics
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
  The name of the 'call' sample
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
  The name of the 'call' sample
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The name of the 'call' sample
CALL_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
  The state of the 'call' sample (i.e.
CALL_VCF - Variable in class picard.vcf.GenotypeConcordance
callAllele1 - Variable in class picard.vcf.GenotypeConcordance.Alleles
callAllele2 - Variable in class picard.vcf.GenotypeConcordance.Alleles
callAlleles() - Method in class picard.vcf.GenotypeConcordance.Alleles
CallingMetricAccumulator - Class in picard.vcf
  Collects variants and generates metrics about them.
CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.CallingMetricAccumulator
CallingMetricAccumulator.Result - Class in picard.vcf
callState - Variable in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
callVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
CAN_SKIP - picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
canMerge(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
  Checks if this instance can be merged with another Other must have all the fields that this instance has, and the fields that are annotated as MergeByAssertEquals must contain the same value
CANNOT_SKIP_FOUND_NO_MC - picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
CANNOT_SKIP_FOUND_OQ - picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
canSkip() - Method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
canSkipSAMFile(File, int, boolean, File) - Static method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
  Checks if we can skip the SAM/BAM/CRAM file when reverting origin base qualities and adding mate cigars.
capFromAbove(double[], double) - Static method in class picard.util.MathUtil
  Returns the array capped (from above) by the value of top
capFromBelow(double[], double) - Static method in class picard.util.MathUtil
  Returns the array capped (from below) by the value of floor
CappedHaplotypeProbabilities - Class in picard.fingerprint
CappedHaplotypeProbabilities(HaplotypeProbabilities, double) - Constructor for class picard.fingerprint.CappedHaplotypeProbabilities
CASAVA_1_8 - picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
Casava18ReadNameEncoder - Class in picard.fastq
  A read name encoder conforming to the standard described by Illumina Casava 1.8.
Casava18ReadNameEncoder(String, String, String) - Constructor for class picard.fastq.Casava18ReadNameEncoder
CATEGORY - Variable in class picard.analysis.AlignmentSummaryMetrics
  One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregated for both first and second reads in a pair.
CATEGORY - Variable in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
  One of either WHOLE_GENOME or NON_ZERO_REGIONS
CATEGORY - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
  Grouping categories for controls.
Cbcl - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
CbclData - Class in picard.illumina.parser
  This class provides that data structure for cbcls.
CbclData(int[], int) - Constructor for class picard.illumina.parser.CbclData
CbclReader - Class in picard.illumina.parser.readers
  ------------------------------------- CBCL Header ----------------------------------- Bytes 0 - 1 Version number, current version is 1 unsigned 16 bits little endian integer Bytes 2 - 5 Header size unsigned 32 bits little endian integer Byte 6 Number of bits per basecall unsigned Byte 7 Number of bits per q-score unsigned
CbclReader(List<File>, Map<Integer, File>, int[], int, List<AbstractIlluminaPositionFileReader.PositionInfo>, int[]) - Constructor for class picard.illumina.parser.readers.CbclReader
CC - picard.fingerprint.DiploidGenotype
CDS_END - picard.annotation.RefFlatReader.RefFlatColumns
CDS_START - picard.annotation.RefFlatReader.RefFlatColumns
CenteredConstrained - picard.util.BaitDesigner.DesignStrategy
  Implementation that "constrains" baits to be within the target region when possible.
CG - picard.fingerprint.DiploidGenotype
CHAIN - Variable in class picard.fingerprint.LiftOverHaplotypeMap
CHAIN - Variable in class picard.util.LiftOverIntervalList
CHAIN - Variable in class picard.vcf.LiftoverVcf
CHART_OUTPUT - Variable in class picard.analysis.CollectBaseDistributionByCycle
CHART_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
CHART_OUTPUT - Variable in class picard.analysis.CollectRnaSeqMetrics
CHART_OUTPUT - Variable in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
CHART_OUTPUT - Variable in class picard.analysis.MeanQualityByCycle
CHART_OUTPUT - Variable in class picard.analysis.QualityScoreDistribution
CHECK_FIRST_N_RECORDS - Variable in class picard.vcf.FixVcfHeader
CheckDuplicateMarking - Class in picard.sam.markduplicates
CheckDuplicateMarking() - Constructor for class picard.sam.markduplicates.CheckDuplicateMarking
CheckDuplicateMarking.Mode - Enum in picard.sam.markduplicates
CheckFingerprint - Class in picard.fingerprint
  Checks the sample identity of the sequence/genotype data in the provided file (SAM/BAM or VCF) against a set of known genotypes in the supplied genotype file (in VCF format).
CheckFingerprint() - Constructor for class picard.fingerprint.CheckFingerprint
checkFingerprints(List<Path>, List<Path>, String, boolean) - Method in class picard.fingerprint.FingerprintChecker
  Top level method to take a set of one or more SAM files and one or more Genotype files and compare each read group in each SAM file to each set of fingerprint genotypes.
checkFingerprintsFromPaths(List<Path>, List<Path>, String, String) - Method in class picard.fingerprint.FingerprintChecker
  Top level method to take a set of one or more observed genotype (VCF) files and one or more expected genotype (VCF) files and compare one or more sample in the observed genotype file with one or more in the expected file and generate results for each set.
CheckIlluminaDirectory - Class in picard.illumina
  Program to check a lane of an Illumina output directory.
CheckIlluminaDirectory() - Constructor for class picard.illumina.CheckIlluminaDirectory
checkOutOfBounds(int) - Method in class picard.analysis.CounterManager
  Method checks that new locus position is not out of bounds of Counter arrays and there is enough space in them to hold information on at least one more read of length `CounterManager.readLength`.
checkRInstallation(boolean) - Static method in class picard.cmdline.CommandLineProgram
  Check if R is installed
CheckTerminatorBlock - Class in picard.sam
  Simple class to check the terminator block of a SAM file.
CheckTerminatorBlock() - Constructor for class picard.sam.CheckTerminatorBlock
checkTileCount() - Method in class picard.illumina.parser.ParameterizedFileUtil
checkTileCount() - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
  The Chi-squared pvalue of the observed counts vector relative to the expected counts, (3x2 table)
CHIMERA_KB_MIN - Variable in class picard.analysis.CollectJumpingLibraryMetrics
ChimeraUtil - Class in picard.analysis
ChimeraUtil() - Constructor for class picard.analysis.ChimeraUtil
CHIMERIC - picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
CHIMERIC_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
  The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs.
CHIP_TYPE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The chip type name
CHIP_WELL_BARCODE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The chip well barcode of the Illumina array being assayed
CHIP_WELL_BARCODE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
CHROM - Variable in class picard.analysis.FingerprintingDetailMetrics
  The chromosome on which the SNP resides.
CHROMOSOME - picard.annotation.RefFlatReader.RefFlatColumns
CHROMOSOME_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
CigarOperatorsInReadStratifier(CigarOperator) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
CircularByteBuffer - Class in picard.util
  Implementation of a circular byte buffer that uses a large byte[] internally and supports basic read/write operations from/to other byte[]s passed as arguments.
CircularByteBuffer(int) - Constructor for class picard.util.CircularByteBuffer
  Constructs a buffer capable of holding the given number of bytes.
ClassFinder - Class in picard.cmdline
  Utility class that can scan for classes in the classpath and find all the ones annotated with a particular annotation.
ClassFinder() - Constructor for class picard.cmdline.ClassFinder
ClassFinder(File) - Constructor for class picard.cmdline.ClassFinder
ClassFinder(ClassLoader) - Constructor for class picard.cmdline.ClassFinder
CLASSIFICATION - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
  The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.)
classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, int, int, boolean) - Static method in class picard.vcf.GenotypeConcordance
classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, Optional<GenotypeConcordanceCounts>, Optional<GenotypeConcordanceCounts>, int, int, boolean) - Static method in class picard.vcf.GenotypeConcordance
  Attempts to determine the concordance state given the truth and all variant context and optionally increments the genotype concordance count for the given variant type (SNP or INDEL).
CleanSam - Class in picard.sam
CleanSam() - Constructor for class picard.sam.CleanSam
cleanUp() - Method in class picard.util.ThreadPoolExecutorWithExceptions
  Calls `shutdownNow, adjusts the core size to 0 and low timeout to ensure threads get killed and garbage collected.
clear() - Method in class picard.analysis.CounterManager
  Clears all inner Counter arrays
clear() - Method in class picard.illumina.parser.readers.CbclReader
CLEAR_DT - Variable in class picard.sam.markduplicates.MarkDuplicates
CLIP_ADAPTERS - Variable in class picard.fastq.BamToBfq
CLIP_ADAPTERS - Variable in class picard.sam.MergeBamAlignment
CLIP_OVERLAPPING_READS - Variable in class picard.analysis.directed.CollectTargetedMetrics
CLIP_OVERLAPPING_READS - Variable in class picard.sam.MergeBamAlignment
clipForOverlappingReads(SAMRecord, SAMRecord, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
  Checks to see whether the ends of the reads overlap and clips reads if necessary.
CLIPPING_ACTION - Variable in class picard.sam.SamToFastq
CLIPPING_ATTRIBUTE - Variable in class picard.sam.SamToFastq
CLIPPING_MIN_LENGTH - Variable in class picard.sam.SamToFastq
ClippingUtility - Class in picard.util
  Utilities to clip the adapter sequence from a SAMRecord read
ClippingUtility() - Constructor for class picard.util.ClippingUtility
Clocs - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
ClocsFileFaker - Class in picard.illumina.parser.fakers
ClocsFileFaker() - Constructor for class picard.illumina.parser.fakers.ClocsFileFaker
ClocsFileReader - Class in picard.illumina.parser.readers
  The clocs file format is one of 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
ClocsFileReader(File) - Constructor for class picard.illumina.parser.readers.ClocsFileReader
clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
clone() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
close() - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
close() - Method in class picard.arrays.illumina.IlluminaBPMFile
close() - Method in class picard.arrays.illumina.InfiniumEGTFile
close() - Method in class picard.arrays.illumina.InfiniumGTCFile
close() - Method in interface picard.illumina.BasecallsConverter.ConvertedClusterDataWriter
  Closes the writer.
close() - Method in class picard.illumina.parser.BaseIlluminaDataProvider
close() - Method in class picard.illumina.parser.MultiTileFilterParser
close() - Method in class picard.illumina.parser.MultiTileLocsParser
close() - Method in class picard.illumina.parser.PerTileParser
close() - Method in class picard.illumina.parser.readers.BarcodeFileReader
close() - Method in class picard.illumina.parser.readers.BclReader
close() - Method in class picard.illumina.parser.readers.CbclReader
close() - Method in class picard.illumina.parser.readers.ClocsFileReader
close() - Method in class picard.illumina.parser.readers.LocsFileReader
close() - Method in class picard.illumina.parser.readers.PosFileReader
close() - Method in class picard.sam.AbstractAlignmentMerger
close() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
close() - Method in class picard.util.AbstractInputParser
  Closes this stream and releases any system resources associated with it.
close() - Method in class picard.util.AsyncIterator
  Stops the thread and then calls synchronouslyClose() to allow implementation to do any one time clean up.
close() - Method in class picard.util.BasicInputParser
  Closes the underlying stream
close() - Method in class picard.util.CircularByteBuffer
  Signals that the buffer is closed and no further writes will occur.
close() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
close() - Method in class picard.util.TabbedTextFileWithHeaderParser
  Release all resources associated with the parser.
close() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
close() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
close() - Method in class picard.vcf.processor.VariantIteratorProducer
  Closes any latent file handles that may have been opened by calls to `VariantIteratorProducer.iterators()`.
closeWriter() - Method in class picard.sam.FixMateInformation
closeWriters() - Method in class picard.illumina.BasecallsConverter
  Closes all writers.
cluster() - Method in class picard.util.GraphUtils.Graph
  returns the cluster map of connected components
CLUSTER - Variable in class picard.fingerprint.ClusteredCrosscheckMetric
  The cluster identifier to which the two groups within this metric (`CrosscheckMetric.LEFT_GROUP_VALUE` and `CrosscheckMetric.RIGHT_GROUP_VALUE`) belong.
CLUSTER_DENSITY - Variable in class picard.illumina.IlluminaLaneMetrics
  The number of clusters per unit area on the this lane expressed in units of [cluster / mm^2].
CLUSTER_FILE - Variable in class picard.arrays.GtcToVcf
CLUSTER_FILE - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
CLUSTER_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
CLUSTER_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
CLUSTER_FILE_NAME - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The name of the cluster file used
CLUSTER_ID - picard.illumina.parser.IlluminaMetricsCode
CLUSTER_SIZE - Variable in class picard.fingerprint.ClusteredCrosscheckMetric
  The number of different groups that are assigned to this cluster.
ClusterCrosscheckMetrics - Class in picard.fingerprint
  Summary
ClusterCrosscheckMetrics() - Constructor for class picard.fingerprint.ClusterCrosscheckMetrics
ClusterData - Class in picard.illumina.parser
  Store the information from Illumina files for a single cluster with one or more reads.
ClusterData(ReadData...) - Constructor for class picard.illumina.parser.ClusterData
  Used for testing, reads is set directly with no copying to the input array
ClusterData(ReadType[]) - Constructor for class picard.illumina.parser.ClusterData
  Creates a ClusterData with one read for each type provided
ClusterDataToSamConverter - Class in picard.illumina
  Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords, as appropriate, and optionally marking adapter sequence.
ClusterDataToSamConverter(String, Map<Integer, String>, ReadStructure, List<AdapterPair>, ClusterDataToSamConverter.PopulateBarcode, boolean) - Constructor for class picard.illumina.ClusterDataToSamConverter
  Constructor
ClusteredCrosscheckMetric - Class in picard.fingerprint
  A metric class to hold the result of `ClusterCrosscheckMetrics` fingerprints.
ClusteredCrosscheckMetric() - Constructor for class picard.fingerprint.ClusteredCrosscheckMetric
ClusteredCrosscheckMetric(CrosscheckMetric) - Constructor for class picard.fingerprint.ClusteredCrosscheckMetric
clusterVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
code() - Method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateType
CODING - picard.annotation.LocusFunction
CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Number of bases in primary alignments that align to a non-UTR coding base for some gene, and not ribosomal sequence.
codingEnd - Variable in class picard.annotation.Gene.Transcript
codingStart - Variable in class picard.annotation.Gene.Transcript
COLLECT_ALIGNMENT_INFORMATION - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
CollectAlignmentRefArgCollection() - Constructor for class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
CollectAlignmentSummaryMetrics - Class in picard.analysis
  A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
CollectAlignmentSummaryMetrics - picard.analysis.CollectMultipleMetrics.Program
CollectAlignmentSummaryMetrics() - Constructor for class picard.analysis.CollectAlignmentSummaryMetrics
CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection - Class in picard.analysis
CollectArraysVariantCallingMetrics - Class in picard.arrays
  Collects summary and per-sample metrics about variant calls in a VCF file.
CollectArraysVariantCallingMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics
CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics - Class in picard.arrays
CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics - Class in picard.arrays
CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics - Class in picard.arrays
CollectBaseDistributionByCycle - Class in picard.analysis
CollectBaseDistributionByCycle - picard.analysis.CollectMultipleMetrics.Program
CollectBaseDistributionByCycle() - Constructor for class picard.analysis.CollectBaseDistributionByCycle
CollectDuplicateMetrics - Class in picard.sam.markduplicates
  Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.
CollectDuplicateMetrics() - Constructor for class picard.sam.markduplicates.CollectDuplicateMetrics
collectErrorMessages(List<String>, String[]) - Method in class picard.illumina.ExtractBarcodesProgram
CollectGcBiasMetrics - Class in picard.analysis
  Tool to collect information about GC bias in the reads in a given BAM file.
CollectGcBiasMetrics - picard.analysis.CollectMultipleMetrics.Program
CollectGcBiasMetrics() - Constructor for class picard.analysis.CollectGcBiasMetrics
CollectHiSeqXPfFailMetrics - Class in picard.illumina.quality
  Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter.
CollectHiSeqXPfFailMetrics() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric - Class in picard.illumina.quality
  a metric class for describing FP failing reads from an Illumina HiSeqX lane *
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric - Class in picard.illumina.quality
  Metrics produced by the GetHiSeqXPFFailMetrics program.
CollectHiSeqXPfFailMetrics.ReadClassifier - Class in picard.illumina.quality
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason - Enum in picard.illumina.quality
CollectHsMetrics - Class in picard.analysis.directed
  This tool takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection.
CollectHsMetrics() - Constructor for class picard.analysis.directed.CollectHsMetrics
CollectIlluminaBasecallingMetrics - Class in picard.illumina
  A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.
CollectIlluminaBasecallingMetrics() - Constructor for class picard.illumina.CollectIlluminaBasecallingMetrics
CollectIlluminaLaneMetrics - Class in picard.illumina
  Command-line wrapper around `CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector`.
CollectIlluminaLaneMetrics() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector - Class in picard.illumina
  Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
CollectIndependentReplicateMetrics - Class in picard.analysis.replicates
  A CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam.
CollectIndependentReplicateMetrics() - Constructor for class picard.analysis.replicates.CollectIndependentReplicateMetrics
CollectInsertSizeMetrics - Class in picard.analysis
  Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
CollectInsertSizeMetrics - picard.analysis.CollectMultipleMetrics.Program
CollectInsertSizeMetrics() - Constructor for class picard.analysis.CollectInsertSizeMetrics
CollectionStratifier(Collection<ReadBaseStratification.RecordAndOffsetStratifier<?>>) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
CollectJumpingLibraryMetrics - Class in picard.analysis
  Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
CollectJumpingLibraryMetrics() - Constructor for class picard.analysis.CollectJumpingLibraryMetrics
collectLaneMetrics(File, File, String, MetricsFile<MetricBase, Comparable<?>>, MetricsFile<MetricBase, Comparable<?>>, ReadStructure, String, ValidationStringency) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
  Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
CollectMultipleMetrics - Class in picard.analysis
  Class that is designed to instantiate and execute multiple metrics programs that extend SinglePassSamProgram while making only a single pass through the SAM file and supplying each program with the records as it goes.
CollectMultipleMetrics() - Constructor for class picard.analysis.CollectMultipleMetrics
CollectMultipleMetrics.Program - Enum in picard.analysis
CollectMultipleMetrics.ProgramInterface - Interface in picard.analysis
CollectOxoGMetrics - Class in picard.analysis
  Class for trying to quantify the CpCG->CpCA error rate.
CollectOxoGMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics
CollectOxoGMetrics.CpcgMetrics - Class in picard.analysis
  Metrics class for outputs.
CollectQualityYieldMetrics - Class in picard.analysis
  Command line program to calculate quality yield metrics
CollectQualityYieldMetrics - picard.analysis.CollectMultipleMetrics.Program
CollectQualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics
CollectQualityYieldMetrics.QualityYieldMetrics - Class in picard.analysis
  A set of metrics used to describe the general quality of a BAM file
CollectQualityYieldMetrics.QualityYieldMetricsCollector - Class in picard.analysis
CollectRawWgsMetrics - Class in picard.analysis
  Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, same implementation as `CollectWgsMetrics`, with different defaults: lacks baseQ and mappingQ filters and has much higher coverage cap.
CollectRawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics
CollectRawWgsMetrics.RawWgsMetrics - Class in picard.analysis
CollectRnaSeqMetrics - Class in picard.analysis
CollectRnaSeqMetrics() - Constructor for class picard.analysis.CollectRnaSeqMetrics
CollectRrbsMetrics - Class in picard.analysis
  Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.
CollectRrbsMetrics() - Constructor for class picard.analysis.CollectRrbsMetrics
CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection - Class in picard.analysis
CollectRrbsMetricsReferenceArgumentCollection() - Constructor for class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
CollectSamErrorMetrics - Class in picard.sam.SamErrorMetric
  Program to collect error metrics on bases stratified in various ways.
CollectSamErrorMetrics() - Constructor for class picard.sam.SamErrorMetric.CollectSamErrorMetrics
CollectSequencingArtifactMetrics - Class in picard.analysis.artifacts
  Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep.
CollectSequencingArtifactMetrics - picard.analysis.CollectMultipleMetrics.Program
CollectSequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.CollectSequencingArtifactMetrics
CollectTargetedMetrics<METRIC extends MultilevelMetrics,​COLLECTOR extends TargetMetricsCollector<METRIC>> - Class in picard.analysis.directed
  Both CollectTargetedPCRMetrics and CollectHsSelection share virtually identical program structures except for the name of their targeting mechanisms (e.g.
CollectTargetedMetrics() - Constructor for class picard.analysis.directed.CollectTargetedMetrics
CollectTargetedPcrMetrics - Class in picard.analysis.directed
  This tool calculates a set of PCR-related metrics from an aligned SAM or BAM file containing targeted sequencing data.
CollectTargetedPcrMetrics() - Constructor for class picard.analysis.directed.CollectTargetedPcrMetrics
CollectVariantCallingMetrics - Class in picard.vcf
  Collects summary and per-sample metrics about variant calls in a VCF file.
CollectVariantCallingMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics
CollectVariantCallingMetrics.VariantCallingDetailMetrics - Class in picard.vcf
  A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
CollectVariantCallingMetrics.VariantCallingSummaryMetrics - Class in picard.vcf
  A collection of metrics relating to snps and indels within a variant-calling file (VCF).
CollectWgsMetrics - Class in picard.analysis
  Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
CollectWgsMetrics() - Constructor for class picard.analysis.CollectWgsMetrics
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection - Class in picard.analysis
CollectWgsMetrics.WgsMetricsCollector - Class in picard.analysis
CollectWgsMetricsIntervalArgumentCollection() - Constructor for class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
CollectWgsMetricsWithNonZeroCoverage - Class in picard.analysis
CollectWgsMetricsWithNonZeroCoverage() - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage - Class in picard.analysis
  Metrics for evaluating the performance of whole genome sequencing experiments.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category - Enum in picard.analysis
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector - Class in picard.analysis
COLOR_STATUS - Static variable in class picard.cmdline.CommandLineDefaults
  Implementation note, this is duplicate code stolen from HTSJDK's Default.java /** Decides if we want to write colors to the terminal.
columnLabels() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
columnLabels() - Method in class picard.util.TabbedTextFileWithHeaderParser
columnLabelsList() - Method in class picard.util.TabbedTextFileWithHeaderParser
CombineGenotypingArrayVcfs - Class in picard.arrays
  A simple program to combine multiple genotyping array VCFs into one VCF The input VCFs must have the same sequence dictionary and same list of variant loci.
CombineGenotypingArrayVcfs() - Constructor for class picard.arrays.CombineGenotypingArrayVcfs
combiningResultsBy(VariantProcessor.ResultMerger<R>) - Method in class picard.vcf.processor.VariantProcessor.Builder
CommandLineDefaults - Class in picard.cmdline
  Embodies defaults for global values that affect how the Picard Command Line operates.
CommandLineDefaults() - Constructor for class picard.cmdline.CommandLineDefaults
CommandLineProgram - Class in picard.cmdline
  Abstract class to facilitate writing command-line programs.
CommandLineProgram() - Constructor for class picard.cmdline.CommandLineProgram
CommandLineSyntaxTranslater - Class in picard.cmdline
  Class for handling translation of Picard-style command line argument syntax to POSIX-style argument syntax; used for running tests written with Picard style syntax against the Barclay command line parser.
CommandLineSyntaxTranslater() - Constructor for class picard.cmdline.CommandLineSyntaxTranslater
COMMENT - Variable in class picard.sam.AddCommentsToBam
COMMENT - Variable in class picard.sam.FastqToSam
COMMENT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
COMMENT - Variable in class picard.sam.MergeSamFiles
COMMENT - Variable in class picard.util.IntervalListTools
COMMENT - Variable in class picard.vcf.GatherVcfs
COMMENT - Variable in class picard.vcf.MergeVcfs
compare(int, int) - Static method in class picard.util.MathUtil
COMPARE_MQ - Variable in class picard.sam.util.SAMComparisonArgumentCollection
CompareGtcFiles - Class in picard.arrays.illumina
  A simple tool to compare two Illumina GTC files.
CompareGtcFiles() - Constructor for class picard.arrays.illumina.CompareGtcFiles
CompareMetrics - Class in picard.analysis
  Compare two metrics files.
CompareMetrics() - Constructor for class picard.analysis.CompareMetrics
compareMetricValues(Object, Object, String) - Method in class picard.analysis.CompareMetrics
CompareSAMs - Class in picard.sam
  Rudimentary SAM comparer.
CompareSAMs() - Constructor for class picard.sam.CompareSAMs
compareTo(SequencingArtifactMetrics.BaitBiasDetailMetrics) - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
compareTo(SequencingArtifactMetrics.PreAdapterDetailMetrics) - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
compareTo(Gene) - Method in class picard.annotation.Gene
compareTo(HaplotypeBlock) - Method in class picard.fingerprint.HaplotypeBlock
compareTo(MatchResults) - Method in class picard.fingerprint.MatchResults
  Provides a natural sort so that better matches (by LOD) sort earlier.
compareTo(Snp) - Method in class picard.fingerprint.Snp
compareTo(Pair<X, Y>) - Method in class picard.sam.util.Pair
compareTo(PrimaryAlignmentKey) - Method in class picard.sam.util.PrimaryAlignmentKey
compareTo(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
CompareVariantContextToLocus(SAMSequenceDictionary, VariantContext, Locus) - Static method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
  Compares a VariantContext to a Locus providing information regarding possible overlap, or relative location
complement() - Method in enum picard.analysis.artifacts.Transition
  Return the complementary transition.
COMPRESS_OUTPUTS - Variable in class picard.illumina.ExtractBarcodesProgram
COMPRESS_OUTPUTS_PER_RG - Variable in class picard.sam.SamToFastq
COMPRESS_OUTPUTS_PER_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
COMPRESSION_LEVEL - Variable in class picard.cmdline.CommandLineProgram
computeQScore(long) - Method in class picard.sam.SamErrorMetric.ErrorMetric
  compute a qscore given the number of errors and the total number of bases.
computeQScore(long, long) - Method in class picard.sam.SamErrorMetric.ErrorMetric
  compute a qscore given the number of errors and the total number of bases.
CON_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.
CON_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.
CONCAT - picard.util.IntervalListTools.Action
CONCAT_ALL - picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
consensusStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratify by tags used during duplex and single index consensus calling.
ConsensusStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
contains(Snp) - Method in class picard.fingerprint.HaplotypeBlock
  Returns true if the SNP is contained within the haplotype block, false otherwise.
contamination - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
CONTAMINATION - Variable in class picard.fingerprint.ExtractFingerprint
CONTAMINATION - Variable in class picard.fingerprint.IdentifyContaminant
CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The sequence context to which the analysis is constrained.
CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The sequence context to which the analysis is constrained.
CONTEXT - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The sequence context being reported on.
CONTEXT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
CONTEXT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
CONTEXTS - Variable in class picard.analysis.CollectOxoGMetrics
CONTEXTS_TO_PRINT - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
contig() - Method in class picard.vcf.processor.VcfFileSegment
CONTINGENCY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
CONTINGENCY_STATE_HEADER_LINE - Static variable in class picard.vcf.GenotypeConcordance
CONTINGENCY_STATE_TAG - Static variable in class picard.vcf.GenotypeConcordance
CONTINGENCY_VALUES - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
  The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference.
CONTROL - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
  Various control intensities that are present on the infinium chips.
CONTROL_INFO - Static variable in class picard.arrays.illumina.ArraysControlInfo
convert(File, File, File, Boolean) - Static method in class picard.sam.SamFormatConverter
  Convert a file from one of sam/bam/cram format to another based on the extension of output.
convertClusterToOutputRecord(ClusterData) - Method in interface picard.illumina.BasecallsConverter.ClusterDataConverter
  Creates the OUTPUT_RECORDs from the cluster
convertClusterToOutputRecord(ClusterData) - Method in class picard.illumina.ClusterDataToSamConverter
  Creates the SAMRecord for each read in the cluster
CONVERTED_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
  Number of times this CpG site was converted (TG for + strand, CA for - strand)
converter - Variable in class picard.illumina.BasecallsConverter
ConvertHaplotypeDatabaseToVcf - Class in picard.fingerprint
ConvertHaplotypeDatabaseToVcf() - Constructor for class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
convertMetric(TargetMetrics) - Method in class picard.analysis.directed.HsMetricCollector
convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetedPcrMetricsCollector
convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetMetricsCollector
convertPicardStyleToPosixStyle(String[]) - Static method in class picard.cmdline.CommandLineSyntaxTranslater
ConvertSequencingArtifactToOxoG - Class in picard.analysis.artifacts
ConvertSequencingArtifactToOxoG() - Constructor for class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
convertSolexaQualityAscii_1_1_ToPhredBinary(byte[]) - Static method in class picard.util.IlluminaUtil
  Converts from Solexa ASCII to Phred binary in place.
copy() - Method in class picard.illumina.BarcodeMetric
  Creates a copy of metric initialized with only non-accumulated and non-calculated values set
COPY_TO_TAG - picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
copyFromBaseClass(T, S) - Static method in class picard.util.ReflectionUtil
CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
  Number of aligned reads that are mapped to the correct strand.
correspondingInterval() - Method in class picard.vcf.processor.VcfFileSegment
COUNT - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
  The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs
COUNT_OUTPUT - Variable in class picard.util.IntervalListTools
COUNT_UNPAIRED - Variable in class picard.analysis.CollectWgsMetrics
counter - Variable in class picard.analysis.AbstractWgsMetricsCollector
  The number of processed genomic bases
CounterManager - Class in picard.analysis
  Class for managing a list of Counters of integer, provides methods to access data from Counters with respect to an offset.
CounterManager(int, int) - Constructor for class picard.analysis.CounterManager
  Constructor creates new CounterManager without any Counters, counters are added to CounterManager via newCounter() method
CounterManager.Counter - Class in picard.analysis
  Class represents an integer array with methods to increment and get the values from it with respect to offset of outer `CounterManager`.
CountingAdapterFilter - Class in picard.filter
  Counting filter that discards reads are unaligned or aligned with MQ==0 and whose 5' ends look like adapter Sequence
CountingAdapterFilter() - Constructor for class picard.filter.CountingAdapterFilter
CountingDuplicateFilter - Class in picard.filter
  Counting filter that discards reads that have been marked as duplicates.
CountingDuplicateFilter() - Constructor for class picard.filter.CountingDuplicateFilter
CountingFilter - Class in picard.filter
  A SamRecordFilter that counts the number of bases in the reads which it filters out.
CountingFilter() - Constructor for class picard.filter.CountingFilter
CountingMapQFilter - Class in picard.filter
  Counting filter that discards reads below a configurable mapping quality threshold.
CountingMapQFilter(int) - Constructor for class picard.filter.CountingMapQFilter
CountingPairedFilter - Class in picard.filter
  Counting filter that discards reads that are unpaired in sequencing and paired reads whose mates are not mapped.
CountingPairedFilter() - Constructor for class picard.filter.CountingPairedFilter
COVARIATE - Variable in class picard.sam.SamErrorMetric.ErrorMetric
  The value of the covariate define the bases included in this metric
Coverage(Interval, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector.Coverage
  Constructs a new coverage object for the provided mapping with the desired padding either side.
COVERAGE_CAP - Variable in class picard.analysis.CollectWgsMetrics
COVERAGE_CAP - Variable in class picard.analysis.directed.CollectTargetedMetrics
coverageCap - Variable in class picard.analysis.AbstractWgsMetricsCollector
  Positions with coverage exceeding this value are treated as if they had coverage at this value
coverageCap - Variable in class picard.analysis.WgsMetrics
  The maximum depth/coverage to consider.
CpcgMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics.CpcgMetrics
CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
  Number of CpG sites that were converted (TG for +, CA for -)
CPG_BASES_SEEN - Variable in class picard.analysis.RrbsSummaryMetrics
  Number of CpG sites encountered
cram - picard.sam.RevertSam.FileType
CREATE_INDEX - Variable in class picard.cmdline.CommandLineProgram
CREATE_MD5_FILE - Variable in class picard.cmdline.CommandLineProgram
CreateBafRegressMetricsFile - Class in picard.arrays
  A simple program to create a standard picard metrics file from the output of bafRegress
CreateBafRegressMetricsFile() - Constructor for class picard.arrays.CreateBafRegressMetricsFile
createBarcodeExtractor() - Method in class picard.illumina.ExtractBarcodesProgram
CreateExtendedIlluminaManifest - Class in picard.arrays.illumina
  Create an Extended Illumina Manifest by performing a liftover to Build 37.
CreateExtendedIlluminaManifest() - Constructor for class picard.arrays.illumina.CreateExtendedIlluminaManifest
createNewCigarsIfMapsOffEndOfReference(SAMRecord) - Static method in class picard.sam.AbstractAlignmentMerger
  Soft-clip an alignment that hangs off the end of its reference sequence.
createRecord(IlluminaManifestRecord) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
createSamFileHeader() - Method in class picard.sam.FastqToSam
  Creates a simple header with the values provided on the command line.
createSamFileWriter(SAMFileHeader) - Method in class picard.sam.FixMateInformation
CreateSeqDictReferenceArgumentCollection() - Constructor for class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
CreateSequenceDictionary - Class in picard.sam
  Create a SAM/BAM file from a fasta containing reference sequence.
CreateSequenceDictionary() - Constructor for class picard.sam.CreateSequenceDictionary
CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection - Class in picard.sam
createSnpAndIndelBitSets(File, SAMSequenceDictionary) - Static method in class picard.util.DbSnpBitSetUtil
  Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
createSnpAndIndelBitSets(File, SAMSequenceDictionary, IntervalList) - Static method in class picard.util.DbSnpBitSetUtil
  Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
createSnpAndIndelBitSets(File, SAMSequenceDictionary, IntervalList, Optional<Log>) - Static method in class picard.util.DbSnpBitSetUtil
  Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
createVCSetFromFingerprint(Fingerprint, ReferenceSequenceFile, String) - Static method in class picard.fingerprint.FingerprintUtils
  A utility function that takes a fingerprint and returns a VariantContextSet with variants representing the haplotypes in the fingerprint
CreateVerifyIDIntensityContaminationMetricsFile - Class in picard.arrays
  A simple program to create a standard picard metrics file from the output of VerifyIDIntensity
CreateVerifyIDIntensityContaminationMetricsFile() - Constructor for class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
createWorkUnit(DocumentedFeature, ClassDoc, Class<?>) - Method in class picard.util.help.PicardHelpDoclet
CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
  The categorical cross entropy of the counts of genotypes relative to expected (big is bad)
CROSSCHECK_BY - Variable in class picard.fingerprint.CrosscheckFingerprints
CROSSCHECK_LIBRARIES - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
  Deprecated.
CROSSCHECK_MODE - Variable in class picard.fingerprint.CrosscheckFingerprints
CROSSCHECK_SAMPLES - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
  Deprecated.
CrosscheckFingerprints - Class in picard.fingerprint
  Checks that all data in the set of input files appear to come from the same individual.
CrosscheckFingerprints() - Constructor for class picard.fingerprint.CrosscheckFingerprints
CrosscheckMetric - Class in picard.fingerprint
  A class to hold the result of crosschecking fingerprints.
CrosscheckMetric() - Constructor for class picard.fingerprint.CrosscheckMetric
CrosscheckMetric.DataType - Enum in picard.fingerprint
CrosscheckMetric.FingerprintResult - Enum in picard.fingerprint
CrosscheckReadGroupFingerprints - Class in picard.fingerprint
  Deprecated.
  6/6/2017 Use `CrosscheckFingerprints` instead.
CrosscheckReadGroupFingerprints() - Constructor for class picard.fingerprint.CrosscheckReadGroupFingerprints
  Deprecated.
CsvInputParser - Class in picard.util
CsvInputParser(boolean, File...) - Constructor for class picard.util.CsvInputParser
  Constructor
CsvInputParser(boolean, InputStream...) - Constructor for class picard.util.CsvInputParser
  Constructor
CT - picard.fingerprint.DiploidGenotype
CtoA - picard.analysis.artifacts.Transition
CtoC - picard.analysis.artifacts.Transition
CtoG - picard.analysis.artifacts.Transition
CtoT - picard.analysis.artifacts.Transition
currentReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies bases into the current (uppercase) base as it was read from the sequencer (i.e.
CUSTOM_AMPLICON_SET - Variable in class picard.analysis.directed.TargetedPcrMetrics
  The name of the amplicon set used in this metrics collection run
CUSTOM_AMPLICON_SET_NAME - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
customCommandLineValidation() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
customCommandLineValidation() - Method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
customCommandLineValidation() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
customCommandLineValidation() - Method in class picard.analysis.CollectBaseDistributionByCycle
customCommandLineValidation() - Method in class picard.analysis.CollectGcBiasMetrics
customCommandLineValidation() - Method in class picard.analysis.CollectInsertSizeMetrics
  Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.analysis.CollectMultipleMetrics
customCommandLineValidation() - Method in class picard.analysis.CollectOxoGMetrics
customCommandLineValidation() - Method in class picard.analysis.CollectRnaSeqMetrics
customCommandLineValidation() - Method in class picard.analysis.CollectRrbsMetrics
customCommandLineValidation() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
customCommandLineValidation() - Method in class picard.analysis.CompareMetrics
customCommandLineValidation() - Method in class picard.analysis.directed.CollectTargetedMetrics
customCommandLineValidation() - Method in class picard.analysis.MeanQualityByCycle
customCommandLineValidation() - Method in class picard.analysis.QualityScoreDistribution
customCommandLineValidation() - Method in class picard.arrays.CollectArraysVariantCallingMetrics
customCommandLineValidation() - Method in class picard.arrays.GtcToVcf
customCommandLineValidation() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
customCommandLineValidation() - Method in class picard.cmdline.CommandLineProgram
  Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.fastq.BamToBfq
customCommandLineValidation() - Method in class picard.fingerprint.CheckFingerprint
customCommandLineValidation() - Method in class picard.fingerprint.CrosscheckFingerprints
customCommandLineValidation() - Method in class picard.fingerprint.CrosscheckReadGroupFingerprints
  Deprecated.
customCommandLineValidation() - Method in class picard.illumina.CheckIlluminaDirectory
customCommandLineValidation() - Method in class picard.illumina.ExtractBarcodesProgram
  Parses all barcodes from input files and validates all barcodes are the same length and unique
customCommandLineValidation() - Method in class picard.illumina.ExtractIlluminaBarcodes
customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToFastq
customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToSam
  Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.illumina.MarkIlluminaAdapters
customCommandLineValidation() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
customCommandLineValidation() - Method in class picard.sam.AddOrReplaceReadGroups
customCommandLineValidation() - Method in class picard.sam.CreateSequenceDictionary
  Use reference filename to create URI to go into header if URI was not passed on cmd line.
customCommandLineValidation() - Method in class picard.sam.DownsampleSam
customCommandLineValidation() - Method in class picard.sam.FastqToSam
customCommandLineValidation() - Method in class picard.sam.FilterSamReads
customCommandLineValidation() - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
customCommandLineValidation() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
customCommandLineValidation() - Method in class picard.sam.MergeBamAlignment
  Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.sam.MergeSamFiles
customCommandLineValidation() - Method in class picard.sam.PositionBasedDownsampleSam
customCommandLineValidation() - Method in class picard.sam.RevertSam
  Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.
customCommandLineValidation() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
customCommandLineValidation() - Method in class picard.sam.SamToFastq
  Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.sam.SamToFastqWithTags
customCommandLineValidation() - Method in class picard.sam.SplitSamByNumberOfReads
customCommandLineValidation() - Method in class picard.sam.ValidateSamFile
customCommandLineValidation() - Method in class picard.sam.ViewSam
customCommandLineValidation() - Method in class picard.util.BaitDesigner
customCommandLineValidation() - Method in class picard.util.IntervalListTools
customCommandLineValidation() - Method in class picard.vcf.FixVcfHeader
customCommandLineValidation() - Method in class picard.vcf.GenotypeConcordance
customCommandLineValidation() - Method in class picard.vcf.MendelianViolations.FindMendelianViolations
  Validates that the sex chromosomes don't overlap and parses the pseudo-autosomal regions into usable objects to ensure their parsability
cycle - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
CYCLE - Variable in class picard.analysis.BaseDistributionByCycleMetrics
CYCLE_SUBDIRECTORY_PATTERN - Static variable in class picard.illumina.parser.IlluminaFileUtil

## D

DATA_TYPE - Variable in class picard.fingerprint.CrosscheckMetric
DATA_TYPES - Variable in class picard.illumina.CheckIlluminaDirectory
DATA_TYPES_WITH_BARCODE - Static variable in class picard.illumina.BasecallsConverter
DATA_TYPES_WITHOUT_BARCODE - Static variable in class picard.illumina.BasecallsConverter
dataFile - Variable in class picard.illumina.parser.MultiTileFileUtil
dateCreated - Variable in class picard.arrays.illumina.InfiniumEGTFile
DB_SNP - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
DB_SNP - Variable in class picard.analysis.CollectMultipleMetrics
DB_SNP - Variable in class picard.analysis.CollectOxoGMetrics
DBSNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics
DBSNP_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
DBSNP_INS_DEL_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The Insertion/Deletion ratio of the indel calls made at dbSNP sites
DBSNP_TITV - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites
DbSnpBitSets() - Constructor for class picard.util.DbSnpBitSetUtil.DbSnpBitSets
DbSnpBitSetUtil - Class in picard.util
  Utility class to use with DbSnp files to determine is a locus is a dbSnp site.
DbSnpBitSetUtil(File, SAMSequenceDictionary) - Constructor for class picard.util.DbSnpBitSetUtil
  Constructor that creates a bit set with bits set to true for all variant types.
DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>) - Constructor for class picard.util.DbSnpBitSetUtil
  Constructor that creates a bit set with bits set to true for the given variant types.
DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>, IntervalList) - Constructor for class picard.util.DbSnpBitSetUtil
  Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>, IntervalList, Optional<Log>) - Constructor for class picard.util.DbSnpBitSetUtil
  Constructor.
DbSnpBitSetUtil.DbSnpBitSets - Class in picard.util
  Little tuple class to contain one bitset for SNPs and another for Indels.
DEBUG_FREQUENCY - Variable in class picard.util.FifoBuffer
decode() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
decode() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
decode() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
deduceIdealSplitWeight(IntervalList, int) - Method in interface picard.util.IntervalList.IntervalListScatterer
  A method that determines the ideal target "weight" of the output IntervalList.
deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
deepCopy() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilities
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
DEFAULT_ADAPTER_LENGTH - Static variable in class picard.util.AdapterMarker
DEFAULT_ADAPTER_SEQUENCE - Static variable in class picard.analysis.AdapterUtility
DEFAULT_BIG_DUPLICATE_SET_SIZE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
DEFAULT_EXPECTED_ORIENTATIONS - Static variable in class picard.analysis.ChimeraUtil
DEFAULT_GENOTYPING_ERROR_RATE - Static variable in class picard.fingerprint.FingerprintChecker
DEFAULT_INSERT_SIZE_LIMIT - Static variable in class picard.analysis.ChimeraUtil
DEFAULT_MAX_DUPLICATE_SET_SIZE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
DEFAULT_MINIMUM_BASE_QUALITY - Static variable in class picard.fingerprint.FingerprintChecker
DEFAULT_MINIMUM_MAPPING_QUALITY - Static variable in class picard.fingerprint.FingerprintChecker
DEFAULT_NUM_ADAPTERS_TO_KEEP - Static variable in class picard.util.AdapterMarker
DEFAULT_OPTICAL_DUPLICATE_DISTANCE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Static variable in class picard.util.AdapterMarker
DEFAULT_QUEUE_SIZE - Static variable in class picard.util.AsyncIterator
DEFAULT_READ_NAME_REGEX - Static variable in class picard.sam.util.ReadNameParser
  The read name regular expression (regex) is used to extract three pieces of information from the read name: tile, x location, and y location.
DEFAULT_TAGS_TO_DROP - Static variable in class picard.util.LiftoverUtils
DEFAULT_TAGS_TO_REVERSE - Static variable in class picard.util.LiftoverUtils
  Default list of attributes that need to be reversed or dropped from the INFO field when alleles have been swapped.
defaultEndBiasBases - Static variable in class picard.analysis.directed.RnaSeqMetricsCollector
DefaultSkipEmptyFiles - Static variable in class picard.illumina.parser.ParameterizedFileUtil
DEFINITE_GENOTYPES - Variable in class picard.fingerprint.FingerprintMetrics
  Number of haplotypes that had enough evidence to make a definite genotype call (genotype LOD > Threshold
deletion - picard.util.VariantType
DELETIONS_Q - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
  The (phred) rate of deletions.
deletionsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratify by Deletions in the read cigars.
DelimitedTextFileWithHeaderIterator - Class in picard.util
  Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.
DelimitedTextFileWithHeaderIterator(BasicInputParser) - Constructor for class picard.util.DelimitedTextFileWithHeaderIterator
DelimitedTextFileWithHeaderIterator.Row - Class in picard.util
demultiplex - Variable in class picard.illumina.BasecallsConverter
DENSITY_ID - picard.illumina.parser.IlluminaMetricsCode
DepthFilter - Class in picard.vcf.filter
  Filters out a record if all variant samples have depth lower than the given value.
DepthFilter(int) - Constructor for class picard.vcf.filter.DepthFilter
DESCRIPTION - Variable in class picard.sam.FastqToSam
descriptors - Variable in class picard.illumina.parser.ReadStructure
DESIGN_NAME - Variable in class picard.util.BaitDesigner
DESIGN_ON_TARGET_STRAND - Variable in class picard.util.BaitDesigner
DESIGN_STRATEGY - Variable in class picard.util.BaitDesigner
DETAIL_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
DETAIL_OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
DETAILED_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
detailedMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
DETAILS - Variable in class picard.metrics.GcBiasMetrics
determineFormats(Set<IlluminaDataType>, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
  For all requestedDataTypes return a map of file format to set of provided data types that covers as many requestedDataTypes as possible and chooses the most preferred available formats possible
determineQualityFormat(FastqReader, FastqReader, FastqQualityFormat) - Static method in class picard.sam.FastqToSam
  Looks at fastq input(s) and attempts to determine the proper quality format Closes the reader(s) by side effect
determineState(VariantContext, String, VariantContext, String, int, int, Boolean) - Static method in class picard.vcf.GenotypeConcordance
  A method to determine the truth and call states for a pair of variant contexts representing truth and call.
DEV_R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
DEV_THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
DEV_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
DEV_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
DEVIATIONS - Variable in class picard.analysis.CollectInsertSizeMetrics
devR - Variable in class picard.arrays.illumina.InfiniumEGTFile
devTheta - Variable in class picard.arrays.illumina.InfiniumEGTFile
DiagnosticsAndQCProgramGroup - Class in picard.cmdline.programgroups
  Tools that collect sequencing quality-related and comparative metrics
DiagnosticsAndQCProgramGroup() - Constructor for class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
DiploidGenotype - Enum in picard.fingerprint
  A genotype produced by one of the concrete implementations of AbstractAlleleCaller.
DiploidHaplotype - Enum in picard.fingerprint
  Simple enum to represent the three possible combinations of major/major, major/minor and minor/minor haplotypes for a diploid individual.
DISABLE_SORT - Variable in class picard.vcf.LiftoverVcf
DISAGREES_WITH_REF_AND_MATE_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
  The (phred) rate of bases that disagree with both the reference and their mate (which agree with each other)
DISAGREES_WITH_REFERENCE_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
  The (phred) rate of bases that disagree with the reference, but agree with their mate
DISCORDANT - picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
DISCRIMINATORY_POWER - Variable in class picard.fingerprint.FingerprintMetrics
  The difference in fingerprinting LOD between LOD_SELF_CHECK and the LOD score found when fingerprinting it against a random permutation of the probablity vectors (PLs) in each of the haplotypes.
DiskBasedReadEndsForMarkDuplicatesMap - Class in picard.sam.markduplicates.util
  Disk-based implementation of ReadEndsForMarkDuplicatesMap.
DiskBasedReadEndsForMarkDuplicatesMap(int, ReadEndsForMarkDuplicatesCodec) - Constructor for class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
distance(BarcodeEditDistanceQuery) - Method in enum picard.illumina.DistanceMetric
DISTANCE_MODE - Variable in class picard.illumina.ExtractBarcodesProgram
distance0(SingleBarcodeDistanceMetric) - Method in enum picard.illumina.DistanceMetric
DistanceMetric - Enum in picard.illumina
divide(double[], double[]) - Static method in class picard.util.MathUtil
  Calculates the ratio of two arrays of the same length.
divide(double, double) - Static method in class picard.util.MathUtil
  Divide two Doubles but return 0.0 if the denominator is 0
DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS - Variable in class picard.arrays.GtcToVcf
DO_NOT_CHANGE - picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
DO_NOT_CHANGE_INVALID - picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
DOC_CAT_BASE_CALLING - Static variable in class picard.util.help.HelpConstants
  Definition of the group names / descriptions for documentation/help purposes.
DOC_CAT_BASE_CALLING_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_CAT_DIAGNOSTICS_AND_QC - Static variable in class picard.util.help.HelpConstants
DOC_CAT_DIAGNOSTICS_AND_QC_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION - Static variable in class picard.util.help.HelpConstants
DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_CAT_INTERVALS_MANIPULATION - Static variable in class picard.util.help.HelpConstants
DOC_CAT_INTERVALS_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_CAT_OTHER - Static variable in class picard.util.help.HelpConstants
DOC_CAT_OTHER_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_CAT_READ_DATA_MANIPULATION - Static variable in class picard.util.help.HelpConstants
DOC_CAT_READ_DATA_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_CAT_REFERENCE - Static variable in class picard.util.help.HelpConstants
DOC_CAT_REFERENCE_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_CAT_TEST - Static variable in class picard.util.help.HelpConstants
DOC_CAT_TEST_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_CAT_VARIANT_EVALUATION - Static variable in class picard.util.help.HelpConstants
DOC_CAT_VARIANT_EVALUATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_CAT_VARIANT_FILTERING - Static variable in class picard.util.help.HelpConstants
DOC_CAT_VARIANT_FILTERING_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_CAT_VARIANT_MANIPULATION - Static variable in class picard.util.help.HelpConstants
DOC_CAT_VARIANT_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
DOC_SUPERCAT_EXCLUDE - Static variable in class picard.util.help.HelpConstants
DOC_SUPERCAT_TOOLS - Static variable in class picard.util.help.HelpConstants
  List of "supercategory" values used for doc purposes.
DOC_SUPERCAT_UTILITIES - Static variable in class picard.util.help.HelpConstants
DONT_MERGE_ABUTTING - Variable in class picard.util.IntervalListTools
DontTag - picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
doPaired(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
  More complicated method that takes two fastq files and builds pairing information in the SAM.
doUnpaired(FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
  Creates a simple SAM file from a single fastq file.
DownsampleSam - Class in picard.sam
  Summary
DownsampleSam() - Constructor for class picard.sam.DownsampleSam
doWork() - Method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
doWork() - Method in class picard.analysis.CollectJumpingLibraryMetrics
  Calculates the detailed statistics about the jumping library and then generates the results.
doWork() - Method in class picard.analysis.CollectMultipleMetrics
doWork() - Method in class picard.analysis.CollectOxoGMetrics
doWork() - Method in class picard.analysis.CollectRrbsMetrics
doWork() - Method in class picard.analysis.CollectWgsMetrics
doWork() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
doWork() - Method in class picard.analysis.CompareMetrics
doWork() - Method in class picard.analysis.directed.CollectTargetedMetrics
  Asserts that files are readable and writable and then fires off an HsMetricsCalculator instance to do the real work.
doWork() - Method in class picard.analysis.replicates.CollectIndependentReplicateMetrics
doWork() - Method in class picard.analysis.SinglePassSamProgram
  Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.
doWork() - Method in class picard.annotation.SortGff
doWork() - Method in class picard.arrays.CollectArraysVariantCallingMetrics
doWork() - Method in class picard.arrays.CombineGenotypingArrayVcfs
doWork() - Method in class picard.arrays.CreateBafRegressMetricsFile
doWork() - Method in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
doWork() - Method in class picard.arrays.GtcToVcf
doWork() - Method in class picard.arrays.illumina.BpmToNormalizationManifestCsv
doWork() - Method in class picard.arrays.illumina.CompareGtcFiles
doWork() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
doWork() - Method in class picard.arrays.MergePedIntoVcf
doWork() - Method in class picard.arrays.VcfToAdpc
doWork() - Method in class picard.cmdline.CommandLineProgram
  Do the work after command line has been parsed.
doWork() - Method in class picard.fastq.BamToBfq
doWork() - Method in class picard.fingerprint.CalculateFingerprintMetrics
doWork() - Method in class picard.fingerprint.CheckFingerprint
doWork() - Method in class picard.fingerprint.ClusterCrosscheckMetrics
doWork() - Method in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
doWork() - Method in class picard.fingerprint.CrosscheckFingerprints
doWork() - Method in class picard.fingerprint.CrosscheckReadGroupFingerprints
  Deprecated.
doWork() - Method in class picard.fingerprint.ExtractFingerprint
doWork() - Method in class picard.fingerprint.IdentifyContaminant
doWork() - Method in class picard.fingerprint.LiftOverHaplotypeMap
doWork() - Method in class picard.illumina.CheckIlluminaDirectory
doWork() - Method in class picard.illumina.CollectIlluminaBasecallingMetrics
doWork() - Method in class picard.illumina.CollectIlluminaLaneMetrics
doWork() - Method in class picard.illumina.ExtractIlluminaBarcodes
doWork() - Method in class picard.illumina.IlluminaBasecallsToFastq
doWork() - Method in class picard.illumina.IlluminaBasecallsToSam
doWork() - Method in class picard.illumina.MarkIlluminaAdapters
doWork() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
doWork() - Method in class picard.reference.ExtractSequences
doWork() - Method in class picard.reference.NonNFastaSize
doWork() - Method in class picard.reference.NormalizeFasta
doWork() - Method in class picard.sam.AddCommentsToBam
doWork() - Method in class picard.sam.AddOATag
doWork() - Method in class picard.sam.AddOrReplaceReadGroups
doWork() - Method in class picard.sam.BamIndexStats
  Main method for the program.
doWork() - Method in class picard.sam.BuildBamIndex
  Main method for the program.
doWork() - Method in class picard.sam.CalculateReadGroupChecksum
doWork() - Method in class picard.sam.CheckTerminatorBlock
doWork() - Method in class picard.sam.CleanSam
  Do the work after command line has been parsed.
doWork() - Method in class picard.sam.CompareSAMs
  Do the work after command line has been parsed.
doWork() - Method in class picard.sam.CreateSequenceDictionary
  Do the work after command line has been parsed.
doWork() - Method in class picard.sam.DownsampleSam
doWork() - Method in class picard.sam.FastqToSam
doWork() - Method in class picard.sam.FilterSamReads
doWork() - Method in class picard.sam.FixMateInformation
doWork() - Method in class picard.sam.GatherBamFiles
doWork() - Method in class picard.sam.markduplicates.CheckDuplicateMarking
doWork() - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
  Method that does most of the work.
doWork() - Method in class picard.sam.markduplicates.MarkDuplicates
  Main work method.
doWork() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
  Main work method.
doWork() - Method in class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
  Main work method.
doWork() - Method in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
doWork() - Method in class picard.sam.MergeBamAlignment
doWork() - Method in class picard.sam.MergeSamFiles
  Combines multiple SAM/BAM/CRAM files into one.
doWork() - Method in class picard.sam.PositionBasedDownsampleSam
doWork() - Method in class picard.sam.ReorderSam
doWork() - Method in class picard.sam.ReplaceSamHeader
  Do the work after command line has been parsed.
doWork() - Method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
doWork() - Method in class picard.sam.RevertSam
doWork() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
doWork() - Method in class picard.sam.SamFormatConverter
doWork() - Method in class picard.sam.SamToFastq
doWork() - Method in class picard.sam.SetNmMdAndUqTags
doWork() - Method in class picard.sam.SortSam
doWork() - Method in class picard.sam.SplitSamByLibrary
doWork() - Method in class picard.sam.SplitSamByNumberOfReads
doWork() - Method in class picard.sam.ValidateSamFile
  Do the work after command line has been parsed.
doWork() - Method in class picard.sam.ViewSam
doWork() - Method in class picard.util.AccumulateQualityYieldMetrics
doWork() - Method in class picard.util.BaitDesigner
doWork() - Method in class picard.util.BedToIntervalList
doWork() - Method in class picard.util.FifoBuffer
doWork() - Method in class picard.util.IntervalListToBed
doWork() - Method in class picard.util.IntervalListTools
doWork() - Method in class picard.util.LiftOverIntervalList
  Do the work after command line has been parsed.
doWork() - Method in class picard.util.ScatterIntervalsByNs
doWork() - Method in class picard.vcf.AccumulateVariantCallingMetrics
doWork() - Method in class picard.vcf.CollectVariantCallingMetrics
doWork() - Method in class picard.vcf.filter.FilterVcf
doWork() - Method in class picard.vcf.FixVcfHeader
doWork() - Method in class picard.vcf.GatherVcfs
doWork() - Method in class picard.vcf.GenotypeConcordance
doWork() - Method in class picard.vcf.LiftoverVcf
doWork() - Method in class picard.vcf.MakeSitesOnlyVcf
doWork() - Method in class picard.vcf.MakeVcfSampleNameMap
doWork() - Method in class picard.vcf.MendelianViolations.FindMendelianViolations
doWork() - Method in class picard.vcf.MergeVcfs
doWork() - Method in class picard.vcf.RenameSampleInVcf
doWork() - Method in class picard.vcf.SortVcf
doWork() - Method in class picard.vcf.SplitVcfs
doWork() - Method in class picard.vcf.UpdateVcfSequenceDictionary
doWork() - Method in class picard.vcf.VcfFormatConverter
doWork() - Method in class picard.vcf.VcfToIntervalList
draw() - Method in class picard.analysis.TheoreticalSensitivity.RouletteWheel
DROP_MISSING_CONTIGS - Variable in class picard.util.BedToIntervalList
DUAL_INDEXED - picard.util.IlluminaUtil.IlluminaAdapterPair
DUPE - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  The record passes validation but is a duplicate (another assay at the same locus with the same alleles)
DUPE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
DUPLEX_CONSENSUS - picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
  Consensus read which has two or more observations in both directions.
DUPLEX_SINGLETON - picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
  Read which has two observations, one from each direction.
DUPLEX_UMI - Variable in class picard.sam.markduplicates.MarkDuplicates
DUPLICATE_MARKINGS_DIFFER - Variable in class picard.sam.SamComparisonMetric
  The number of primary records for which duplicate markings are different.
DUPLICATE_SCORING_STRATEGY - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
DUPLICATE_SET_INDEX_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
  The attribute in the SAM/BAM file used to store which read was selected as representative out of a duplicate set
DUPLICATE_SET_SIZE_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
  The attribute in the SAM/BAM file used to store the size of a duplicate set
DUPLICATE_SETS_IGNORING_UMI - Variable in class picard.sam.markduplicates.UmiMetrics
  Number of duplicate sets found before taking UMIs into account
DUPLICATE_SETS_WITH_UMI - Variable in class picard.sam.markduplicates.UmiMetrics
  Number of duplicate sets found after taking UMIs into account
DUPLICATE_TYPE_LIBRARY - Static variable in class picard.sam.markduplicates.MarkDuplicates
  The duplicate type tag value for duplicate type: library.
DUPLICATE_TYPE_SEQUENCING - Static variable in class picard.sam.markduplicates.MarkDuplicates
  The duplicate type tag value for duplicate type: sequencing (optical & pad-hopping, or "co-localized").
DUPLICATE_TYPE_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
  The optional attribute in SAM/BAM/CRAM files used to store the duplicate type.
duplicateSetSize - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
DuplicationMetrics - Class in picard.sam
  Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
DuplicationMetrics() - Constructor for class picard.sam.DuplicationMetrics
dynamic - picard.sam.RevertSam.FileType

## E

EarliestFragmentPrimaryAlignmentSelectionStrategy - Class in picard.sam
  When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read.
EarliestFragmentPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
EmpiricalPhasingMetricsOutReader - Class in picard.illumina.parser.readers
EmpiricalPhasingMetricsOutReader(File) - Constructor for class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics - Class in picard.illumina.parser.readers
EMPTY - picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
EMPTY - picard.vcf.GenotypeConcordanceStates.ContingencyState
EMPTY - Static variable in class picard.vcf.GenotypeConcordanceScheme
EMPTY_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
  The empty (no contingency info) count across all variants
EmptyOutputArgumentCollection - Class in picard.cmdline.argumentcollections
EmptyOutputArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.EmptyOutputArgumentCollection
encode(ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
encode(ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
encode(RepresentativeReadIndexer) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
encodeDictionary(BufferedWriter, Iterator<SAMSequenceRecord>) - Static method in class picard.util.SequenceDictionaryUtils
  Encodes a sequence dictionary
encodeMappingInformation(SAMRecord) - Static method in class picard.sam.AbstractAlignmentMerger
  Encodes mapping information from a record into a string according to the format sepcified in the Sam-Spec under the SA tag.
end - Variable in class picard.annotation.Gene.Transcript.Exon
end - Variable in class picard.illumina.parser.Range
end() - Method in class picard.annotation.Gene.Transcript
END_BIAS_BASES - Variable in class picard.analysis.CollectRnaSeqMetrics
ENFORCE_SAME_SAMPLES - Variable in class picard.vcf.FixVcfHeader
equals(Object) - Method in class picard.annotation.Gene
equals(Object) - Method in class picard.annotation.Gene.Transcript
equals(Object) - Method in class picard.fingerprint.FingerprintIdDetails
equals(Object) - Method in class picard.fingerprint.HaplotypeBlock
equals(Object) - Method in class picard.fingerprint.Snp
equals(Object) - Method in class picard.illumina.parser.Range
equals(Object) - Method in class picard.illumina.parser.ReadDescriptor
equals(Object) - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
equals(Object) - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
equals(Object) - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
equals(Object) - Method in class picard.illumina.parser.ReadStructure
equals(Object) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
equals(Object) - Method in class picard.sam.util.Pair
  Calculate whether this pair object is equal to another object.
equals(Object) - Method in class picard.sam.util.PrimaryAlignmentKey
equals(Object) - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
ERROR_BAR_WIDTH - Variable in class picard.analysis.GcBiasDetailMetrics
  The radius of error bars in this bin based on the number of observations made.
ERROR_BASES - Variable in class picard.sam.SamErrorMetric.BaseErrorMetric
  The number of bases that disagree with the reference
ERROR_METRICS - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).
ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The estimated error rate due to this artifact.
ERROR_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
ERROR_VALUE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
ErrorMetric - Class in picard.sam.SamErrorMetric
  Created by farjoun on 6/26/18.
ErrorMetric() - Constructor for class picard.sam.SamErrorMetric.ErrorMetric
ErrorMetric(String, long) - Constructor for class picard.sam.SamErrorMetric.ErrorMetric
ErrorSummaryMetrics - Class in picard.analysis.artifacts
  Summary metrics produced by `CollectSequencingArtifactMetrics` as a roll up of the context-specific error rates, to provide global error rates per type of base substitution.
ErrorSummaryMetrics() - Constructor for class picard.analysis.artifacts.ErrorSummaryMetrics
escapePeriods(String) - Static method in class picard.illumina.parser.ParameterizedFileUtil
  Escape the period character.
ESTIMATE - Variable in class picard.arrays.BafRegressMetrics
  The estimate of contamination from the model (on the 0.0-1.0 scale)
ESTIMATED_LIBRARY_SIZE - Variable in class picard.sam.DuplicationMetrics
  The estimated number of unique molecules in the library based on PE duplication.
EstimateLibraryComplexity - Class in picard.sam.markduplicates
  Attempts to estimate library complexity from sequence alone.
EstimateLibraryComplexity() - Constructor for class picard.sam.markduplicates.EstimateLibraryComplexity
estimateLibrarySize(long, long) - Static method in class picard.sam.DuplicationMetrics
  Estimates the size of a library based on the number of paired end molecules observed and the number of unique pairs observed.
estimateRoi(long, double, long, long) - Static method in class picard.sam.DuplicationMetrics
  Estimates the ROI (return on investment) that one would see if a library was sequenced to x higher coverage than the observed coverage.
exception - Variable in class picard.util.ThreadPoolExecutorWithExceptions
excludeAligned - picard.sam.FilterSamReads.Filter
excludeReadList - picard.sam.FilterSamReads.Filter
excludeTagValues - picard.sam.FilterSamReads.Filter
excludingNonOverlaps(VcfFileSegmentGenerator, OverlapDetector<T>) - Static method in class picard.vcf.processor.VcfFileSegmentGenerator
  Returns a decorated `VcfFileSegmentGenerator` that filters out `VcfFileSegment`s that have no overlap with the provided `OverlapDetector`.
executeFromClasspath(String, String...) - Static method in class picard.util.RExecutor
  Executes the given R script that is stored in a file on the classpath.
executeFromFile(File, String...) - Static method in class picard.util.RExecutor
  Executes the given R script that is stored in a file by a call to Rscript.
EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE - Static variable in class picard.vcf.LiftoverVcf
EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND - Variable in class picard.fingerprint.CheckFingerprint
EXIT_CODE_WHEN_MISMATCH - Variable in class picard.fingerprint.CrosscheckFingerprints
EXIT_CODE_WHEN_NO_VALID_CHECKS - Variable in class picard.fingerprint.CheckFingerprint
EXIT_CODE_WHEN_NO_VALID_CHECKS - Variable in class picard.fingerprint.CrosscheckFingerprints
Exon(int, int) - Constructor for class picard.annotation.Gene.Transcript.Exon
EXON_COUNT - picard.annotation.RefFlatReader.RefFlatColumns
EXON_ENDS - picard.annotation.RefFlatReader.RefFlatColumns
EXON_STARTS - picard.annotation.RefFlatReader.RefFlatColumns
exons - Variable in class picard.annotation.Gene.Transcript
EXP_CLUSTERS_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
EXPECT_ALL_GROUPS_TO_MATCH - Variable in class picard.fingerprint.CrosscheckFingerprints
EXPECT_ALL_READ_GROUPS_TO_MATCH - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
  Deprecated.
EXPECTED_GENDER - Variable in class picard.arrays.GtcToVcf
EXPECTED_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
EXPECTED_GENOTYPE - Variable in class picard.analysis.FingerprintingDetailMetrics
  The expected genotype of the sample at the SNP locus.
EXPECTED_HET - Variable in class picard.fingerprint.FingerprintMetrics
  Expected number of heterozygous calls
EXPECTED_HOM_ALLELE1 - Variable in class picard.fingerprint.FingerprintMetrics
  Expected number of major allele homozygous calls
EXPECTED_HOM_ALLELE2 - Variable in class picard.fingerprint.FingerprintMetrics
  Expected number of major allele homozygous calls
EXPECTED_INSERT_SIZE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
EXPECTED_MATCH - picard.fingerprint.CrosscheckMetric.FingerprintResult
EXPECTED_MISMATCH - picard.fingerprint.CrosscheckMetric.FingerprintResult
EXPECTED_ORIENTATIONS - Variable in class picard.sam.MergeBamAlignment
EXPECTED_PAIR_ORIENTATIONS - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
EXPECTED_SAMPLE_ALIAS - Variable in class picard.fingerprint.CheckFingerprint
EXPECTED_VERSION - Static variable in class picard.illumina.parser.readers.FilterFileReader
  Expected Version
EXTENDED_ILLUMINA_MANIFEST - Variable in class picard.arrays.GtcToVcf
EXTENDED_ILLUMINA_MANIFEST_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
EXTENDED_ILLUMINA_MANIFEST_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
EXTENDED_MANIFEST_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The version of the Extended Illumina Manifest used for calling this sample
extendedIterator() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
extension - Variable in class picard.illumina.parser.ParameterizedFileUtil
  The file extension for this class, file extension does not have the standard meaning in this instance.
EXTENSION - Static variable in class picard.arrays.illumina.InfiniumEGTFile
EXTRA_ARGUMENT - Variable in class picard.analysis.CollectMultipleMetrics
EXTRACT_CONTAMINATED - Variable in class picard.fingerprint.IdentifyContaminant
EXTRACT_CONTAMINATION - Variable in class picard.fingerprint.ExtractFingerprint
ExtractBarcodesProgram - Class in picard.illumina
ExtractBarcodesProgram() - Constructor for class picard.illumina.ExtractBarcodesProgram
ExtractFingerprint - Class in picard.fingerprint
  Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
ExtractFingerprint() - Constructor for class picard.fingerprint.ExtractFingerprint
ExtractIlluminaBarcodes - Class in picard.illumina
  Determine the barcode for each read in an Illumina lane.
ExtractIlluminaBarcodes() - Constructor for class picard.illumina.ExtractIlluminaBarcodes
ExtractIlluminaBarcodes.PerTileBarcodeExtractor - Class in picard.illumina
  Extracts barcodes and accumulates metrics for an entire tile.
ExtractSequences - Class in picard.reference
  Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.
ExtractSequences() - Constructor for class picard.reference.ExtractSequences

## F

F - Static variable in class picard.sam.markduplicates.util.ReadEnds
F1F2 - picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
F1R2 - picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
F2R1 - picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
FAIL_REF - Static variable in class picard.arrays.illumina.InfiniumVcfFields
FAKE_FILES - Variable in class picard.illumina.CheckIlluminaDirectory
fakeBciFile(File, List<Integer>) - Method in class picard.illumina.parser.fakers.BciFileFaker
fakeBciFile(File, TileIndex) - Method in class picard.illumina.parser.fakers.BclIndexFaker
fakeFile(File, int, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
fakeFile(File, Integer) - Method in class picard.illumina.parser.fakers.FileFaker
fakeFile(File, List<Integer>, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BciFileFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BclFileFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BclIndexFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.ClocsFileFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FileFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FilterFileFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.LocsFileFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.PosFileFaker
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileBclFileUtil
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileFileUtil
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.ParameterizedFileUtil
  Given the expected tiles/expected cycles for this file type create a set of fake files such that the verification criteria are met.
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTileFileUtil
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
fakeMultiTileBclFile(File, TileIndex) - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
faker - Variable in class picard.illumina.parser.ParameterizedFileUtil
FAMILY_ID - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The family ID assigned to the trio for which these metrics are calculated.
FASTQ - Variable in class picard.sam.FastqToSam
FASTQ - Variable in class picard.sam.SamToFastq
FASTQ2 - Variable in class picard.sam.FastqToSam
FastqToSam - Class in picard.sam
  Converts a FASTQ file to an unaligned BAM or SAM file.
FastqToSam() - Constructor for class picard.sam.FastqToSam
FastWgsMetricsCollector - Class in picard.analysis
  Class represents fast algorithm for collecting data from `AbstractLocusInfo` with a list of aligned `EdgingRecordAndOffset` objects.
FastWgsMetricsCollector(CollectWgsMetrics, int, IntervalList) - Constructor for class picard.analysis.FastWgsMetricsCollector
  Creates a collector and initializes the inner data structures
FATHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The ID of the father within the trio.
Female - picard.pedigree.Sex
FEMALE_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
FF - Static variable in class picard.sam.markduplicates.util.ReadEnds
FifoBuffer - Class in picard.util
  Summary
FifoBuffer() - Constructor for class picard.util.FifoBuffer
  Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
FifoBuffer(InputStream, PrintStream) - Constructor for class picard.util.FifoBuffer
  Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
FILE - picard.fingerprint.CrosscheckMetric.DataType
FILE_EXTENSION - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
FILE_EXTENSION - Variable in class picard.analysis.CollectMultipleMetrics
FILE_EXTENSION - Static variable in class picard.arrays.CreateBafRegressMetricsFile
FILE_EXTENSION - Static variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
FILE_EXTENSION - Variable in class picard.illumina.CollectIlluminaLaneMetrics
FILE_NAME_PATTERN - Static variable in class picard.illumina.parser.BaseIlluminaDataProvider
FileFaker - Class in picard.illumina.parser.fakers
FileFaker() - Constructor for class picard.illumina.parser.fakers.FileFaker
filesAvailable() - Method in class picard.illumina.parser.MultiTileBclFileUtil
filesAvailable() - Method in class picard.illumina.parser.MultiTileFileUtil
filesAvailable() - Method in class picard.illumina.parser.ParameterizedFileUtil
  Determine whether or not files are available
filesAvailable() - Method in class picard.illumina.parser.PerTileFileUtil
filesAvailable() - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
filesAvailable() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
fileToTile(String) - Static method in class picard.illumina.parser.BaseIlluminaDataProvider
fileToTile(String) - Method in class picard.illumina.parser.ParameterizedFileUtil
  Returns only lane and tile information as PerTileFt's do not have End information.
FILL_POOLS - Variable in class picard.util.BaitDesigner
filter(VariantContext) - Method in class picard.vcf.filter.AlleleBalanceFilter
filter(VariantContext) - Method in class picard.vcf.filter.FisherStrandFilter
filter(VariantContext) - Method in class picard.vcf.filter.QdFilter
filter(VariantContext) - Method in interface picard.vcf.filter.VariantFilter
  Check to see if the VariantContext should have a filter applied to it.
filter(VariantContext, Genotype) - Method in class picard.vcf.filter.DepthFilter
filter(VariantContext, Genotype) - Method in interface picard.vcf.filter.GenotypeFilter
  Test whether or not the genotype should be filtered out.
filter(VariantContext, Genotype) - Method in class picard.vcf.filter.GenotypeQualityFilter
Filter - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
FILTER - Variable in class picard.sam.FilterSamReads
FILTER_CANNOT_LIFTOVER_REV_COMP - Static variable in class picard.vcf.LiftoverVcf
  Filter name to use when a target cannot be lifted over.
FILTER_INDEL_STRADDLES_TWO_INTERVALS - Static variable in class picard.vcf.LiftoverVcf
  Filter name to use when an indel cannot be lifted over since it straddles two intervals in a chain which means that it is unclear what are the right alleles to be used.
FILTER_MISMATCHING_REF_ALLELE - Static variable in class picard.vcf.LiftoverVcf
  Filter name to use when a target is lifted over, but the reference allele doesn't match the new reference.
FILTER_NAME - Static variable in class picard.vcf.filter.QdFilter
FILTER_NO_TARGET - Static variable in class picard.vcf.LiftoverVcf
  Filter name to use when a target cannot be lifted over.
FILTER_UNPAIRED_READS - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
FilterApplyingVariantIterator - Class in picard.vcf.filter
  Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying iterator.
FilterApplyingVariantIterator(Iterator<VariantContext>, Collection<VariantFilter>, Collection<GenotypeFilter>) - Constructor for class picard.vcf.filter.FilterApplyingVariantIterator
  Constructs an iterator from an underlying iterator and the provided (possibly empty) collections of variant and genotype filters.
FILTERED_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of indels that are filtered
FILTERED_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of SNPs that are filtered
FilterFileFaker - Class in picard.illumina.parser.fakers
  Created by jcarey on 3/13/14.
FilterFileFaker() - Constructor for class picard.illumina.parser.fakers.FilterFileFaker
FilterFileReader - Class in picard.illumina.parser.readers
  Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not.
FilterFileReader(File) - Constructor for class picard.illumina.parser.readers.FilterFileReader
filterOut(SAMRecord) - Method in class picard.filter.CountingFilter
filterOut(SAMRecord, SAMRecord) - Method in class picard.filter.CountingFilter
FilterSamReads - Class in picard.sam
  Summary
FilterSamReads() - Constructor for class picard.sam.FilterSamReads
FilterSamReads.Filter - Enum in picard.sam
filterSuspectSites() - Method in class picard.fingerprint.Fingerprint
  Attempts to filter out haplotypes that may have suspect genotyping by removing haplotypes that reach a minimum confidence score yet have a significant fraction of observations from a third or fourth allele.
FilterVcf - Class in picard.vcf.filter
  Applies a set of hard filters to Variants and to Genotypes within a VCF.
FilterVcf() - Constructor for class picard.vcf.filter.FilterVcf
  Constructor to default to having index creation on.
finalizeAndWriteMetrics(LibraryIdGenerator, MetricsFile<DuplicationMetrics, Double>, File) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
  Writes the metrics given by the libraryIdGenerator to the outputFile.
finalizeMetrics(Map<String, BarcodeMetric>, BarcodeMetric) - Static method in class picard.illumina.ExtractBarcodesProgram
find(String, Class<?>) - Method in class picard.cmdline.ClassFinder
  Scans the classpath for classes within the specified package and sub-packages that extend the parentType.
findAdapterPairAndIndexForSingleRead(byte[], int) - Method in class picard.util.AdapterMarker
  Return the adapter to be trimmed from a read represented as an array of bytes[]
findAdapterPairAndIndexForSingleRead(byte[], int, double, int) - Method in class picard.util.AdapterMarker
  Return the adapter to be trimmed from a read represented as an array of bytes[]
findAdapterPairAndIndexForSingleRead(byte[], int, double, int, AdapterPair...) - Static method in class picard.util.ClippingUtility
  Return the adapter to be trimmed from a read represented as an array of bytes[]
findByKey(int) - Static method in enum picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
findIndexOfClipSequence(byte[], byte[], int, double) - Static method in class picard.util.ClippingUtility
  Finds the first index of the adapterSequence sequence in the read sequence requiring at least minMatch bases of pairwise alignment with a maximum number of errors dictated by maxErrorRate.
FindMendelianViolations - Class in picard.vcf.MendelianViolations
  Summary
FindMendelianViolations() - Constructor for class picard.vcf.MendelianViolations.FindMendelianViolations
findOpticalDuplicates(List<? extends PhysicalLocation>, PhysicalLocation) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
  Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of one another.
findPreferredFormat(IlluminaDataType, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
  Given a data type find the most preferred file format even if files are not available
findTile(int) - Method in class picard.illumina.parser.TileIndex
findTileMetricsFiles(File, int) - Static method in class picard.illumina.parser.TileMetricsUtil
  Finds all of the tile metrics files for a given run directory and cycle count.
findUnmatchedTypes(Set<IlluminaDataType>, Map<IlluminaFileUtil.SupportedIlluminaFormat, Set<IlluminaDataType>>) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
  Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them
Fingerprint - Class in picard.fingerprint
  class to represent a genetic fingerprint as a set of HaplotypeProbabilities objects that give the relative probabilities of each of the possible haplotypes at a locus.
Fingerprint(String, Path, String) - Constructor for class picard.fingerprint.Fingerprint
FINGERPRINT_DETAIL_FILE_SUFFIX - Static variable in class picard.fingerprint.CheckFingerprint
FINGERPRINT_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
FINGERPRINT_GENOTYPES_VCF_FILE - Variable in class picard.arrays.GtcToVcf
FINGERPRINT_SUMMARY_FILE_SUFFIX - Static variable in class picard.fingerprint.CheckFingerprint
FingerprintChecker - Class in picard.fingerprint
  Major class that coordinates the activities involved in comparing genetic fingerprint data whether the source is from a genotyping platform or derived from sequence data.
FingerprintChecker(File) - Constructor for class picard.fingerprint.FingerprintChecker
  Creates a fingerprint checker that will work with the set of haplotypes stored in the supplied file.
FingerprintChecker(HaplotypeMap) - Constructor for class picard.fingerprint.FingerprintChecker
  Creates a fingerprint checker that will work with the set of haplotyped provided.
fingerprintFiles(Collection<Path>, int, int, TimeUnit) - Method in class picard.fingerprint.FingerprintChecker
  Fingerprints one or more SAM/BAM/VCF files at all available loci within the haplotype map, using multiple threads to speed up the processing.
FingerprintIdDetails - Class in picard.fingerprint
  class to hold the details of a element of fingerprinting PU tag
FingerprintIdDetails() - Constructor for class picard.fingerprint.FingerprintIdDetails
FingerprintIdDetails(SAMReadGroupRecord, String) - Constructor for class picard.fingerprint.FingerprintIdDetails
FingerprintIdDetails(String, String) - Constructor for class picard.fingerprint.FingerprintIdDetails
FingerprintingDetailMetrics - Class in picard.analysis
  Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
FingerprintingDetailMetrics() - Constructor for class picard.analysis.FingerprintingDetailMetrics
FingerprintingSummaryMetrics - Class in picard.analysis
  Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs.
FingerprintingSummaryMetrics() - Constructor for class picard.analysis.FingerprintingSummaryMetrics
FingerprintMetrics - Class in picard.fingerprint
  Class for holding metrics on a single fingerprint.
FingerprintMetrics() - Constructor for class picard.fingerprint.FingerprintMetrics
FingerprintResults - Class in picard.fingerprint
  Class that is used to represent the results of comparing a read group within a SAM file, or a sample within a VCF against one or more set of fingerprint genotypes.
FingerprintResults(Path, String, String) - Constructor for class picard.fingerprint.FingerprintResults
fingerprintSamFile(Path, IntervalList) - Method in class picard.fingerprint.FingerprintChecker
  Deprecated.
  use `FingerprintChecker.fingerprintSamFile(Path, Function)` instead.
fingerprintSamFile(Path, Function<HaplotypeBlock, HaplotypeProbabilities>) - Method in class picard.fingerprint.FingerprintChecker
  Generates a Fingerprint per read group in the supplied SAM file using the loci provided in the interval list.
FingerprintUtils - Class in picard.fingerprint
  A set of utilities used in the fingerprinting environment
FingerprintUtils() - Constructor for class picard.fingerprint.FingerprintUtils
FingerprintUtils.VariantContextSet - Class in picard.fingerprint
  A class that holds VariantContexts sorted by genomic position
fingerprintVcf(Path) - Method in class picard.fingerprint.FingerprintChecker
finish() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
finish() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
finish() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
finish() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
finish() - Method in class picard.analysis.CollectBaseDistributionByCycle
finish() - Method in class picard.analysis.CollectGcBiasMetrics
finish() - Method in class picard.analysis.CollectInsertSizeMetrics
finish() - Method in class picard.analysis.CollectQualityYieldMetrics
finish() - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
finish() - Method in class picard.analysis.CollectRnaSeqMetrics
finish() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
finish() - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
finish() - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
finish() - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
finish() - Method in class picard.analysis.MeanQualityByCycle
finish() - Method in class picard.analysis.QualityScoreDistribution
finish() - Method in class picard.analysis.SinglePassSamProgram
  Should be implemented by subclasses to do one-time finalization work.
finish() - Method in class picard.metrics.MultiLevelCollector
  Call finish on all PerUnitMetricCollectors
finish() - Method in interface picard.metrics.PerUnitMetricCollector
  When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
finish() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
FIRST - picard.illumina.parser.TileTemplateRead
FIRST - picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
FIRST_OF_PAIR - picard.analysis.AlignmentSummaryMetrics.Category
FIRST_READ_TRANSCRIPTION_STRAND - picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
firstTile(Integer) - Method in class picard.illumina.BasecallsConverterBuilder
  Configures the first tile that the converter will begin processing at.
FisherStrandFilter - Class in picard.vcf.filter
  Filters records based on the phred scaled p-value from the Fisher Strand test stored in the FS attribute.
FisherStrandFilter(double) - Constructor for class picard.vcf.filter.FisherStrandFilter
FIVE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
FIVE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToSam
FIVE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
FIVE_PRIME_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
FixedOffset - picard.util.BaitDesigner.DesignStrategy
  Design that places baits at fixed offsets over targets, allowing them to hang off the ends as dictated by the target size and offset.
fixGenotypes(GenotypesContext, List<Allele>, List<Allele>) - Static method in class picard.util.LiftoverUtils
FixMateInformation - Class in picard.sam
  Summary
FixMateInformation() - Constructor for class picard.sam.FixMateInformation
fixNmMdAndUq(SAMRecord, ReferenceSequenceFileWalker, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
  Calculates and sets the NM, MD, and and UQ tags from the record and the reference
fixUq(SAMRecord, ReferenceSequenceFileWalker, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
  Calculates and sets UQ tag from the record and the reference
FixVcfHeader - Class in picard.vcf
  Tool for replacing or fixing up a VCF header.
FixVcfHeader() - Constructor for class picard.vcf.FixVcfHeader
FLAG_DUPLICATES - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
flip() - Method in class picard.fingerprint.Snp
  Returns a new SNP object with the alleles swapped and MAF corrected.
floatToByteArray(float) - Static method in class picard.arrays.illumina.InfiniumDataFile
  Utility method to convert a float to a byte array
FLOWCELL_BARCODE - Variable in class picard.fastq.BamToBfq
FLOWCELL_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
flowCellTileStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies base into their read's tile which is parsed from the read-name.
FlowCellTileStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
flowCellXStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies base into their read's tile which is parsed from the read-name.
FlowCellXStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
flowCellYStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies base into their read's tile which is parsed from the read-name.
FlowCellYStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
FLUIDIGM - picard.util.IlluminaUtil.IlluminaAdapterPair
FN - picard.vcf.GenotypeConcordanceStates.ContingencyState
FN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
  The FN (false negative) count across all variants
FN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
FOLD_80_BASE_PENALTY - Variable in class picard.analysis.directed.PanelMetricsBase
  The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
FOLD_80_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
  The fold over-coverage necessary to raise 80% of bases to the mean coverage level.
FOLD_90_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
  The fold over-coverage necessary to raise 90% of bases to the mean coverage level.
FOLD_95_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
  The fold over-coverage necessary to raise 95% of bases to the mean coverage level.
FOLD_ENRICHMENT - Variable in class picard.analysis.directed.HsMetrics
  The fold by which the baited region has been amplified above genomic background.
FOLD_ENRICHMENT - Variable in class picard.analysis.directed.TargetedPcrMetrics
  The fold by which the amplicon region has been amplified above genomic background.
FOLD_ENRICHMENT - Variable in class picard.analysis.directed.TargetMetrics
  The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)
foldInto(CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics, Collection<CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics>) - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
foldInto(T, Collection<T>) - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
FORCE_GC - Variable in class picard.illumina.IlluminaBasecallsToFastq
formatFloatForVcf(float) - Static method in class picard.arrays.GtcToVcf
formatToDataTypes - Variable in class picard.illumina.parser.IlluminaDataProviderFactory
  A Map of file formats to the dataTypes they will provide for this run.
forVcf(File) - Method in class picard.vcf.processor.VcfFileSegmentGenerator
FOUND_NO_EVIDENCE - picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
FP - picard.vcf.GenotypeConcordanceStates.ContingencyState
FP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
  The FP (false positive) count across all variants
FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
FP_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The sex, as reported for the fingerprinted sample
FP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
FP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
FP_TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
FR - Static variable in class picard.sam.markduplicates.util.ReadEnds
FRACTION - Variable in class picard.sam.PositionBasedDownsampleSam
FRAGMENTS - Variable in class picard.analysis.JumpingLibraryMetrics
  The number of fragments in the SAM file
FREE - picard.illumina.DistanceMetric
freeDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
  +++lifted from Commons Lang Text +++
fromBases(byte[]) - Static method in enum picard.fingerprint.DiploidGenotype
  Converts a pair of bases into a DiploidGenotype regardless of base order or case
fromBases(byte, byte) - Static method in enum picard.fingerprint.DiploidGenotype
  Converts a pair of bases into a DiploidGenotype regardless of base order or case
fromCode(int) - Static method in enum picard.pedigree.Sex
  Decodes the Sex from a numeric code.
fromFile(File, boolean) - Static method in class picard.pedigree.PedFile
  Attempts to read a pedigree file into memory.
fromSexMap(Map<String, Sex>) - Static method in class picard.pedigree.PedFile
  Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.
fromString(String) - Static method in enum picard.pedigree.Sex
  Decodes the Sex from a String.
fullString() - Method in class picard.arrays.illumina.ArraysControlInfo
FWD_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.
FWD_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The number of REF_BASE:REF_BASE alignments at sites with the given reference context.
FWD_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).

## G

G - picard.analysis.artifacts.Transition.Base
G - picard.illumina.parser.IntensityChannel
G_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The number of alt (A/T) basecalls observed at sites where the genome reference == G.
G_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs.
G_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
G_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The number of ref basecalls observed at sites where the genome reference == G.
GA4GH_CLIENT_SECRETS - Variable in class picard.cmdline.CommandLineProgram
GA4GHScheme - Class in picard.vcf
  The scheme is defined in the constructor.
GA4GHScheme() - Constructor for class picard.vcf.GA4GHScheme
GA4GHSchemeWithMissingAsHomRef - Class in picard.vcf
  The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
GA4GHSchemeWithMissingAsHomRef() - Constructor for class picard.vcf.GA4GHSchemeWithMissingAsHomRef
GatherBamFiles - Class in picard.sam
  Concatenate efficiently BAM files that resulted from a scattered parallel analysis.
GatherBamFiles() - Constructor for class picard.sam.GatherBamFiles
GatherVcfs - Class in picard.vcf
  Simple little class that combines multiple VCFs that have exactly the same set of samples and nonoverlapping sets of loci.
GatherVcfs() - Constructor for class picard.vcf.GatherVcfs
GC - Variable in class picard.analysis.GcBiasDetailMetrics
  The G+C content of the reference sequence represented by this bin.
GC_DROPOUT - Variable in class picard.analysis.directed.PanelMetricsBase
  A measure of how undercovered >= 50% GC regions are relative to the mean.
GC_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
  Illumina-style GC dropout metric.
GC_NC_0_19 - Variable in class picard.analysis.GcBiasSummaryMetrics
  Normalized coverage over quintile of GC content ranging from 0 - 19.
GC_NC_20_39 - Variable in class picard.analysis.GcBiasSummaryMetrics
  Normalized coverage over each quintile of GC content ranging from 20 - 39.
GC_NC_40_59 - Variable in class picard.analysis.GcBiasSummaryMetrics
  Normalized coverage over each quintile of GC content ranging from 40 - 59.
GC_NC_60_79 - Variable in class picard.analysis.GcBiasSummaryMetrics
  Normalized coverage over each quintile of GC content ranging from 60 - 79.
GC_NC_80_100 - Variable in class picard.analysis.GcBiasSummaryMetrics
  Normalized coverage over each quintile of GC content ranging from 80 - 100.
GC_SCORE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
GcBiasDetailMetrics - Class in picard.analysis
  Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
GcBiasDetailMetrics() - Constructor for class picard.analysis.GcBiasDetailMetrics
GcBiasMetrics - Class in picard.metrics
GcBiasMetrics() - Constructor for class picard.metrics.GcBiasMetrics
GcBiasMetricsCollector - Class in picard.analysis
  Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.
GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean) - Constructor for class picard.analysis.GcBiasMetricsCollector
GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean, boolean) - Constructor for class picard.analysis.GcBiasMetricsCollector
GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector - Class in picard.analysis
GcBiasSummaryMetrics - Class in picard.analysis
  High level metrics that capture how biased the coverage in a certain lane is.
GcBiasSummaryMetrics() - Constructor for class picard.analysis.GcBiasSummaryMetrics
GcBiasUtils - Class in picard.analysis
  Utilities to calculate GC Bias Created by kbergin on 9/23/15.
GcBiasUtils() - Constructor for class picard.analysis.GcBiasUtils
gcContentStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  A stratifier that uses GC (of the read) to stratify.
GCContentStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
GCS - picard.nio.PathProvider
gencallVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
GENDER_CONCORDANCE_PF - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  Whether or not the three sexs agree
GENDER_GTC - Variable in class picard.arrays.GtcToVcf
Gene - Class in picard.annotation
  Holds annotation of a gene for storage in an OverlapDetector.
Gene(String, int, int, boolean, String) - Constructor for class picard.annotation.Gene
GENE_NAME - picard.annotation.RefFlatReader.RefFlatColumns
Gene.Transcript - Class in picard.annotation
  A single transcript of a gene.
Gene.Transcript.Exon - Class in picard.annotation
  1-based, inclusive representation of an exon.
GeneAnnotationReader - Class in picard.annotation
  Load gene annotations into an OverlapDetector of Gene objects.
GeneAnnotationReader() - Constructor for class picard.annotation.GeneAnnotationReader
generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) - Method in class picard.sam.SamToFastq
generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) - Method in class picard.sam.SamToFastqWithTags
generateNoMatchBarcode(ReadStructure) - Static method in class picard.illumina.BarcodeExtractor
generateReadName(ClusterData, Integer) - Method in class picard.fastq.Casava18ReadNameEncoder
generateReadName(ClusterData, Integer) - Method in class picard.fastq.IlluminaReadNameEncoder
generateReadName(ClusterData, Integer) - Method in interface picard.fastq.ReadNameEncoder
  Generates a read name string for the provided cluster.
generateShortName(ClusterData) - Method in class picard.fastq.Casava18ReadNameEncoder
generateShortName(ClusterData) - Method in class picard.fastq.IlluminaReadNameEncoder
generateShortName(ClusterData) - Method in interface picard.fastq.ReadNameEncoder
  Generates a short read name that includes a minimal amount of information, this is used primarily for read sorting.
generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectRawWgsMetrics
generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectWgsMetrics
generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
generatingAccumulatorsBy(VariantProcessor.AccumulatorGenerator<A, R>) - Static method in class picard.vcf.processor.VariantProcessor.Builder
GENOME_ASSEMBLY - Variable in class picard.sam.CreateSequenceDictionary
GENOME_BUILD_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
GENOME_SIZE - Variable in class picard.analysis.directed.PanelMetricsBase
  The number of bases in the reference genome used for alignment.
GENOME_TERRITORY - Variable in class picard.analysis.WgsMetrics
  The number of non-N bases in the genome reference over which coverage will be evaluated.
genotype - Variable in class picard.arrays.illumina.InfiniumGTCRecord
GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The genotype concordance for all possible states.
GENOTYPE_LOD_THRESHOLD - Variable in class picard.fingerprint.CalculateFingerprintMetrics
GENOTYPE_LOD_THRESHOLD - Variable in class picard.fingerprint.CheckFingerprint
GenotypeConcordance - Class in picard.vcf
  Summary
GenotypeConcordance() - Constructor for class picard.vcf.GenotypeConcordance
GenotypeConcordance.Alleles - Class in picard.vcf
  A simple structure to return the results of getAlleles.
GenotypeConcordanceContingencyMetrics - Class in picard.vcf
  Class that holds metrics about the Genotype Concordance contingency tables.
GenotypeConcordanceContingencyMetrics() - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
  Empty constructor - needed for unit tests
GenotypeConcordanceContingencyMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
GenotypeConcordanceCounts - Class in picard.vcf
  A class to store the counts for various truth and call state classifications relative to a reference.
GenotypeConcordanceCounts() - Constructor for class picard.vcf.GenotypeConcordanceCounts
GenotypeConcordanceDetailMetrics - Class in picard.vcf
  Class that holds detail metrics about Genotype Concordance
GenotypeConcordanceDetailMetrics() - Constructor for class picard.vcf.GenotypeConcordanceDetailMetrics
GenotypeConcordanceScheme - Class in picard.vcf
  This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
GenotypeConcordanceScheme() - Constructor for class picard.vcf.GenotypeConcordanceScheme
GenotypeConcordanceSchemeFactory - Class in picard.vcf
  Created by kbergin on 6/19/15.
GenotypeConcordanceSchemeFactory() - Constructor for class picard.vcf.GenotypeConcordanceSchemeFactory
GenotypeConcordanceStateCodes - Enum in picard.vcf
  Created by kbergin on 7/30/15.
GenotypeConcordanceStates - Class in picard.vcf
  A class to store the various classifications for: 1.
GenotypeConcordanceStates() - Constructor for class picard.vcf.GenotypeConcordanceStates
GenotypeConcordanceStates.CallState - Enum in picard.vcf
  These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence.
GenotypeConcordanceStates.ContingencyState - Enum in picard.vcf
  A specific state for a 2x2 contingency table.
GenotypeConcordanceStates.TruthAndCallStates - Class in picard.vcf
  A minute class to store the truth and call state respectively.
GenotypeConcordanceStates.TruthState - Enum in picard.vcf
  These states represent the relationship between a truth genotype and the reference sequence.
GenotypeConcordanceSummaryMetrics - Class in picard.vcf
  Class that holds summary metrics about Genotype Concordance
GenotypeConcordanceSummaryMetrics() - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
  Empty constructor - needed for unit tests
GenotypeConcordanceSummaryMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
GenotypeFilter - Interface in picard.vcf.filter
  An interface for classes that perform Genotype filtration.
GenotypeQualityFilter - Class in picard.vcf.filter
  Genotype filter that filters out genotypes below a given quality threshold.
GenotypeQualityFilter(int) - Constructor for class picard.vcf.filter.GenotypeQualityFilter
GENOTYPES - Variable in class picard.fingerprint.CheckFingerprint
genotypeScore - Variable in class picard.arrays.illumina.InfiniumGTCRecord
GENOTYPING_ERROR_RATE - Variable in class picard.fingerprint.CrosscheckFingerprints
GenotypingArraysProgramGroup - Class in picard.cmdline.programgroups
  Miscellaneous tools, e.g.
GenotypingArraysProgramGroup() - Constructor for class picard.cmdline.programgroups.GenotypingArraysProgramGroup
get(int) - Method in class picard.analysis.CounterManager.Counter
get(int) - Method in class picard.illumina.parser.readers.BclIndexReader
get(int) - Method in class picard.illumina.parser.ReadStructure.Substructure
get3PrimeAdapter() - Method in interface picard.util.AdapterPair
get3PrimeAdapter() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
get3PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
get3PrimeAdapterBytes() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
get3PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
get3PrimeAdapterBytesInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
get3PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
get3PrimeAdapterInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
get3PrimeSoftClippedBases(Cigar, boolean) - Static method in class picard.analysis.AlignmentSummaryMetricsCollector
  returns the length of the soft clip on the 3' end If there are no-non-clipping operators, method will return 0 as it is unclear which clips should be considered on the "3'" end.
get5PrimeAdapter() - Method in interface picard.util.AdapterPair
get5PrimeAdapter() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
get5PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
get5PrimeAdapterBytes() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
get5PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
get5PrimeAdapterBytesInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
get5PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
get5PrimeAdapterInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
getAaCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
getAbCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
getActualTiles(List<IlluminaFileUtil.SupportedIlluminaFormat>) - Method in class picard.illumina.parser.IlluminaFileUtil
  Get the available tiles for the given formats, if the formats have tile lists that differ then throw an exception, if any of the format
getAddressA() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getAddressAId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getAddressB() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getAddressBId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getAlignedReadHistogram() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
getAllele1() - Method in enum picard.fingerprint.DiploidGenotype
getAllele1() - Method in class picard.fingerprint.Snp
getAllele2() - Method in enum picard.fingerprint.DiploidGenotype
getAllele2() - Method in class picard.fingerprint.Snp
getAlleleA() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getAlleleAProbeSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getAlleleAProbeSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getAlleleB() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getAlleleBProbeSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getAlleleBProbeSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getAlleles() - Method in class picard.fingerprint.Snp
getAlleleString() - Method in class picard.fingerprint.Snp
getAllNormalizationIds() - Method in class picard.arrays.illumina.IlluminaBPMFile
getAllPossibleHeaderNames() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
getAllPossibleHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
getAllReadsCollector() - Method in class picard.metrics.MultiLevelCollector
  Get the PerUnitMetricCollector that collects reads for all levels
getAllSnps() - Method in class picard.fingerprint.HaplotypeMap
  Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
getAllTiles() - Method in class picard.illumina.parser.readers.CbclReader
getAssayFormat() - Method in class picard.arrays.illumina.IlluminaManifest
getAssayHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
getAssayHeaderNameToIndex() - Method in class picard.arrays.illumina.IlluminaManifest
getAssayType() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getAttributesToReverse() - Method in class picard.sam.AbstractAlignmentMerger
  Gets the set of attributes to be reversed on reads marked as negative strand.
getAttributesToReverseComplement() - Method in class picard.sam.AbstractAlignmentMerger
  Gets the set of attributes to be reverse complemented on reads marked as negative strand.
getAutoCallDate() - Method in class picard.arrays.illumina.InfiniumGTCFile
getAutoCallVersion() - Method in class picard.arrays.illumina.InfiniumGTCFile
getAvailableTiles() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
  Return the list of tiles available for this flowcell and lane.
getB37Chr() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getB37Pos() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getbAlleleFreqs() - Method in class picard.arrays.illumina.InfiniumGTCFile
getBarcode() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
getBarcodeValue(SAMRecord) - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
getBaseCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
getBaseQualityHistogram() - Method in class picard.analysis.directed.TargetMetricsCollector
getBases() - Method in class picard.illumina.parser.BclData
getBases() - Method in class picard.illumina.parser.ReadData
getBasesExcludedBy(CountingFilter) - Method in class picard.analysis.CollectWgsMetrics
  If INTERVALS is specified, this will count bases beyond the interval list when the read overlaps the intervals and extends beyond the edge.
getBbCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
getBciFile() - Method in class picard.illumina.parser.readers.BclIndexReader
getBeadSetId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getByteBufferIterator(int, int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
getByteIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
getBytesAvailableToRead() - Method in class picard.util.CircularByteBuffer
  Returns the number of bytes that are in the buffer at the time of the method invocation.
getCallRate() - Method in class picard.arrays.illumina.InfiniumGTCFile
getCapacity() - Method in class picard.util.CircularByteBuffer
  Returns the total capacity of the buffer (empty+filled).
getCategory() - Method in class picard.arrays.illumina.ArraysControlInfo
getChainedPgIds(SAMFileHeader) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
  We have to re-chain the program groups based on this algorithm.
getChr() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getChrom() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getChrom() - Method in class picard.fingerprint.Snp
getChromosomes() - Method in class picard.arrays.illumina.InfiniumNormalizationManifest
getClasses() - Method in class picard.cmdline.ClassFinder
  Fetches the set of classes discovered so far.
getClusterCount() - Method in class picard.illumina.parser.Tile
  Returns the number of on this tile.
getClusterDensity() - Method in class picard.illumina.parser.Tile
  Returns the cluster density of this tile, in units of [cluster/mm^2].
getClusterFile() - Method in class picard.arrays.illumina.InfiniumGTCFile
getCode() - Method in enum picard.vcf.GenotypeConcordanceStates.CallState
getCode() - Method in enum picard.vcf.GenotypeConcordanceStates.TruthState
getCollector(int, IntervalList) - Method in class picard.analysis.CollectWgsMetrics
  Creates `AbstractWgsMetricsCollector` implementation according to `CollectWgsMetrics.USE_FAST_ALGORITHM` value.
getCollector(int, IntervalList) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
getColumnNames() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
getColumnNames() - Method in class picard.util.TabbedTextFileWithHeaderParser
getCommandLine() - Method in class picard.cmdline.CommandLineProgram
getCommandLineParser() - Method in class picard.cmdline.CommandLineProgram
getCommandLineParserForArgs(String[]) - Method in class picard.cmdline.CommandLineProgram
getCompressedBlockSize() - Method in class picard.illumina.parser.readers.BaseBclReader.TileData
getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceScheme
  Get the concordance state array associate with the given truth state and call state tuple.
getConcordanceStateArray(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
  Get the concordance state array associate with the given truth state and call state tuple.
getContingencyStateCounts(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
  Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[]) - Method in class picard.vcf.GenotypeConcordanceScheme
  Get the contingency state array as a set
getContingencyStateString(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
  Get the contingency state array as a parse-able string
getControl() - Method in class picard.arrays.illumina.ArraysControlInfo
getControlConfig() - Method in class picard.arrays.illumina.IlluminaBPMFile
getCount(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
  Returns the count defined by the truth state set and call state set.
getCount(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
  Returns the count defined by the truth state set and call state set.
getCounterSize() - Method in class picard.vcf.GenotypeConcordanceCounts
getCoverageByTarget() - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
  Returns the accumulated coverage per target.
getCurrentLine() - Method in class picard.util.BasicInputParser
  Provides access to the current (just parsed) line in pre-parsed format.
getCurrentLine() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
getCurrentLine() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
getCurrentLineNumber() - Method in class picard.util.BasicInputParser
  NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the next line, not the most recent line returned by next().
getCurrentLineNumber() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
getCurrentLineNumber() - Method in class picard.util.TabbedTextFileWithHeaderParser
getCustomerStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getCycleData() - Method in class picard.illumina.parser.readers.CbclReader
getCycleFromDir(File) - Static method in class picard.illumina.parser.PerTilePerCycleFileUtil
getCycleIndexRanges() - Method in class picard.illumina.parser.OutputMapping
getCycleIndexRanges() - Method in class picard.illumina.parser.ReadStructure.Substructure
getCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
getDataTypesFromReadStructure(ReadStructure, boolean, File) - Static method in class picard.illumina.BasecallsConverter
  Given a read structure return the data types that need to be parsed for this run
getDateFromVcfOtherHeaderLine(VCFHeader, String, SimpleDateFormat) - Static method in class picard.arrays.illumina.InfiniumVcfFields
getDateManufactured() - Method in class picard.arrays.illumina.IlluminaManifest
getDefaultHeaders() - Method in class picard.cmdline.CommandLineProgram
getDefaultSampleID() - Method in class picard.fingerprint.FingerprintChecker
getDensity() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
getDepthHistogram() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
getDepthHistogram() - Method in class picard.analysis.directed.TargetMetricsCollector
getDepths() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
  Gets the coverage depths as an array of ints.
getDescription() - Method in class picard.cmdline.programgroups.BaseCallingProgramGroup
getDescription() - Method in class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
getDescription() - Method in class picard.cmdline.programgroups.GenotypingArraysProgramGroup
getDescription() - Method in class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
getDescription() - Method in class picard.cmdline.programgroups.OtherProgramGroup
getDescription() - Method in class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
getDescription() - Method in class picard.cmdline.programgroups.ReferenceProgramGroup
getDescription() - Method in class picard.cmdline.programgroups.Testing
getDescription() - Method in class picard.cmdline.programgroups.VariantEvaluationProgramGroup
getDescription() - Method in class picard.cmdline.programgroups.VariantFilteringProgramGroup
getDescription() - Method in class picard.cmdline.programgroups.VariantManipulationProgramGroup
getDescriptorFileName() - Method in class picard.arrays.illumina.IlluminaManifest
getDescriptorLengths() - Method in class picard.illumina.parser.ReadStructure.Substructure
getDetectedCycles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
getDictionaryForMergedBam() - Method in class picard.sam.AbstractAlignmentMerger
getDictionaryForMergedBam() - Method in class picard.sam.SamAlignmentMerger
getDiploidHaplotype(Snp, DiploidGenotype) - Method in class picard.fingerprint.HaplotypeBlock
  Gets the diploid haplotype for this haplotype block given the provided SNP and SNP genotype.
getDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
getDuplicateMarkingsDiffer() - Method in class picard.sam.util.SamComparison
getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) - Method in class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) - Method in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
getDx() - Method in class picard.arrays.illumina.InfiniumGTCFile
getException() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
getExpClusters() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getExpClusters() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getExpectedTiles() - Method in class picard.illumina.parser.IlluminaFileUtil
  Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.bin
getExtendedManifestVersion() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
getExtension() - Static method in class picard.illumina.IlluminaLaneMetrics
  This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
getExtension() - Static method in class picard.illumina.IlluminaPhasingMetrics
  This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
getExtension() - Static method in class picard.vcf.MendelianViolations.MendelianViolationMetrics
getFamilyId() - Method in class picard.pedigree.PedFile.PedTrio
getFaqLink() - Static method in class picard.cmdline.CommandLineProgram
getField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
getField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
getFields() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
getFields() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
getFile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
getFile() - Method in class picard.illumina.parser.TileIndex
getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
getFileName() - Method in class picard.util.AbstractInputParser
getFileName() - Method in class picard.util.BasicInputParser
  Gets the name of the file being parsed
getFiles() - Method in class picard.illumina.parser.PerTileFileUtil
getFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
getFiles(int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
  Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in.
getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTileFileUtil
getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
  Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created on util instantiation, doesn't contain any of these tiles/cycles).
getFilesForCycle(int) - Method in class picard.illumina.parser.readers.CbclReader
getFilteredBases() - Method in class picard.filter.CountingFilter
  Gets the number of bases that have been filtered out thus far.
getFilteredRecords() - Method in class picard.filter.CountingFilter
  Gets the number of records that have been filtered out thus far.
getFingerprintFile() - Method in class picard.fingerprint.MatchResults
getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType) - Static method in class picard.fingerprint.Fingerprint
getFingerprintMetrics(Fingerprint) - Method in class picard.fingerprint.CalculateFingerprintMetrics
getFingerprintPanels() - Method in class picard.fingerprint.Snp
getFirstSnp() - Method in class picard.fingerprint.HaplotypeBlock
  Gets the arbitrarily first SNP in the haplotype.
getFlag() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getFloatIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
getForceSort() - Method in class picard.sam.SamAlignmentMerger
getFracA() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getFracC() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getFracG() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getFracT() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getFractionUnexpectedAlleleObs() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
getGender() - Method in class picard.arrays.illumina.InfiniumGTCFile
getGene() - Method in class picard.annotation.Gene.Transcript
getGenesForPickTranscripts() - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
  Derived class may override this method in order to return a different set of genes for picking transcripts for computing coverage, or to cache the value returned by geneOverlapDetector.getAll(), because it can be expensive to compute repeatedly.
getGenomeBuild() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getGenotype(String, InfiniumGTCRecord, IlluminaManifestRecord, Allele, Allele) - Method in class picard.arrays.GtcToVcf
getGenotypeBytes() - Method in class picard.arrays.illumina.InfiniumGTCFile
getGenotypeScores() - Method in class picard.arrays.illumina.InfiniumGTCFile
getGreen() - Method in class picard.arrays.illumina.ArraysControlInfo
getGroupMap(DocWorkUnit) - Method in class picard.util.help.PicardHelpDoclet
  Adds a super-category so that we can custom-order the categories in the doc index
getHaplotype() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns the haplotype for which the probabilities apply.
getHaplotype(String) - Method in class picard.fingerprint.HaplotypeMap
  Queries a HaplotypeBlock by Snp name.
getHaplotype(String, int) - Method in class picard.fingerprint.HaplotypeMap
  Queries a HaplotypeBlock by Snp chromosome and position.
getHaplotype(Snp) - Method in class picard.fingerprint.HaplotypeMap
  Queries a HaplotypeBlock by Snp object.
getHaplotypeFrequencies() - Method in class picard.fingerprint.HaplotypeBlock
  Gets the set of haplotype frequencies.
getHaplotypeFrequency(int) - Method in class picard.fingerprint.HaplotypeBlock
  Gets the frequency of the i'th diploid haplotype where haplotypes are ordered accorinding to DiploidHaplotype.
getHaplotypes() - Method in class picard.fingerprint.HaplotypeMap
  Returns an unmodifiable collection of all the haplotype blocks in the map.
getHeader() - Method in class picard.fingerprint.FingerprintChecker
getHeader() - Method in class picard.fingerprint.HaplotypeMap
getHeader() - Method in class picard.sam.AbstractAlignmentMerger
getHeaderContents() - Method in class picard.arrays.illumina.IlluminaManifest
getHeaderSize() - Method in class picard.illumina.parser.readers.CbclReader
getHelpDoc() - Method in enum picard.analysis.CollectMultipleMetrics.Program
getHelpDoc() - Method in enum picard.illumina.DistanceMetric
getHelpDoc() - Method in enum picard.sam.FilterSamReads.Filter
getHelpDoc() - Method in enum picard.sam.markduplicates.CheckDuplicateMarking.Mode
getHelpDoc() - Method in enum picard.sam.RevertSam.FileType
getHelpDoc() - Method in enum picard.util.IntervalList.IntervalListScatterMode
getHelpDoc() - Method in enum picard.util.IntervalListTools.Action
getHet(int, int) - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
getHeterogyzousGenotype() - Method in class picard.fingerprint.Snp
getHetPercent() - Method in class picard.arrays.illumina.InfiniumGTCFile
getHgGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getHighQualityDepthHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
getHistogram(long[], String, String) - Method in class picard.analysis.AbstractWgsMetricsCollector
getHom(int) - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
getHom(int) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
getHomozygousAllele1Genotype() - Method in class picard.fingerprint.Snp
getHomozygousAllele2Genotype() - Method in class picard.fingerprint.Snp
getIdentifier() - Method in class picard.arrays.illumina.InfiniumDataFile
getIlmnId() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getIlmnId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getIlmnStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getIlmnStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getImagingDate() - Method in class picard.arrays.illumina.InfiniumGTCFile
getImagingUser() - Method in class picard.arrays.illumina.InfiniumGTCFile
getIndelCounter() - Method in class picard.vcf.GenotypeConcordance
getIndelElement(SamLocusIterator.RecordAndOffset) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
getIndex() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getIndex() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getIndexTemplateName() - Method in class picard.util.help.PicardHelpDoclet
  Return the name of the freemarker template to be used for the index generated by Barclay.
getIndices() - Method in class picard.illumina.parser.ReadStructure.Substructure
getIndividualId() - Method in class picard.pedigree.PedFile.PedTrio
getInfo() - Method in class picard.fingerprint.Fingerprint
getInputFile() - Method in class picard.fingerprint.FingerprintResults
getInputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
getInputStream() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
getIntegerField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
getIntegerField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
getIntegerFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
getIntegerIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
getIntensityOnly() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getIntervalFile() - Method in class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
getIntervalFile() - Method in interface picard.cmdline.argumentcollections.IntervalArgumentCollection
getIntervalList() - Method in class picard.fingerprint.HaplotypeMap
  Returns an IntervalList with an entry for every SNP in every Haplotype in the map.
getIntervalsToExamine() - Method in class picard.analysis.CollectWgsMetrics
  Gets the intervals over which we will calculate metrics.
getLane() - Method in class picard.illumina.parser.ClusterData
getLane() - Method in class picard.illumina.parser.IlluminaFileUtil
  Return the lane we're inspecting
getLane() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
getLaneFactories() - Method in class picard.illumina.BasecallsConverter
  Gets the data provider factory used to create the underlying data provider.
getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
getLaneNumber() - Method in class picard.illumina.parser.Tile
  Returns the number of this tile's parent lane.
getLaneTileCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
getLastThreeFields(String, char, int[]) - Static method in class picard.sam.util.ReadNameParser
  Given a string, splits the string by the delimiter, and returns the the last three fields parsed as integers.
getLeft() - Method in class picard.sam.util.Pair
getLibraryId() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
getLibraryId() - Method in class picard.sam.markduplicates.util.ReadEnds
getLibraryId() - Method in interface picard.sam.util.PhysicalLocation
getLibraryId() - Method in class picard.sam.util.PhysicalLocationInt
getLibraryId(SAMRecord) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
  Get the library ID for the given SAM record.
getLibraryIdGenerator() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
getLibraryIdsMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
getLibraryName(SAMFileHeader, SAMRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
  Gets the library name from the header for the record.
getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence
getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
getLine() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getLine() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
  Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
getLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
getLociCount() - Method in class picard.arrays.illumina.IlluminaManifest
getLociToGenotype(Collection<Fingerprint>) - Method in class picard.fingerprint.FingerprintChecker
  Takes a set of fingerprints and returns an IntervalList containing all the loci that can be productively examined in sequencing data to compare to one or more of the fingerprints.
getLocusEntries() - Method in class picard.arrays.illumina.IlluminaBPMFile
getLocusIterator(SamReader) - Method in class picard.analysis.CollectWgsMetrics
  Creates `AbstractLocusIterator` implementation according to `CollectWgsMetrics.USE_FAST_ALGORITHM` value.
getLocusMaxReads() - Method in class picard.fingerprint.FingerprintChecker
getLocusResults() - Method in class picard.fingerprint.MatchResults
getLOD() - Method in class picard.fingerprint.MatchResults
getLodMostProbableGenotype() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns the LOD score between the most probable haplotype and the second most probable.
getLodNT() - Method in class picard.fingerprint.MatchResults
getLodTN() - Method in class picard.fingerprint.MatchResults
getLog_of_base() - Method in class picard.util.MathUtil.LogMath
getLogFromProbability(double[]) - Static method in class picard.util.MathUtil
  Takes a complete set of mutually exclusive Likelihoods and converts them to logLikelihoods.
getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
getLogRDev() - Method in class picard.arrays.illumina.InfiniumGTCFile
getLogRRatios() - Method in class picard.arrays.illumina.InfiniumGTCFile
getLogValue(double) - Method in class picard.util.MathUtil.LogMath
  Returns the log-representation of the provided decimal value.
getLogValue(double[]) - Method in class picard.util.MathUtil.LogMath
  Returns the log-representation of the provided decimal array.
getLongIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
getMaf() - Method in class picard.fingerprint.HaplotypeBlock
  Returns the minor allele frequency of this haplotype.
getMaf() - Method in class picard.fingerprint.Snp
getMajorGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getManifestFile() - Method in class picard.arrays.illumina.IlluminaManifest
getManifestFileHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
getManifestFileParser() - Method in class picard.arrays.illumina.IlluminaManifest
getManifestName() - Method in class picard.arrays.illumina.IlluminaBPMFile
getManifestName() - Method in class picard.arrays.illumina.InfiniumEGTFile
getMapInfo() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getMappingsDiffer() - Method in class picard.sam.util.SamComparison
getMappingsMatch() - Method in class picard.sam.util.SamComparison
getMaskedBaseCount(byte[], int, int) - Static method in class picard.util.BaitDesigner
  Returns the total of soft or hard masked bases in the interval of bases.
getMatchedBarcode() - Method in class picard.illumina.parser.ClusterData
getMatchResults() - Method in class picard.fingerprint.FingerprintResults
getMaternalId() - Method in class picard.pedigree.PedFile.PedTrio
getMaxPairErrorRate() - Method in class picard.util.AdapterMarker
getMaxSingleEndErrorRate() - Method in class picard.util.AdapterMarker
getMedianPhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
getMedianPrePhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
getMessage(int) - Method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
getMetric() - Method in interface picard.sam.SamErrorMetric.BaseCalculator
  Returns the metric generated by the observed loci
getMetric() - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
  Returns the metric generated by the observed loci
getMetric() - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
  Returns the metric generated by the observed loci
getMetric() - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
  Returns the metric generated by the observed loci
getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
getMetrics() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
getMetrics() - Method in class picard.illumina.BarcodeExtractor
getMetrics() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
getMetrics() - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
getMetrics(CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.AbstractWgsMetricsCollector
  Creates CollectWgsMetrics.WgsMetrics - the object holding the result of CollectWgsMetrics
getMetricsByLibrary(String) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
getMetricsByLibraryMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
getMetricsCode() - Method in enum picard.illumina.parser.IlluminaMetricsCode
getMetricsFile() - Method in class picard.cmdline.CommandLineProgram
  Gets a MetricsFile with default headers already written into it.
getMetricValue() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
getMinimumBaseQuality() - Method in class picard.illumina.BarcodeExtractor
getMinPairMatchBases() - Method in class picard.util.AdapterMarker
getMinSingleEndMatchBases() - Method in class picard.util.AdapterMarker
getMismatches() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
getMismatchesToSecondBest() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
getMissingLeft() - Method in class picard.sam.util.SamComparison
getMissingRight() - Method in class picard.sam.util.SamComparison
getMostLikelyGenotype(Snp) - Method in class picard.fingerprint.HaplotypeProbabilities
  Gets the genotype for this Snp given the most likely haplotype.
getMostLikelyHaplotype() - Method in class picard.fingerprint.HaplotypeProbabilities
  Gets the most likely haplotype given the probabilities.
getName() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getName() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getName() - Method in class picard.cmdline.programgroups.BaseCallingProgramGroup
getName() - Method in class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
getName() - Method in class picard.cmdline.programgroups.GenotypingArraysProgramGroup
getName() - Method in class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
getName() - Method in class picard.cmdline.programgroups.OtherProgramGroup
getName() - Method in class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
getName() - Method in class picard.cmdline.programgroups.ReferenceProgramGroup
getName() - Method in class picard.cmdline.programgroups.Testing
getName() - Method in class picard.cmdline.programgroups.VariantEvaluationProgramGroup
getName() - Method in class picard.cmdline.programgroups.VariantFilteringProgramGroup
getName() - Method in class picard.cmdline.programgroups.VariantManipulationProgramGroup
getName() - Method in class picard.fingerprint.Snp
getName() - Method in interface picard.util.AdapterPair
getName() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
getNearProbeDistance() - Method in class picard.analysis.directed.TargetMetricsCollector
  Gets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
getNextReadPair(PeekableIterator<SAMRecord>) - Static method in class picard.util.QuerySortedReadPairIteratorUtil
  Get the next read pair (where both have the same read name).
getNodes() - Method in class picard.util.GraphUtils.Graph
getNoMatchMetric() - Method in class picard.illumina.BarcodeExtractor
getNoMatchMetric() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
getNonLogValue(double) - Method in class picard.util.MathUtil.LogMath
  Returns the decimal representation of the provided log values.
getNonOpticalDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
getNormalizationId() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getNormalizedXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
getNormalizedYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
getNumAdaptersToKeep() - Method in class picard.util.AdapterMarker
getNumAlignedBases(SAMRecord) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
getNumAssays() - Method in class picard.arrays.illumina.IlluminaManifest
getNumBasesPassingMinimumBaseQuality(SAMRecord, AlignmentBlock, int) - Static method in class picard.analysis.directed.TargetMetricsCollector
  Get the the number of bases in the given alignment block and record that have base quality greater or equal to the minimum
getNumberOfClusters(File) - Static method in class picard.illumina.parser.readers.BclReader
getNumberOfOpticalDuplicateClusters() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
getNumberOfSnps() - Method in class picard.arrays.illumina.InfiniumGTCFile
getNumCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
getNumClustersInTile() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
getNumDescriptors() - Method in class picard.illumina.parser.ReadStructure
getNumDuplicates() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
getNumDuplicates() - Method in class picard.sam.markduplicates.util.MarkQueue
  Returns the number of duplicates detected
getNumIntensityOnly() - Method in class picard.arrays.illumina.InfiniumGTCFile
getNumNoCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
getNumReads() - Method in class picard.illumina.parser.ClusterData
getNumRecordsWithNoMateCigar() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
  Useful for statistics after the iterator has been exhausted and closed.
getNumTiles() - Method in class picard.illumina.parser.readers.BclIndexReader
getNumTiles() - Method in class picard.illumina.parser.TileIndex
getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns the number of observations of alleles supporting the first/major haplotype allele.
getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
  Returns the number of bases/reads that support the first allele.
getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns the number of observations of alleles supporting the second/minor haplotype allele.
getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
  Returns the number of bases/reads that support the second allele.
getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
getOffset() - Method in class picard.arrays.illumina.InfiniumFileTOC
getOffsetX() - Method in class picard.arrays.illumina.InfiniumTransformation
getOffsetY() - Method in class picard.arrays.illumina.InfiniumTransformation
getOpticalDupesByLibraryId() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
getOpticalDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
getOpticalDuplicatesByLibraryIdMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
getOptionalDoubleFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
getOptionalIntegerFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
getOptionalValueFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
getOrientationByte(boolean, boolean) - Static method in class picard.sam.markduplicates.util.ReadEnds
  Returns a single byte that encodes the orientation of the two reads in a pair.
getOutputArgumentCollection() - Method in class picard.analysis.SinglePassSamProgram
getOutputArgumentCollection() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
getOutputCycles() - Method in class picard.illumina.parser.OutputMapping
getOutputDescriptors() - Method in class picard.illumina.parser.OutputMapping
getOutputFile() - Method in class picard.cmdline.argumentcollections.EmptyOutputArgumentCollection
getOutputFile() - Method in interface picard.cmdline.argumentcollections.OutputArgumentCollection
getOutputFile() - Method in class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
getOutputFileName(File) - Static method in class picard.sam.CalculateReadGroupChecksum
  Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.
getOutputIndexForCycle(int) - Method in class picard.illumina.parser.OutputMapping
  Return an index that where: index.arrayIndex - represents either the read number the cycle will be output too, or (in some cases) an array index into a two dimensional array of byte[][] where the top level array corresponds to read number index.elementIndex - represents the element a cycle will appear in inside it's give read, or the element in an array as described above
getOutputReadLengths() - Method in class picard.illumina.parser.OutputMapping
getOutputReadStructure() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
  Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input readStructure
getOutputReadStructure() - Method in class picard.illumina.parser.OutputMapping
getOutputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
getOutputStream() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
getP05Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
getP05Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
getP10GC() - Method in class picard.arrays.illumina.InfiniumGTCFile
getP50GC() - Method in class picard.arrays.illumina.InfiniumGTCFile
getP50Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
getP50Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
getP95Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
getP95Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
getPackageList() - Static method in class picard.cmdline.PicardCommandLine
  The packages we wish to include in our command line
getPaternalId() - Method in class picard.pedigree.PedFile.PedTrio
getPerTilePerCycleFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
  For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through all the files for these tiles in expectedBase Side Effect: Assigns numCycles
getPGRecord(SAMFileHeader) - Method in class picard.cmdline.CommandLineProgram
getPhasingCode(int, IlluminaMetricsCode) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
  Phasing codes are between 200 and 299 (inclusive).
getPhasingMap() - Method in class picard.illumina.parser.Tile
getPhasingMetricsForTiles(long, Collection<Tile>, boolean) - Static method in class picard.illumina.IlluminaPhasingMetrics
  Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
getPhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
getPhenotype() - Method in class picard.pedigree.PedFile.PedTrio
getPlatformUnit() - Method in class picard.fingerprint.FingerprintIdDetails
getPloidy() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getPloidy() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getPloidy() - Method in class picard.arrays.illumina.InfiniumGTCFile
getPloidyType() - Method in class picard.arrays.illumina.InfiniumGTCFile
getPmtGreen() - Method in class picard.arrays.illumina.InfiniumGTCFile
getPmtRed() - Method in class picard.arrays.illumina.InfiniumGTCFile
getPoorQualityFrequencies() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
  Returns a view of number of qualities that failed, where the key is the quality score and the value is the number of observations.
getPopulationLikelihood() - Method in class picard.fingerprint.MatchResults
getPos() - Method in class picard.fingerprint.Snp
getPosition() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getPositionInfo() - Method in class picard.illumina.parser.CbclData
getPositions() - Method in class picard.arrays.illumina.InfiniumNormalizationManifest
getPosteriorLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns the probabilities, in order, of the AA, Aa and aa haplotypes.
getPosteriorProbabilities() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns the probabilities, in order, of the AA, Aa and aa haplotypes.
getPrePhasingMap() - Method in class picard.illumina.parser.Tile
getPrePhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
getPrintableId() - Method in class picard.fingerprint.Fingerprint
getPriorProbablities() - Method in class picard.fingerprint.HaplotypeProbabilities
getProbabilityFromLog(double[]) - Static method in class picard.util.MathUtil
  Takes a complete set of mutually exclusive logLikelihoods and converts them to probabilities with no rescaling.
getProbeIntervals() - Method in class picard.analysis.directed.CollectHsMetrics
getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedMetrics
getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
getProbeSetName() - Method in class picard.analysis.directed.CollectHsMetrics
getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedMetrics
getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
getProgramProperty(Class) - Static method in class picard.cmdline.PicardCommandLine
getProgramRecord() - Method in class picard.sam.AbstractAlignmentMerger
getQualities() - Method in class picard.illumina.parser.BclData
getQualities() - Method in class picard.illumina.parser.ReadData
getQuerynameSortedAlignedRecords() - Method in class picard.sam.AbstractAlignmentMerger
getQuerynameSortedAlignedRecords() - Method in class picard.sam.SamAlignmentMerger
  Reads the aligned SAM records into a SortingCollection and returns an iterator over that collection
getRawControlXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
getRawControlXIntensity(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
getRawControlYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
getRawControlYIntensity(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
getRawXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
getRawYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
getRead(int) - Method in class picard.illumina.parser.ClusterData
getReadBarcodeValue(SAMRecord, String) - Static method in class picard.sam.markduplicates.EstimateLibraryComplexity
getReadEnds() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
  Gets the set of read ends
getReadEndSetForOpticalDuplicates() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
  Gets the read ends for optical duplicate tracking
getReadGroup() - Method in class picard.fingerprint.FingerprintResults
getReadGroup() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
getReadGroup() - Method in class picard.sam.markduplicates.util.ReadEnds
getReadGroup() - Method in interface picard.sam.util.PhysicalLocation
getReadGroup() - Method in class picard.sam.util.PhysicalLocationInt
getReadGroupLibraryName(SAMReadGroupRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
getReadHistogram() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
getReadType() - Method in class picard.illumina.parser.ReadData
getRecord() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
getRecord(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
getRecordReadName() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
getRed() - Method in class picard.arrays.illumina.ArraysControlInfo
getRefAllele() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getReferenceFasta() - Method in class picard.fingerprint.FingerprintChecker
getReferenceFile() - Method in class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
getReferenceFile() - Method in class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
getReferenceFile() - Method in class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
getReferenceFile() - Method in interface picard.cmdline.argumentcollections.ReferenceArgumentCollection
getReferenceFile() - Method in class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
getReferenceFile() - Method in class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
getReferenceFile() - Method in class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
getReferenceSequence() - Method in class picard.metrics.SAMRecordAndReference
getReferenceStrand() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getRefStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getRefStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns a representative SNP for this haplotype.
getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
  Returns the SNP who's genotype was used to construct the likelihoods.
getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
getReserved1() - Method in class picard.arrays.illumina.InfiniumTransformation
getReserved2() - Method in class picard.arrays.illumina.InfiniumTransformation
getReserved3() - Method in class picard.arrays.illumina.InfiniumTransformation
getReserved4() - Method in class picard.arrays.illumina.InfiniumTransformation
getReserved5() - Method in class picard.arrays.illumina.InfiniumTransformation
getReserved6() - Method in class picard.arrays.illumina.InfiniumTransformation
getRight() - Method in class picard.sam.util.Pair
getRIlmn() - Method in class picard.arrays.illumina.InfiniumGTCFile
getRsId() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getRunFile(File, Pattern) - Method in class picard.illumina.parser.ParameterizedFileUtil
getSamFileHeader() - Method in class picard.analysis.CollectWgsMetrics
  This method should only be called after `CollectWgsMetrics.getSamReader()` is called.
getSample() - Method in class picard.fingerprint.Fingerprint
getSample() - Method in class picard.fingerprint.FingerprintIdDetails
getSample() - Method in class picard.fingerprint.MatchResults
getSampleAlias() - Method in class picard.fingerprint.FingerprintResults
getSampleLikelihood() - Method in class picard.fingerprint.MatchResults
getSampleName() - Method in class picard.arrays.illumina.InfiniumGTCFile
getSamplePlate() - Method in class picard.arrays.illumina.InfiniumGTCFile
getSampleWell() - Method in class picard.arrays.illumina.InfiniumGTCFile
getSamReader() - Method in class picard.analysis.CollectWgsMetrics
  Gets the SamReader from which records will be examined.
getSamReader() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
getSamRecord() - Method in class picard.metrics.SAMRecordAndReference
getSamRecordIndex() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
  A number of convenience functions
getScaleX() - Method in class picard.arrays.illumina.InfiniumTransformation
getScaleY() - Method in class picard.arrays.illumina.InfiniumTransformation
getScannerName() - Method in class picard.arrays.illumina.InfiniumGTCFile
getScannerVersion() - Method in class picard.arrays.illumina.InfiniumGTCFile
getScheme(boolean) - Method in class picard.vcf.GenotypeConcordanceSchemeFactory
getSensitivity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
  Returns the sensitivity defined by the scheme across the subset of truth states.
getSentrixBarcode() - Method in class picard.arrays.illumina.InfiniumGTCFile
getSequentialFileList(File) - Static method in class picard.sam.FastqToSam
  Get a list of FASTQs that are sequentially numbered based on the first (base) fastq.
getSex() - Method in class picard.pedigree.PedFile.PedTrio
getSexConcordance(String, String, String) - Static method in class picard.arrays.CollectArraysVariantCallingMetrics
getShear() - Method in class picard.arrays.illumina.InfiniumTransformation
getSingleBarcodeDistanceQuery(int, int) - Method in class picard.util.BarcodeEditDistanceQuery
getSingletonSample(VariantContext) - Static method in class picard.vcf.CallingMetricAccumulator
getSizeOf() - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
getSizeOf() - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
getSnp() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getSnp() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getSnp(String) - Method in class picard.fingerprint.HaplotypeBlock
  Gets a SNP by name if it belongs to this haplotype.
getSnp(String, int) - Method in class picard.fingerprint.HaplotypeMap
  Queries a Snp by chromosome and position.
getSnpAlleleA() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getSnpAlleleB() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getSnpCounter() - Method in class picard.vcf.GenotypeConcordance
getSnpGenotype(Snp, DiploidHaplotype) - Method in class picard.fingerprint.HaplotypeBlock
  Gets the expected genotype of the provided SNP given the provided haplotype of this haplotype block.
getSnpManifest() - Method in class picard.arrays.illumina.InfiniumGTCFile
getSnpRefAllele() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
getSnps() - Method in class picard.fingerprint.HaplotypeBlock
  Returns an unmodifiable, unordered, collection of all SNPs in this haplotype block.
getSolexaQualityCharFromFourQualities(String[], int, FormatUtil) - Static method in class picard.util.IlluminaUtil
  Get a Solexa ASCII quality value from an array of strings that are integer qualities in this order: [cycle-1-A, cycle-1-C, cycle-1-G, cycle-1-T, cycle-2-A, ...].
getSource() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getSource() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getSource() - Method in class picard.fingerprint.Fingerprint
getSourceSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getSourceSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getSourceStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getSourceStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getSourceVersion() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getSourceVersion() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getSpecies() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getSpecies() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getSpecificity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
  Returns the specificity defined by the scheme across the subset of truth states.
getStandardUsagePreamble() - Method in class picard.cmdline.CommandLineProgram
getStandardUsagePreamble(Class<?>) - Static method in class picard.cmdline.CommandLineProgram
  A typical command line program will call this to get the beginning of the usage message, and then typically append a description of the program, like this: public String USAGE = getStandardUsagePreamble(getClass()) + "Frobnicate the freebozle."
getSuffix() - Method in interface picard.sam.SamErrorMetric.BaseCalculator
  The suffix that pertains to the implementation of aggregation
getSuffix() - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
getSuffix() - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
  The suffix that pertains to the implementation of aggregation
getSuffix() - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
  The suffix that pertains to the implementation of aggregation
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
getSuffix() - Method in interface picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier
getSuffix() - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
  The suffix that pertains to the implementation of aggregation
getSum() - Method in class picard.vcf.GenotypeConcordanceCounts
  Returns the sum of all pairs of tuples defined by the truth state set and call state set.
getSum(Set<GenotypeConcordanceStates.TruthState>, Set<GenotypeConcordanceStates.CallState>) - Method in class picard.vcf.GenotypeConcordanceCounts
  Returns the sum of all pairs of tuples defined by the truth state set and call state set.
getSuperCategoryMap() - Static method in class picard.util.help.HelpConstants
getSuperCategoryProperty(String) - Static method in class picard.util.help.HelpConstants
  Given a group name, return a supercategory string for use by the online doc system to determine which supercateogry the group is in.
getTagFilterPrefix() - Method in class picard.util.help.PicardHelpDocWorkUnitHandler
getTemplateName(DocWorkUnit) - Method in class picard.util.help.PicardHelpDocWorkUnitHandler
getTheta() - Method in class picard.arrays.illumina.InfiniumTransformation
getThetaIlmn() - Method in class picard.arrays.illumina.InfiniumGTCFile
getThresholdForSelectingAdaptersToKeep() - Method in class picard.util.AdapterMarker
getTile() - Method in class picard.illumina.parser.CbclData
getTile() - Method in class picard.illumina.parser.ClusterData
getTile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
getTile() - Method in interface picard.sam.util.PhysicalLocation
getTile() - Method in class picard.sam.util.PhysicalLocationInt
getTiledFiles(File, Pattern) - Static method in class picard.illumina.BasecallsConverter
  Applies an lane and tile based regex to return all files matching that regex for each tile.
getTiledFiles(File, Pattern) - Method in class picard.illumina.parser.ParameterizedFileUtil
  Return all files that match pattern of the given file type in the given base directory
getTileFromReadName(String) - Static method in class picard.util.IlluminaUtil
  Parse the tile # from the read name.
getTileInfo() - Method in class picard.illumina.parser.readers.BaseBclReader.CycleData
getTileNum() - Method in class picard.illumina.parser.readers.BaseBclReader.TileData
getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
getTileNumber() - Method in class picard.illumina.parser.Tile
  Returns the number/name of this tile.
getTileOfNextCluster() - Method in class picard.illumina.parser.MultiTileParser
getTileOfNextCluster() - Method in class picard.illumina.parser.PerTileParser
  Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next.
getTiles() - Method in class picard.illumina.parser.MultiTileBclFileUtil
getTiles() - Method in class picard.illumina.parser.MultiTileFileUtil
getTiles() - Method in class picard.illumina.parser.ParameterizedFileUtil
  Return a list of all tiles available for this file format and run
getTiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
  Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files.
getTiles() - Method in class picard.illumina.parser.TileIndex
getTileTemplateRead() - Method in class picard.illumina.parser.TilePhasingValue
getToMarkQueueMinimumDistance() - Method in class picard.sam.markduplicates.util.MarkQueue
  Returns the minimum genomic distance such that we can be assured that all duplicates have been considered.
getTopGenomicSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getTopGenomicSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
getTotal() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
getTotalCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
getTotalInserts() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns the total number of observations of any allele.
getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
  Gets the total number of observations presented at this locus.
getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
getTotalOutputCycles() - Method in class picard.illumina.parser.OutputMapping
getTranscriptCoordinate(int) - Method in class picard.annotation.Gene.Transcript
  Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.
getUnfilteredBaseQHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
getUnfilteredDepthHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
getUniqueNormalizationIds() - Method in class picard.arrays.illumina.IlluminaBPMFile
getUnmappedBoth() - Method in class picard.sam.util.SamComparison
getUnmappedLeft() - Method in class picard.sam.util.SamComparison
getUnmappedRight() - Method in class picard.sam.util.SamComparison
getUnsupportedBuilds() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
getUtil(IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.IlluminaFileUtil
  Given a file type, get the Parameterized File Util object associated with it
getValidationStringency() - Method in class picard.fingerprint.FingerprintChecker
getValueFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
getVar(int, int) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
getVariantTypeFromOrdinal(int) - Static method in enum picard.util.VariantType
  Gets the enum for a given ordinal
getVersion() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
getVersion() - Method in class picard.arrays.illumina.InfiniumTransformation
getVersion() - Method in class picard.cmdline.CommandLineProgram
getVersion() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
getWordCount() - Method in class picard.util.AbstractInputParser
getX() - Method in class picard.illumina.parser.ClusterData
getX() - Method in interface picard.sam.util.PhysicalLocation
getX() - Method in class picard.sam.util.PhysicalLocationInt
getXCoordinate() - Method in class picard.illumina.parser.CbclData
getY() - Method in class picard.illumina.parser.ClusterData
getY() - Method in interface picard.sam.util.PhysicalLocation
getY() - Method in class picard.sam.util.PhysicalLocationInt
getYCoordinate() - Method in class picard.illumina.parser.CbclData
getZeroBasedTileNumber() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
GG - picard.fingerprint.DiploidGenotype
Graph() - Constructor for class picard.util.GraphUtils.Graph
GraphUtils - Class in picard.util
  Created by farjoun on 11/2/16.
GraphUtils() - Constructor for class picard.util.GraphUtils
GraphUtils.Graph<Node extends Comparable<Node>> - Class in picard.util
GREEN - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
  The green intensity value for the control.
GroupAlignmentSummaryMetricsPerUnitMetricCollector(String, String, String) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
GT - picard.fingerprint.DiploidGenotype
GT_FILTERED - picard.vcf.GenotypeConcordanceStates.CallState
GT_FILTERED - picard.vcf.GenotypeConcordanceStates.TruthState
GT_FILTERED_CODE - picard.vcf.GenotypeConcordanceStateCodes
GTA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
GTC_CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The call rate as determined by Autocall/IAAP (and stored in the GTC File)
GTC_CALL_RATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
GTC_CALL_RATE_DETAIL - Static variable in class picard.arrays.illumina.InfiniumVcfFields
GtcToVcf - Class in picard.arrays
  Class to convert an Illumina GTC file into a VCF file.
GtcToVcf() - Constructor for class picard.arrays.GtcToVcf
GtoA - picard.analysis.artifacts.Transition
GtoC - picard.analysis.artifacts.Transition
GtoG - picard.analysis.artifacts.Transition
GtoT - picard.analysis.artifacts.Transition
GTZ - Static variable in class picard.arrays.illumina.InfiniumVcfFields
GVCF_INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
GvcfMetricAccumulator - Class in picard.vcf
  An accumulator for collecting metrics about a single-sample GVCF.
GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.GvcfMetricAccumulator

## H

HAMMING - picard.illumina.DistanceMetric
hammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
handleAdditionalRecords(SAMRecord, Map<SAMReadGroupRecord, List<FastqWriter>>, SAMRecord, SAMRecord) - Method in class picard.sam.SamToFastq
handleAdditionalRecords(SAMRecord, Map<SAMReadGroupRecord, List<FastqWriter>>, SAMRecord, SAMRecord) - Method in class picard.sam.SamToFastqWithTags
handleItem(String) - Method in class picard.cmdline.ClassFinder
  Checks an item to see if it is a class and is annotated with the specified annotation.
HAPLOTYPE_MAP - Variable in class picard.fingerprint.CalculateFingerprintMetrics
HAPLOTYPE_MAP - Variable in class picard.fingerprint.CheckFingerprint
HAPLOTYPE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
HAPLOTYPE_MAP - Variable in class picard.fingerprint.ExtractFingerprint
HAPLOTYPE_MAP - Variable in class picard.fingerprint.IdentifyContaminant
HaplotypeBlock - Class in picard.fingerprint
  Represents information about a group of SNPs that form a haplotype in perfect LD with one another.
HaplotypeBlock(double) - Constructor for class picard.fingerprint.HaplotypeBlock
  Constructs a haplotype block with the provided minor allele frequency.
HaplotypeMap - Class in picard.fingerprint
  A collection of metadata about Haplotype Blocks including multiple in memory "indices" of the data to make it easy to query the correct HaplotypeBlock or Snp by snp names, positions etc.
HaplotypeMap(SAMFileHeader) - Constructor for class picard.fingerprint.HaplotypeMap
  Constructs an empty HaplotypeMap using the provided SAMFileHeader's sequence dictionary.
HaplotypeMap(File) - Constructor for class picard.fingerprint.HaplotypeMap
HaplotypeMap(Collection<HaplotypeBlock>) - Constructor for class picard.fingerprint.HaplotypeMap
  since this constructor doesn't initialize the HaplotypeMap "properly", it should be used carefully!
HaplotypeProbabilities - Class in picard.fingerprint
  Abstract class for storing and calculating various likelihoods and probabilities for haplotype alleles given evidence.
HaplotypeProbabilities(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilities
HaplotypeProbabilities.Genotype - Enum in picard.fingerprint
  Log10(P(evidence| haplotype)) for the 3 different possible haplotypes {aa, ab, bb}
HaplotypeProbabilitiesFromContaminatorSequence - Class in picard.fingerprint
  Represents the probability of the underlying haplotype of the contaminating sample given the data.
HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock, double) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeProbabilitiesFromContaminatorSequence) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
HaplotypeProbabilitiesFromGenotype - Class in picard.fingerprint
  Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.
HaplotypeProbabilitiesFromGenotype(HaplotypeProbabilitiesFromGenotype) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
HaplotypeProbabilitiesFromGenotype(Snp, HaplotypeBlock, double, double, double) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
HaplotypeProbabilitiesFromGenotypeLikelihoods - Class in picard.fingerprint
  Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block.
HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeProbabilitiesFromGenotypeLikelihoods) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
HaplotypeProbabilitiesFromSequence - Class in picard.fingerprint
  Represents the probability of the underlying haplotype given the data.
HaplotypeProbabilitiesFromSequence(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromSequence
HaplotypeProbabilitiesFromSequence(HaplotypeProbabilitiesFromSequence) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromSequence
HaplotypeProbabilityOfNormalGivenTumor - Class in picard.fingerprint
  A wrapper class for any HaplotypeProbabilities instance that will assume that the given evidence is that of a tumor sample and provide an hp for the normal sample that tumor came from.
HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilities, double) - Constructor for class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilityOfNormalGivenTumor) - Constructor for class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
HAPLOTYPES - Variable in class picard.fingerprint.FingerprintMetrics
  Number of haplotypes examined
HAPLOTYPES_CONFIDENTLY_CHECKED - Variable in class picard.analysis.FingerprintingSummaryMetrics
  The subset of genotyped haplotypes for which there was sufficient sequence data to confidently genotype the haplotype.
HAPLOTYPES_CONFIDENTLY_MATCHING - Variable in class picard.analysis.FingerprintingSummaryMetrics
  The subset of confidently checked haplotypes that match the expected genotypes.
HAPLOTYPES_WITH_EVIDENCE - Variable in class picard.fingerprint.FingerprintMetrics
  Number of haplotypes that had evidence in the source file
HAPLOTYPES_WITH_GENOTYPES - Variable in class picard.analysis.FingerprintingSummaryMetrics
  The number of haplotypes that had expected genotypes to compare to.
HARD_CLIP_OVERLAPPING_READS - Variable in class picard.sam.MergeBamAlignment
hasBothParents() - Method in class picard.pedigree.PedFile.PedTrio
  True if this record has paternal and maternal ids, otherwise false.
hasCbcls(File, int) - Static method in class picard.illumina.parser.IlluminaFileUtil
hasColumn(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator
hasColumn(String) - Method in class picard.util.TabbedTextFileWithHeaderParser
hasCoverage() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
  Returns true if any base in the range has coverage of > 0
hasError() - Method in class picard.util.ThreadPoolExecutorWithExceptions
hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns true if evidence has been added, false if the probabilities are just the priors.
hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
hashCode() - Method in class picard.annotation.Gene.Transcript
hashCode() - Method in class picard.fingerprint.FingerprintIdDetails
hashCode() - Method in class picard.fingerprint.HaplotypeBlock
hashCode() - Method in class picard.fingerprint.Snp
hashCode() - Method in class picard.illumina.parser.Range
hashCode() - Method in class picard.illumina.parser.ReadDescriptor
hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
hashCode() - Method in class picard.illumina.parser.ReadStructure
hashCode() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
hashCode() - Method in class picard.sam.util.Pair
  Basic hashcode function.
hashCode() - Method in class picard.sam.util.PrimaryAlignmentKey
hashCode() - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
hasLocation() - Method in interface picard.sam.util.PhysicalLocation
  Default implementation of a method to check whether real location data has been set.
hasNext() - Method in class picard.illumina.parser.MultiTileParser
hasNext() - Method in class picard.illumina.parser.PerTileParser
hasNext() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
  Return true if the file has more elements to return, false otherwise
hasNext() - Method in class picard.illumina.parser.readers.BarcodeFileReader
hasNext() - Method in class picard.illumina.parser.readers.BclReader
hasNext() - Method in class picard.illumina.parser.readers.CbclReader
hasNext() - Method in class picard.illumina.parser.readers.ClocsFileReader
hasNext() - Method in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
hasNext() - Method in class picard.illumina.parser.readers.FilterFileReader
hasNext() - Method in class picard.illumina.parser.readers.LocsFileReader
hasNext() - Method in class picard.illumina.parser.readers.PosFileReader
hasNext() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
hasNext() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
hasNext() - Method in class picard.util.AsyncIterator
hasNext() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
hasNext() - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
hasNext() - Method in class picard.vcf.ByIntervalListVariantContextIterator
hasNext() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
hasNext() - Method in class picard.vcf.PairedVariantSubContextIterator
hasNext() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
hasSampleBarcode() - Method in class picard.illumina.parser.ReadStructure
hasWebDocumentation(Class<?>) - Static method in class picard.cmdline.CommandLineProgram
  Determine if a class has web documentation based on its package name
header - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
HEADER - Variable in class picard.sam.ReplaceSamHeader
HEADER - Variable in class picard.vcf.FixVcfHeader
HEADER_NAMES - Static variable in class picard.arrays.illumina.IlluminaManifest
HEADER_ONLY - Variable in class picard.sam.ViewSam
headerLines() - Method in class picard.vcf.filter.AlleleBalanceFilter
headerLines() - Method in class picard.vcf.filter.FisherStrandFilter
headerLines() - Method in class picard.vcf.filter.QdFilter
headerLines() - Method in interface picard.vcf.filter.VariantFilter
  Return VCF header lines that define filters that may be applied by the VariantFilter.
HelpConstants - Class in picard.util.help
HET_ALLELE12 - picard.fingerprint.HaplotypeProbabilities.Genotype
HET_AS_HOM - Variable in class picard.analysis.FingerprintingSummaryMetrics
  num of hets, observed as homs with LOD > threshold
HET_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
  The Chi-squared pvalue for the number of HETs and HOMs relative to the expected counts (2x2 table)
HET_CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
  The categorical cross entropy of the counts of HETs and HOMs relative to the expected counts (big is bad)
HET_GENOTYPE_FOR_PHASING - Static variable in class picard.fingerprint.HaplotypeMap
HET_HOMVAR_RATIO - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  (count of hets)/(count of homozygous non-ref) for this sample
HET_HOMVAR_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
  (count of hets)/(count of homozygous non-ref) for this sample
HET_PCT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  100 * (count of hets) / (total calls) for this sample
HET_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP))
HET_REF_VAR1 - picard.vcf.GenotypeConcordanceStates.CallState
HET_REF_VAR1 - picard.vcf.GenotypeConcordanceStates.TruthState
HET_REF_VAR1_CODE - picard.vcf.GenotypeConcordanceStateCodes
HET_REF_VAR2 - picard.vcf.GenotypeConcordanceStates.CallState
HET_REF_VAR3 - picard.vcf.GenotypeConcordanceStates.CallState
HET_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN))
HET_SNP_Q - Variable in class picard.analysis.directed.PanelMetricsBase
  The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
HET_SNP_Q - Variable in class picard.analysis.WgsMetrics
  The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
HET_SNP_SENSITIVITY - Variable in class picard.analysis.directed.PanelMetricsBase
  The theoretical HET SNP sensitivity.
HET_SNP_SENSITIVITY - Variable in class picard.analysis.WgsMetrics
  The theoretical HET SNP sensitivity.
HET_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The specificity for all heterozygous variants cannot be calculated
HET_VAR1_VAR2 - picard.vcf.GenotypeConcordanceStates.CallState
HET_VAR1_VAR2 - picard.vcf.GenotypeConcordanceStates.TruthState
HET_VAR1_VAR2_CODE - picard.vcf.GenotypeConcordanceStateCodes
HET_VAR1_VAR3 - picard.vcf.GenotypeConcordanceStates.CallState
HET_VAR3_VAR4 - picard.vcf.GenotypeConcordanceStates.CallState
hetAltDepthDistribution(int) - Static method in class picard.analysis.TheoreticalSensitivity
hetSNPSensitivity(double[], double[], int, double) - Static method in class picard.analysis.TheoreticalSensitivity
hetSNPSensitivity(double[], double[], int, double, boolean) - Static method in class picard.analysis.TheoreticalSensitivity
HG_TO_NCBI - Static variable in class picard.arrays.illumina.IlluminaManifest
HG17 - Static variable in class picard.arrays.illumina.IlluminaManifest
HG18 - Static variable in class picard.arrays.illumina.IlluminaManifest
HG19 - Static variable in class picard.arrays.illumina.IlluminaManifest
highQualityDepthHistogram - Variable in class picard.analysis.WgsMetrics
  Count of sites with a given depth of coverage.
highQualityDepthHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
  Count of sites with a given depth of coverage.
Histogram_FILE - Variable in class picard.analysis.CollectInsertSizeMetrics
HISTOGRAM_FILE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
Histogram_R_SCRIPT - Static variable in class picard.analysis.CollectInsertSizeMetrics
HISTOGRAM_WIDTH - Variable in class picard.analysis.CollectInsertSizeMetrics
HOM_ALLELE1 - picard.fingerprint.HaplotypeProbabilities.Genotype
HOM_ALLELE2 - picard.fingerprint.HaplotypeProbabilities.Genotype
HOM_AS_HET - Variable in class picard.analysis.FingerprintingSummaryMetrics
  num of homs, observed as hets with LOD > threshold
HOM_AS_OTHER_HOM - Variable in class picard.analysis.FingerprintingSummaryMetrics
  num of homs, observed as other homs with LOD > threshold
HOM_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
  The Chi-squared pvalue for `FingerprintMetrics.NUM_HOM_ALLELE1` and `FingerprintMetrics.NUM_HOM_ALLELE2` relative to the expected counts (2x2 table)
HOM_CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
  The categorical cross entropy of `FingerprintMetrics.NUM_HOM_ALLELE1` and `FingerprintMetrics.NUM_HOM_ALLELE2` relative to the expected counts (big is bad)
HOM_REF - picard.vcf.GenotypeConcordanceStates.CallState
HOM_REF - picard.vcf.GenotypeConcordanceStates.TruthState
HOM_REF_CODE - picard.vcf.GenotypeConcordanceStateCodes
HOM_VAR1 - picard.vcf.GenotypeConcordanceStates.CallState
HOM_VAR1 - picard.vcf.GenotypeConcordanceStates.TruthState
HOM_VAR1_CODE - picard.vcf.GenotypeConcordanceStateCodes
HOM_VAR2 - picard.vcf.GenotypeConcordanceStates.CallState
HOM_VAR3 - picard.vcf.GenotypeConcordanceStates.CallState
homoPolymerLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies a base onto the length of the homopolymer preceding it (in the read direction).
homopolymerStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies a base onto the make up (repeating base and following reference base) and length of the homopolymer from whence it came.
HOMVAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP))
HOMVAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN))
HOMVAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The specificity for all homozygous variants cannot be calculated.
HS_LIBRARY_SIZE - Variable in class picard.analysis.directed.HsMetrics
  The estimated number of unique molecules in the selected part of the library.
HS_PENALTY_100X - Variable in class picard.analysis.directed.HsMetrics
  The "hybrid selection penalty" incurred to get 80% of target bases to 100X.
HS_PENALTY_10X - Variable in class picard.analysis.directed.HsMetrics
  The "hybrid selection penalty" incurred to get 80% of target bases to 10X.
HS_PENALTY_20X - Variable in class picard.analysis.directed.HsMetrics
  The "hybrid selection penalty" incurred to get 80% of target bases to 20X.
HS_PENALTY_30X - Variable in class picard.analysis.directed.HsMetrics
  The "hybrid selection penalty" incurred to get 80% of target bases to 30X.
HS_PENALTY_40X - Variable in class picard.analysis.directed.HsMetrics
  The "hybrid selection penalty" incurred to get 80% of target bases to 40X.
HS_PENALTY_50X - Variable in class picard.analysis.directed.HsMetrics
  The "hybrid selection penalty" incurred to get 80% of target bases to 50X.
HsMetricCollector - Class in picard.analysis.directed
  Calculates HS metrics for a given SAM or BAM file.
HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.HsMetricCollector
HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.HsMetricCollector
HsMetrics - Class in picard.analysis.directed
  Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments.
HsMetrics() - Constructor for class picard.analysis.directed.HsMetrics

## I

ID - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
  The ID of this entry
identifyContaminant(Path, double) - Method in class picard.fingerprint.FingerprintChecker
  Generates a per-sample Fingerprint for the contaminant in the supplied SAM file.
IdentifyContaminant - Class in picard.fingerprint
  Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
IdentifyContaminant() - Constructor for class picard.fingerprint.IdentifyContaminant
IGC - Static variable in class picard.arrays.illumina.InfiniumVcfFields
IGNORE - Variable in class picard.sam.ValidateSamFile
IGNORE_FILTER_STATUS - Variable in class picard.vcf.GenotypeConcordance
IGNORE_HISTOGRAM_DIFFERENCES - Variable in class picard.analysis.CompareMetrics
IGNORE_MISSING_MATES - Variable in class picard.sam.FixMateInformation
IGNORE_READ_GROUPS - Variable in class picard.fingerprint.CheckFingerprint
IGNORE_SEQUENCE - Variable in class picard.analysis.CollectMultipleMetrics
IGNORE_SEQUENCE - Variable in class picard.analysis.CollectRnaSeqMetrics
IGNORE_UNEXPECTED_BARCODES - Variable in class picard.illumina.IlluminaBasecallsToFastq
IGNORE_UNEXPECTED_BARCODES - Variable in class picard.illumina.IlluminaBasecallsToSam
IGNORE_WARNINGS - Variable in class picard.sam.ValidateSamFile
ignoreAlignment(SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
ignoreAlignment(SAMRecord) - Method in class picard.sam.SamAlignmentMerger
  For now, we ignore only those alignments that have more than `SamAlignmentMerger.maxGaps` insertions or deletions.
IGNORED_READS - Variable in class picard.analysis.RnaSeqMetrics
  Number of primary alignments that are mapped to a sequence specified on command-line as IGNORED_SEQUENCE.
ignoreUnexpectedBarcodes - Variable in class picard.illumina.BasecallsConverter
ILLUMINA - picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
ILLUMINA_ALLEGED_MINIMUM_QUALITY - Static variable in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
ILLUMINA_BEAD_POOL_MANIFEST_FILE - Variable in class picard.arrays.GtcToVcf
ILLUMINA_BEAD_POOL_MANIFEST_FILE - Variable in class picard.arrays.illumina.CompareGtcFiles
ILLUMINA_BUILD - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ILLUMINA_CHR - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ILLUMINA_FLAGGED - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Flagged by Illumina as a bad assay
ILLUMINA_FLAGGED_BAD_CHR - Static variable in class picard.arrays.illumina.IlluminaManifestRecord
ILLUMINA_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
ILLUMINA_POS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ILLUMINA_STRAND - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ILLUMINA_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
IlluminaAdpcFileWriter - Class in picard.arrays.illumina
  A class to encompass writing an Illumina adpc.bin file.
IlluminaAdpcFileWriter(File) - Constructor for class picard.arrays.illumina.IlluminaAdpcFileWriter
IlluminaAdpcFileWriter.Record - Class in picard.arrays.illumina
IlluminaBasecallingMetrics - Class in picard.illumina
  Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
IlluminaBasecallingMetrics() - Constructor for class picard.illumina.IlluminaBasecallingMetrics
IlluminaBasecallsToFastq - Class in picard.illumina
IlluminaBasecallsToFastq() - Constructor for class picard.illumina.IlluminaBasecallsToFastq
IlluminaBasecallsToFastq.ReadNameFormat - Enum in picard.illumina
  Simple switch to control the read name format to emit.
IlluminaBasecallsToSam - Class in picard.illumina
  IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM, BAM or CRAM file format.
IlluminaBasecallsToSam() - Constructor for class picard.illumina.IlluminaBasecallsToSam
IlluminaBPMFile - Class in picard.arrays.illumina
  A class to parse the contents of an Illumina Bead Pool Manifest (BPM) file A BPM file contains metadata (including the alleles, mapping and normalization information) on an Illumina Genotyping Array Each type of genotyping array has a specific BPM .
IlluminaBPMFile(File) - Constructor for class picard.arrays.illumina.IlluminaBPMFile
IlluminaBPMLocusEntry - Class in picard.arrays.illumina
  A simple class to represent a locus entry in an Illumina Bead Pool Manifest (BPM) file
IlluminaBPMLocusEntry() - Constructor for class picard.arrays.illumina.IlluminaBPMLocusEntry
IlluminaDataProviderFactory - Class in picard.illumina.parser
  IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.
IlluminaDataProviderFactory(File, int, ReadStructure, BclQualityEvaluationStrategy, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
  Create factory with the specified options, one that favors using QSeqs over all other files
IlluminaDataProviderFactory(File, File, int, ReadStructure, BclQualityEvaluationStrategy, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
  Create factory with the specified options, one that favors using QSeqs over all other files
IlluminaDataType - Enum in picard.illumina.parser
  List of data types of interest when parsing Illumina data.
IlluminaFileUtil - Class in picard.illumina.parser
  General utils for dealing with IlluminaFiles as well as utils for specific, support formats.
IlluminaFileUtil(File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
IlluminaFileUtil(File, File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
IlluminaFileUtil.SupportedIlluminaFormat - Enum in picard.illumina.parser
IlluminaGenotype - Enum in picard.arrays.illumina
IlluminaLaneMetrics - Class in picard.illumina
  Embodies characteristics that describe a lane.
IlluminaLaneMetrics() - Constructor for class picard.illumina.IlluminaLaneMetrics
IlluminaLaneMetricsCollector() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
IlluminaLaneTileCode(int, int, int) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
IlluminaManifest - Class in picard.arrays.illumina
  A class to represent an Illumina Manifest file.
IlluminaManifest(File) - Constructor for class picard.arrays.illumina.IlluminaManifest
IlluminaManifest(File, int) - Constructor for class picard.arrays.illumina.IlluminaManifest
IlluminaManifestRecord - Class in picard.arrays.illumina
  A class to represent a record (line) from an Illumina Manifest [Assay] entry
IlluminaManifestRecord.IlluminaStrand - Enum in picard.arrays.illumina
IlluminaMetricsCode - Enum in picard.illumina.parser
  Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code (e.g.
IlluminaPhasingMetrics - Class in picard.illumina
  Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
IlluminaPhasingMetrics() - Constructor for class picard.illumina.IlluminaPhasingMetrics
IlluminaReadNameEncoder - Class in picard.fastq
  A read name encoder following the encoding initially produced by picard fastq writers.
IlluminaReadNameEncoder(String) - Constructor for class picard.fastq.IlluminaReadNameEncoder
IlluminaTileMetrics(int, int, int, float) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
IlluminaTileMetrics(ByteBuffer, TileMetricsOutReader.TileMetricsVersion) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
IlluminaUtil - Class in picard.util
  Misc utilities for working with Illumina specific files and data
IlluminaUtil() - Constructor for class picard.util.IlluminaUtil
IlluminaUtil.IlluminaAdapterPair - Enum in picard.util
  Describes adapters used on each pair of strands
IMAGING_DATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The date that this sample was imaged
IMAGING_DATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
IMPROPER - picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
in - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
in - Variable in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
INCLUDE_BARCODE_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToSam
INCLUDE_BC_IN_RG_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
INCLUDE_BQ_HISTOGRAM - Variable in class picard.analysis.CollectWgsMetrics
INCLUDE_DUPLICATES - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
INCLUDE_DUPLICATES - Variable in class picard.analysis.CollectInsertSizeMetrics
INCLUDE_FILTERED - Variable in class picard.util.IntervalListTools
INCLUDE_FILTERED - Variable in class picard.vcf.VcfToIntervalList
INCLUDE_FILTERED_SHORT_NAME - Static variable in class picard.vcf.VcfToIntervalList
INCLUDE_INDELS - Variable in class picard.analysis.directed.CollectTargetedMetrics
INCLUDE_NO_CALLS - Variable in class picard.analysis.QualityScoreDistribution
INCLUDE_NON_PF_READS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
INCLUDE_NON_PF_READS - Variable in class picard.analysis.CollectOxoGMetrics
INCLUDE_NON_PF_READS - Variable in class picard.fastq.BamToBfq
INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToFastq
INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToSam
INCLUDE_NON_PF_READS - Variable in class picard.sam.SamToFastq
INCLUDE_NON_PRIMARY_ALIGNMENTS - Variable in class picard.sam.SamToFastq
INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.analysis.CollectQualityYieldMetrics
INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.sam.MergeBamAlignment
INCLUDE_SUPPLEMENTAL_ALIGNMENTS - Variable in class picard.analysis.CollectQualityYieldMetrics
INCLUDE_UNPAIRED - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
INCLUDE_UNPAIRED - Variable in class picard.analysis.CollectMultipleMetrics
includeAligned - picard.sam.FilterSamReads.Filter
includeJavascript - picard.sam.FilterSamReads.Filter
includeNonPfReads - Variable in class picard.illumina.BasecallsConverter
includePairedIntervals - picard.sam.FilterSamReads.Filter
includeReadList - picard.sam.FilterSamReads.Filter
includeSupplementalAlignments - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
includeTagValues - picard.sam.FilterSamReads.Filter
INCOMPARABLE_CODE - picard.vcf.GenotypeConcordanceStateCodes
INCONCLUSIVE - picard.fingerprint.CrosscheckMetric.FingerprintResult
INCORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
  Number of aligned reads that are mapped to the incorrect strand.
increment(int) - Method in class picard.analysis.CounterManager.Counter
  Increments value corresponding to reference sequence index
increment(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
  Increments a count for the truth/call state tuple.
increment(GenotypeConcordanceStates.TruthAndCallStates, double) - Method in class picard.vcf.GenotypeConcordanceCounts
incrementReadCount() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
  Increments the # of reads mapping to this target.
INDEL_CONFLICT - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Both insertion and deletion sequence found in reference.
INDEL_EXTENSION_ERROR - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Deprecated.
  - but used in existing extended manifest files.
INDEL_NOT_FOUND - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Neither insertion nor deletion sequence found in reference.
INDEL_OUTPUT - Variable in class picard.vcf.SplitVcfs
INDEL_SEQ_MISMATCH - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Deprecated.
  - but used in existing extended manifest files.
INDEL_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
indelCounter - Variable in class picard.vcf.GenotypeConcordance
IndelErrorCalculator - Class in picard.sam.SamErrorMetric
  A calculator that estimates the error rate of the bases it observes for indels only.
IndelErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.IndelErrorCalculator
IndelErrorMetric - Class in picard.sam.SamErrorMetric
  Metric to be used for InDel errors
IndelErrorMetric() - Constructor for class picard.sam.SamErrorMetric.IndelErrorMetric
IndelErrorMetric(String, long, long, long, long, long) - Constructor for class picard.sam.SamErrorMetric.IndelErrorMetric
indelLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies into the number of bases in an insertion
IndelLengthStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
indels - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
indelsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratify by Indels in the read cigars.
IndelsInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
IndependentReplicateMetric - Class in picard.analysis.replicates
  A class to store information relevant for biological rate estimation
IndependentReplicateMetric() - Constructor for class picard.analysis.replicates.IndependentReplicateMetric
independentReplicationRateFromBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
independentReplicationRateFromTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The biological duplication rate (as a fraction of the duplicates sets) calculated from tripleton sets.
independentReplicationRateFromUmi - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  Given the UMIs one can estimate the rate of biological duplication directly, as this would be the rate of having different UMIs in all duplicate sets.
INDEX_VALIDATION_STRINGENCY - Variable in class picard.sam.ValidateSamFile
INDEXED - picard.util.IlluminaUtil.IlluminaAdapterPair
indexOfMax(double[]) - Static method in class picard.util.MathUtil
  Returns the index of the largest element in the array.
indexOfMax(long[]) - Static method in class picard.util.MathUtil
  Returns the index of the largest element in the array.
indexOfMin(double[]) - Static method in class picard.util.MathUtil
  Returns the index of the smallest element in the array.
indexOfMin(int[]) - Static method in class picard.util.MathUtil
  Returns the index of the smallest element in the array.
IndividualAlignmentSummaryMetricsCollector(AlignmentSummaryMetrics.Category, String, String, String) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  Label the artifacts corresponding to known error modes.
inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  Label the artifacts corresponding to known error modes.
INFERRED_UMI_ENTROPY - Variable in class picard.sam.markduplicates.UmiMetrics
  Entropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs.
INFERRED_UNIQUE_UMIS - Variable in class picard.sam.markduplicates.UmiMetrics
  Number of different inferred UMI sequences derived
InfiniumDataFile - Class in picard.arrays.illumina
  A class to provide methods for accessing Illumina Infinium Data Files.
InfiniumEGTFile - Class in picard.arrays.illumina
  A class to parse the contents of an Illumina Infinium cluster (EGT) file A cluster file contains information about the clustering information used in mapping red / green intensity information to genotype calls
InfiniumEGTFile(File) - Constructor for class picard.arrays.illumina.InfiniumEGTFile
InfiniumFileTOC - Class in picard.arrays.illumina
  A class to encapsulate the table of contents for an Illumina Infinium Data Files.
InfiniumFileTOC() - Constructor for class picard.arrays.illumina.InfiniumFileTOC
InfiniumGTCFile - Class in picard.arrays.illumina
  A class to parse the contents of an Illumina Infinium genotype (GTC) file A GTC file is the output of Illumina's genotype calling software (either Autocall or Autoconvert) and contains genotype calls, confidence scores, basecalls and raw intensities for all calls made on the chip.
InfiniumGTCFile(File, File) - Constructor for class picard.arrays.illumina.InfiniumGTCFile
  Creates an InfiniumGTCFile object and parses the given input file.
InfiniumGTCRecord - Class in picard.arrays.illumina
InfiniumGTCRecord(String) - Constructor for class picard.arrays.illumina.InfiniumGTCRecord
InfiniumNormalizationManifest - Class in picard.arrays.illumina
  A class to parse the contents of an Illumina Infinium Normalization Manifest file An Illumina Infinium Normalization Manifest file contains a subset of the information contained in the Illumina Manifest file in addition to the normalization ID which is needed for normalizating intensities in GtcToVcf
InfiniumNormalizationManifest(File) - Constructor for class picard.arrays.illumina.InfiniumNormalizationManifest
InfiniumTransformation - Class in picard.arrays.illumina
InfiniumTransformation() - Constructor for class picard.arrays.illumina.InfiniumTransformation
InfiniumVcfFields - Class in picard.arrays.illumina
  A class to store fields that are specific to a VCF generated from an Illumina GTC file.
InfiniumVcfFields() - Constructor for class picard.arrays.illumina.InfiniumVcfFields
InfiniumVcfFields.GENOTYPE_VALUES - Enum in picard.arrays.illumina
INFO - Variable in class picard.fingerprint.FingerprintMetrics
  Additional information about the fingerprint
initialize() - Method in class picard.illumina.parser.MultiTileBclParser
initialize() - Method in enum picard.nio.PathProvider
initializeAdditionalWriters() - Method in class picard.sam.SamToFastq
initializeAdditionalWriters() - Method in class picard.sam.SamToFastqWithTags
initiateScheme() - Method in class picard.vcf.GA4GHScheme
initiateScheme() - Method in class picard.vcf.GA4GHSchemeWithMissingAsHomRef
initiateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
INPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
INPUT - Variable in class picard.analysis.CollectMultipleMetrics
INPUT - Variable in class picard.analysis.CollectOxoGMetrics
INPUT - Variable in class picard.analysis.CollectRrbsMetrics
INPUT - Variable in class picard.analysis.CollectWgsMetrics
INPUT - Variable in class picard.analysis.CompareMetrics
INPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
INPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
INPUT - Variable in class picard.analysis.SinglePassSamProgram
INPUT - Variable in class picard.annotation.SortGff
INPUT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
INPUT - Variable in class picard.arrays.CombineGenotypingArrayVcfs
INPUT - Variable in class picard.arrays.CreateBafRegressMetricsFile
INPUT - Variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
INPUT - Variable in class picard.arrays.GtcToVcf
INPUT - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
INPUT - Variable in class picard.arrays.illumina.CompareGtcFiles
INPUT - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
INPUT - Variable in class picard.fastq.BamToBfq
INPUT - Variable in class picard.fingerprint.CalculateFingerprintMetrics
INPUT - Variable in class picard.fingerprint.CheckFingerprint
INPUT - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
INPUT - Variable in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
INPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
INPUT - Variable in class picard.fingerprint.ExtractFingerprint
INPUT - Variable in class picard.fingerprint.IdentifyContaminant
INPUT - Variable in class picard.fingerprint.LiftOverHaplotypeMap
INPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
INPUT - Variable in class picard.illumina.MarkIlluminaAdapters
INPUT - Variable in class picard.reference.NonNFastaSize
INPUT - Variable in class picard.reference.NormalizeFasta
INPUT - Variable in class picard.sam.AddCommentsToBam
INPUT - Variable in class picard.sam.AddOATag
INPUT - Variable in class picard.sam.AddOrReplaceReadGroups
INPUT - Variable in class picard.sam.BamIndexStats
INPUT - Variable in class picard.sam.BuildBamIndex
INPUT - Variable in class picard.sam.CalculateReadGroupChecksum
INPUT - Variable in class picard.sam.CheckTerminatorBlock
INPUT - Variable in class picard.sam.CleanSam
INPUT - Variable in class picard.sam.DownsampleSam
INPUT - Variable in class picard.sam.FilterSamReads
INPUT - Variable in class picard.sam.FixMateInformation
INPUT - Variable in class picard.sam.GatherBamFiles
INPUT - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
INPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
INPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
INPUT - Variable in class picard.sam.MergeSamFiles
INPUT - Variable in class picard.sam.PositionBasedDownsampleSam
INPUT - Variable in class picard.sam.ReorderSam
INPUT - Variable in class picard.sam.ReplaceSamHeader
INPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
INPUT - Variable in class picard.sam.RevertSam
INPUT - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
INPUT - Variable in class picard.sam.SamFormatConverter
INPUT - Variable in class picard.sam.SamToFastq
INPUT - Variable in class picard.sam.SetNmMdAndUqTags
INPUT - Variable in class picard.sam.SortSam
INPUT - Variable in class picard.sam.SplitSamByLibrary
INPUT - Variable in class picard.sam.SplitSamByNumberOfReads
INPUT - Variable in class picard.sam.ValidateSamFile
INPUT - Variable in class picard.sam.ViewSam
INPUT - Variable in class picard.util.AccumulateQualityYieldMetrics
INPUT - Variable in class picard.util.BedToIntervalList
INPUT - Variable in class picard.util.IntervalListToBed
INPUT - Variable in class picard.util.IntervalListTools
INPUT - Variable in class picard.util.LiftOverIntervalList
INPUT - Variable in class picard.vcf.AccumulateVariantCallingMetrics
INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
INPUT - Variable in class picard.vcf.filter.FilterVcf
INPUT - Variable in class picard.vcf.FixVcfHeader
INPUT - Variable in class picard.vcf.GatherVcfs
INPUT - Variable in class picard.vcf.LiftoverVcf
INPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
INPUT - Variable in class picard.vcf.MakeVcfSampleNameMap
INPUT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
INPUT - Variable in class picard.vcf.MergeVcfs
INPUT - Variable in class picard.vcf.RenameSampleInVcf
INPUT - Variable in class picard.vcf.SortVcf
INPUT - Variable in class picard.vcf.SplitVcfs
INPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
INPUT - Variable in class picard.vcf.VcfFormatConverter
INPUT - Variable in class picard.vcf.VcfToIntervalList
INPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
INPUT_PARAMS_FILE - Variable in class picard.illumina.ExtractBarcodesProgram
INPUT_SAMPLE_FILE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
INPUT_SAMPLE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
INPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
inputReadStructure - Variable in class picard.illumina.ExtractBarcodesProgram
  The read structure of the actual Illumina Run, i.e.
insertion - picard.util.VariantType
INSERTIONS_Q - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
  The (phred) rate of insertions.
insertionsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratify by Insertions in the read cigars.
insertLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies into the read-pairs estimated insert-length, as long as it isn't larger than 10x the length of the read
InsertSizeMetrics - Class in picard.analysis
  Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics".
InsertSizeMetrics() - Constructor for class picard.analysis.InsertSizeMetrics
InsertSizeMetricsCollector - Class in picard.analysis.directed
  Collects InsertSizeMetrics on the specified accumulationLevels using
InsertSizeMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, double, Integer, Integer, double, boolean) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector
InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector - Class in picard.analysis.directed
  A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)
instanceMain(String[]) - Method in class picard.cmdline.CommandLineProgram
instanceMain(String[]) - Method in class picard.cmdline.PicardCommandLine
  For testing
instanceMain(String[], List<String>, String) - Method in class picard.cmdline.PicardCommandLine
  The main method.
instanceMainWithExit(String[]) - Method in class picard.cmdline.CommandLineProgram
INTENSITY_ONLY_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
IntensityChannel - Enum in picard.illumina.parser
  The channels in a FourChannelIntensityData object, and the channels produced by a ClusterIntensityFileReader, for cases in which it is desirable to handle these abstractly rather than having the specific names in the source code.
INTERGENIC - picard.annotation.LocusFunction
INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Number of bases in primary alignments that do not align to any gene.
INTERLEAVE - Variable in class picard.sam.SamToFastq
INTEROP_SUBDIRECTORY_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
  The path to the directory containing the tile metrics file relative to the basecalling directory.
interruptAndShutdownExecutors(ThreadPoolExecutorWithExceptions...) - Method in class picard.illumina.BasecallsConverter
INTERSECT - picard.util.IntervalListTools.Action
INTERSECT_INTERVALS - Variable in class picard.vcf.GenotypeConcordance
INTERVAL_COUNT - picard.util.IntervalList.IntervalListScatterMode
  A scatter by interval **count** which attempts to fill each resulting interval list with the same number of intervals, disregarding the base count.
INTERVAL_ITERATOR - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
INTERVAL_LIST - Variable in class picard.reference.ExtractSequences
INTERVAL_LIST - Variable in class picard.sam.AddOATag
INTERVAL_LIST - Variable in class picard.sam.FilterSamReads
INTERVAL_LIST - Variable in class picard.sam.ViewSam
INTERVAL_SUBDIVISION - picard.util.IntervalList.IntervalListScatterMode
  A simple scatter approach in which all output intervals have size equal to the total base count of the source list divide by the scatter count (except for possible variance in the final interval list).
intervalArgumentCollection - Variable in class picard.analysis.CollectWgsMetrics
IntervalArgumentCollection - Interface in picard.cmdline.argumentcollections
  Base interface for an interval argument collection.
IntervalListScatter - Class in picard.util.IntervalList
IntervalListScatter(IntervalListScatterer, IntervalList, int) - Constructor for class picard.util.IntervalList.IntervalListScatter
IntervalListScatterer - Interface in picard.util.IntervalList
  An interface for a class that scatters IntervalLists.
IntervalListScattererByBaseCount - Class in picard.util.IntervalList
  a Baseclass for scatterers that scatter by uniqued base count.
IntervalListScattererByBaseCount() - Constructor for class picard.util.IntervalList.IntervalListScattererByBaseCount
IntervalListScattererByIntervalCount - Class in picard.util.IntervalList
  Scatters `IntervalList` by interval count so that resulting `IntervalList`'s have the same number of intervals in them.
IntervalListScattererByIntervalCount() - Constructor for class picard.util.IntervalList.IntervalListScattererByIntervalCount
IntervalListScattererWithoutSubdivision - Class in picard.util.IntervalList
  A BaseCount Scatterer that avoid breaking-up intervals.
IntervalListScattererWithoutSubdivision() - Constructor for class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
IntervalListScattererWithoutSubdivisionWithOverflow - Class in picard.util.IntervalList
  Like `IntervalListScattererWithoutSubdivision` but will overflow current list if the projected size of the remaining lists is bigger than the "ideal".
IntervalListScattererWithoutSubdivisionWithOverflow() - Constructor for class picard.util.IntervalList.IntervalListScattererWithoutSubdivisionWithOverflow
IntervalListScattererWithSubdivision - Class in picard.util.IntervalList
  An IntervalListScatterer that attempts to place the same number of (uniquified) bases in each output interval list.
IntervalListScattererWithSubdivision() - Constructor for class picard.util.IntervalList.IntervalListScattererWithSubdivision
IntervalListScatterMode - Enum in picard.util.IntervalList
  An enum to control the creation of the various IntervalListScatter objects
IntervalListToBed - Class in picard.util
  Trivially simple command line program to convert an IntervalList file to a BED file.
IntervalListToBed() - Constructor for class picard.util.IntervalListToBed
IntervalListTools - Class in picard.util
  Performs various `IntervalList` manipulations.
IntervalListTools() - Constructor for class picard.util.IntervalListTools
IntervalListTools.Action - Enum in picard.util
intervals - Variable in class picard.analysis.AbstractWgsMetricsCollector
intervals - Variable in class picard.analysis.WgsMetrics
  The intervals over which this metric was computed.
INTERVALS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
INTERVALS - Variable in class picard.analysis.CollectMultipleMetrics
INTERVALS - Variable in class picard.analysis.CollectOxoGMetrics
INTERVALS - Variable in class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
INTERVALS - Variable in class picard.analysis.CollectWgsMetrics
INTERVALS - Variable in class picard.reference.NonNFastaSize
INTERVALS - Variable in class picard.sam.MergeSamFiles
INTERVALS - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
INTERVALS - Variable in class picard.vcf.GenotypeConcordance
IntervalsManipulationProgramGroup - Class in picard.cmdline.programgroups
  Tools that process genomic intervals in various formats.
IntervalsManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
intervalWeight(Interval) - Method in interface picard.util.IntervalList.IntervalListScatterer
  A method that defines the "weight" of an interval list for the purpose of scattering.
intervalWeight(Interval) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
intervalWeight(Interval) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
INTRONIC - picard.annotation.LocusFunction
INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Number of bases in primary alignments that align to an intronic base for some gene, and not a coding or UTR base.
INVERT - Variable in class picard.util.IntervalListTools
IO_SIZE - Variable in class picard.util.FifoBuffer
IS_BISULFITE_SEQUENCE - Variable in class picard.sam.MergeBamAlignment
IS_BISULFITE_SEQUENCE - Variable in class picard.sam.SetNmMdAndUqTags
IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectGcBiasMetrics
IS_BISULFITE_SEQUENCED - Variable in class picard.sam.ValidateSamFile
IS_MIXED - picard.vcf.GenotypeConcordanceStates.CallState
IS_MIXED - picard.vcf.GenotypeConcordanceStates.TruthState
IS_MIXED_CODE - picard.vcf.GenotypeConcordanceStateCodes
IS_ZCALLED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  Whether the sample was zcalled
isAdapter(SAMRecord) - Method in class picard.analysis.AdapterUtility
  Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
isAdapterSequence(byte[]) - Method in class picard.analysis.AdapterUtility
  Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
isAdapterSequence(byte[], boolean) - Method in class picard.analysis.AdapterUtility
  Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
isAmbiguous() - Method in class picard.arrays.illumina.IlluminaManifestRecord
isAvailable - Variable in enum picard.nio.PathProvider
isBlank(byte[]) - Method in class picard.util.AbstractInputParser
  Determines whether a given line is a comment
isBlockGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
isChimeric(SAMRecord, int, Set<SamPairUtil.PairOrientation>) - Static method in class picard.analysis.ChimeraUtil
  Checks whether the given read is part of a chimeric pair.
isChimeric(SAMRecord, SAMRecord, int, Set<SamPairUtil.PairOrientation>) - Static method in class picard.analysis.ChimeraUtil
  Checks whether the given read is part of a chimeric pair.
isClipOverlappingReads() - Method in class picard.sam.AbstractAlignmentMerger
isClosed() - Method in class picard.util.CircularByteBuffer
  Returns true if the buffer is closed, false otherwise.
isClusterRecord() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
isComment(byte[]) - Method in class picard.util.AbstractInputParser
  Determines whether a given line is a comment
isContaminant(HitsForInsert) - Method in class picard.sam.AbstractAlignmentMerger
isContaminant(HitsForInsert) - Method in class picard.sam.SamAlignmentMerger
  Criteria for contaminant reads: 1.
isDbSnpSite(String, int) - Method in class picard.util.DbSnpBitSetUtil
  Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
isDelimiter(byte) - Method in class picard.util.AbstractInputParser
  Determines whether a given character is a delimiter
isDelimiter(byte) - Method in class picard.util.CsvInputParser
  Determines whether a given character is a delimiter
isDelimiter(byte) - Method in class picard.util.TabbedInputParser
  Determines whether a given character is a delimiter
isDupe() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
isEmpty() - Method in class picard.illumina.parser.ReadStructure.Substructure
isEmpty() - Method in class picard.sam.markduplicates.util.MarkQueue
isExpected() - Method in enum picard.fingerprint.CrosscheckMetric.FingerprintResult
isFail() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
isGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
isHeterozygous() - Method in enum picard.fingerprint.DiploidGenotype
isHomomozygous() - Method in enum picard.fingerprint.DiploidGenotype
isIndel() - Method in class picard.arrays.illumina.IlluminaManifestRecord
isIntensityOnly() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
isKeepAlignerProperPairFlags() - Method in class picard.sam.AbstractAlignmentMerger
isKeepValid() - Method in enum picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
isLegacyPicardStyle(String[]) - Static method in class picard.cmdline.CommandLineSyntaxTranslater
isMatch() - Method in enum picard.fingerprint.CrosscheckMetric.FingerprintResult
isMatched() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
isMissing(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
  Returns true if EITHER the truth or call state is MISSING.
isOpticalDuplicate - Variable in class picard.sam.markduplicates.util.ReadEnds
  A *transient* flag marking this read end as being an optical duplicate.
isPaired() - Method in class picard.sam.markduplicates.util.ReadEnds
isPaired() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
isPf() - Method in class picard.illumina.parser.CbclData
isPf() - Method in class picard.illumina.parser.ClusterData
isPhasing(IlluminaMetricsCode) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
isPopulateOaTag() - Method in enum picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
isRefStrandDefinedInManifest() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
isReservedTag(String) - Method in class picard.sam.AbstractAlignmentMerger
isResetMappingInformation() - Method in enum picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
isSkipBlankLines() - Method in class picard.util.AbstractInputParser
isSnp() - Method in class picard.arrays.illumina.IlluminaManifestRecord
isSoloTranscript() - Method in class picard.annotation.Gene.Transcript
isTreatGroupedDelimitersAsOne() - Method in class picard.util.AbstractInputParser
isValidBase(byte) - Static method in enum picard.fingerprint.DiploidGenotype
isVar(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
  Returns true if EITHER the truth or call state is a VAR.
isVariantFile(File) - Static method in class picard.vcf.VcfUtils
  Checks if the suffix is one of those that are allowed for the various formats that contain variants (currently vcf and bcf)
isWGT - Variable in class picard.arrays.illumina.InfiniumEGTFile
iterator - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
iterator() - Method in class picard.annotation.Gene
iterator() - Method in class picard.arrays.illumina.IlluminaManifest
iterator() - Method in class picard.illumina.parser.BaseIlluminaDataProvider
iterator() - Method in class picard.illumina.parser.ReadStructure.Substructure
iterator() - Method in class picard.illumina.parser.TileIndex
iterator() - Method in class picard.util.AbstractInputParser
iterator() - Method in class picard.util.IntervalList.IntervalListScatter
iterator() - Method in class picard.util.TabbedTextFileWithHeaderParser
  Creates the iterator object.
iterators() - Method in class picard.vcf.processor.VariantIteratorProducer
  Renders the embodied regions of the VCF files in the form of `CloseableIterator`s over `VariantContext`s.
Iterators - Class in picard.util
Iterators() - Constructor for class picard.util.Iterators
IUPAC_NUCLEOTIDE_CODES - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator

## J

JAVASCRIPT_FILE - Variable in class picard.sam.FilterSamReads
JAVASCRIPT_FILE - Variable in class picard.vcf.filter.FilterVcf
JUMP_DUPLICATE_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
  The number of outward-facing pairs that are duplicates
JUMP_DUPLICATE_PCT - Variable in class picard.analysis.JumpingLibraryMetrics
  The fraction of outward-facing pairs that are marked as duplicates
JUMP_LIBRARY_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
  The estimated library size for outward-facing pairs
JUMP_MEAN_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
  The mean insert size for outward-facing pairs
JUMP_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
  The number of outward-facing pairs in the SAM file
JUMP_SIZE - Variable in class picard.sam.MergeBamAlignment
  Deprecated.
JUMP_STDEV_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
  The standard deviation on the insert size for outward-facing pairs
JumpingLibraryMetrics - Class in picard.analysis
  High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
JumpingLibraryMetrics() - Constructor for class picard.analysis.JumpingLibraryMetrics

## K

KEEP_FIRST_DUPLICATE - Variable in class picard.sam.RevertSam
klDivergance(double[], double[]) - Static method in class picard.util.MathUtil
  Calculate the KL divergence from measured to distribution // https://en.wikipedia.org/wiki/Kullback%E2%80%93Leibler_divergence

## L

lane - Variable in class picard.illumina.parser.BaseIlluminaDataProvider
lane - Variable in class picard.illumina.parser.ParameterizedFileUtil
lane - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
  The lane, which is determined from the file name
LANE - Variable in class picard.fastq.BamToBfq
LANE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
LANE - Variable in class picard.illumina.ExtractBarcodesProgram
LANE - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The lane for which the metrics were calculated.
LANE - Variable in class picard.illumina.IlluminaLaneMetrics
  This lane's number.
LANE - Variable in class picard.illumina.IlluminaPhasingMetrics
  Illumina flowcell lane number
LANE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
LANE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
laneFactories - Variable in class picard.illumina.BasecallsConverter
laneIsSet() - Method in class picard.illumina.parser.ClusterData
LanePhasingMetricsCollector - Class in picard.illumina
  Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics
LanePhasingMetricsCollector(Collection<Tile>, boolean) - Constructor for class picard.illumina.LanePhasingMetricsCollector
  Constructor takes a lane's collection of Tiles and calculates the median phasing/prephasing for the first and second (if available) reads
LANES - Variable in class picard.illumina.CheckIlluminaDirectory
laneTileCode - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
LEFT_FILE - Variable in class picard.fingerprint.CrosscheckMetric
LEFT_FILE - Variable in class picard.sam.SamComparisonMetric
  Left file used in comparison
LEFT_GROUP_VALUE - Variable in class picard.fingerprint.CrosscheckMetric
LEFT_LANE - Variable in class picard.fingerprint.CrosscheckMetric
LEFT_LIBRARY - Variable in class picard.fingerprint.CrosscheckMetric
LEFT_MOLECULAR_BARCODE_SEQUENCE - Variable in class picard.fingerprint.CrosscheckMetric
LEFT_PRIMER - Variable in class picard.util.BaitDesigner
LEFT_RUN_BARCODE - Variable in class picard.fingerprint.CrosscheckMetric
LEFT_SAMPLE - Variable in class picard.fingerprint.CrosscheckMetric
leftAlignVariant(VariantContextBuilder, int, int, List<Allele>, ReferenceSequence) - Static method in class picard.util.LiftoverUtils
  Normalizes and left aligns a `VariantContextBuilder`.
leftVariantContext - Variable in class picard.vcf.PairedVariantSubContextIterator.VcfTuple
length - Variable in class picard.illumina.parser.Range
length - Variable in class picard.illumina.parser.ReadDescriptor
length() - Method in class picard.annotation.Gene.Transcript
length() - Method in class picard.illumina.parser.ReadStructure.Substructure
leniantHammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
  Deprecated.
LENIENT_DUP - Variable in class picard.sam.util.SAMComparisonArgumentCollection
LENIENT_HAMMING - picard.illumina.DistanceMetric
LENIENT_HEADER - Variable in class picard.sam.util.SAMComparisonArgumentCollection
LENIENT_LOW_MQ_ALIGNMENT - Variable in class picard.sam.util.SAMComparisonArgumentCollection
LENIENT_UNKNOWN_MQ_ALIGNMENT - Variable in class picard.sam.util.SAMComparisonArgumentCollection
lenientHammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
  Similar to Hamming distance but this version doesn't penalize matching bases with low quality for the read.
LIBRARY - picard.analysis.MetricAccumulationLevel
LIBRARY - picard.fingerprint.CrosscheckMetric.DataType
LIBRARY - picard.sam.markduplicates.MarkDuplicates.DuplicateType
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The name of the library being assayed.
LIBRARY - Variable in class picard.metrics.MultilevelMetrics
  The library to which these metrics apply.
LIBRARY - Variable in class picard.sam.DuplicationMetrics
  The library on which the duplicate marking was performed.
LIBRARY - Variable in class picard.sam.markduplicates.UmiMetrics
  Library that was used to generate UMI data.
LIBRARY_NAME - Variable in class picard.illumina.BarcodeMetric
  The name of the library
LIBRARY_NAME - Variable in class picard.illumina.IlluminaBasecallsToSam
LIBRARY_NAME - Variable in class picard.sam.FastqToSam
LIBRARY_NAME - Variable in class picard.sam.RevertSam
LIBRARY_NAME_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
  Column header for the library name.
LIBRARY_NAME_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
LIBRARY_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToSam
libraryId - Variable in class picard.sam.markduplicates.util.ReadEnds
libraryIdGenerator - Variable in class picard.sam.markduplicates.MarkDuplicates
LibraryIdGenerator - Class in picard.sam.markduplicates.util
  A class to generate library Ids and keep duplication metrics by library IDs.
LibraryIdGenerator(SAMFileHeader) - Constructor for class picard.sam.markduplicates.util.LibraryIdGenerator
LIFTOVER_FAILED - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS - Static variable in class picard.fingerprint.LiftOverHaplotypeMap
LIFTOVER_MIN_MATCH - Variable in class picard.vcf.LiftoverVcf
LiftOverHaplotypeMap - Class in picard.fingerprint
  Liftover SNPs in HaplotypeMaps from one reference to another
LiftOverHaplotypeMap() - Constructor for class picard.fingerprint.LiftOverHaplotypeMap
LiftOverIntervalList - Class in picard.util
  This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references.
LiftOverIntervalList() - Constructor for class picard.util.LiftOverIntervalList
LiftoverUtils - Class in picard.util
LiftoverUtils() - Constructor for class picard.util.LiftoverUtils
LiftoverVcf - Class in picard.vcf
  Summary
LiftoverVcf() - Constructor for class picard.vcf.LiftoverVcf
liftSimpleVariantContext(VariantContext, Interval) - Static method in class picard.util.LiftoverUtils
liftVariant(VariantContext, Interval, ReferenceSequence, boolean, boolean) - Static method in class picard.util.LiftoverUtils
  This will take an input VariantContext and lift to the provided interval.
limitingProcessedRegionsTo(IntervalList) - Method in class picard.vcf.processor.VariantProcessor.Builder
LINE_LENGTH - Variable in class picard.reference.ExtractSequences
LINE_LENGTH - Variable in class picard.reference.NormalizeFasta
LINK_LOCS - Variable in class picard.illumina.CheckIlluminaDirectory
  Deprecated.
  It is no longer necessary to create locs file symlinks.
listWeight(IntervalList) - Method in interface picard.util.IntervalList.IntervalListScatterer
  A method that defines the "weight" of an interval for the purpose of scattering.
listWeight(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
listWeight(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
LL_EXPECTED_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
  The Log Likelihood of the sequence data given the expected sample's genotypes.
LL_RANDOM_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
  The Log Likelihood of the sequence data given a random sample from the human population.
LLK - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
  The log likelihood
LLK0 - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
  The log likelihood 0
loadFingerprints(Path, String) - Method in class picard.fingerprint.FingerprintChecker
  Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
loadFingerprintsFromIndexedVcf(Path, String) - Method in class picard.fingerprint.FingerprintChecker
  Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
loadFingerprintsFromNonIndexedVcf(Path, String) - Method in class picard.fingerprint.FingerprintChecker
  Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
loadFingerprintsFromQueriableReader(VCFFileReader, String, Path) - Method in class picard.fingerprint.FingerprintChecker
  Loads genotypes from the supplied reader into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
loadFingerprintsFromVariantContexts(Iterable<VariantContext>, String, Path) - Method in class picard.fingerprint.FingerprintChecker
  Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
loadPropertiesFile(String, Class<?>) - Static method in class picard.util.PropertyUtils
  Attempt to load a Properties object from an on-disk properties file.
loadRefFlat(File, SAMSequenceDictionary) - Static method in class picard.annotation.GeneAnnotationReader
LOCATION_BIN_SIZE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
Locs - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
LocsFileFaker - Class in picard.illumina.parser.fakers
  Created by jcarey on 3/13/14.
LocsFileFaker() - Constructor for class picard.illumina.parser.fakers.LocsFileFaker
LocsFileReader - Class in picard.illumina.parser.readers
  The locs file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
LocsFileReader(File) - Constructor for class picard.illumina.parser.readers.LocsFileReader
LocsFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.LocsFileReader
LOCUS_ACCUMULATION_CAP - Variable in class picard.analysis.CollectWgsMetrics
LOCUS_MAX_READS - Variable in class picard.fingerprint.ExtractFingerprint
LOCUS_MAX_READS - Variable in class picard.fingerprint.IdentifyContaminant
LocusFunction - Enum in picard.annotation
  Describes the behavior of a locus relative to a gene.
LOD - Variable in class picard.analysis.FingerprintingDetailMetrics
  The LOD score for OBSERVED_GENOTYPE vs.
LOD_EXPECTED_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
  The LOD for Expected Sample vs.
LOD_SCORE - Variable in class picard.fingerprint.CrosscheckMetric
LOD_SCORE_NORMAL_TUMOR - Variable in class picard.fingerprint.CrosscheckMetric
LOD_SCORE_TUMOR_NORMAL - Variable in class picard.fingerprint.CrosscheckMetric
LOD_SELF_CHECK - Variable in class picard.fingerprint.FingerprintMetrics
  The fingerprinting LOD score this sample gets when compared to itself (big is good)
LOD_THRESHOLD - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
LOD_THRESHOLD - Variable in class picard.fingerprint.CrosscheckFingerprints
log - Static variable in class picard.illumina.SortedBasecallsConverter
log - Static variable in class picard.util.LiftoverUtils
LOG - Static variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
LOG - Static variable in class picard.vcf.VcfFormatConverter
LOG - Static variable in class picard.vcf.VcfToIntervalList
LOG_10_MATH - Static variable in class picard.util.MathUtil
LOG_2_MATH - Static variable in class picard.util.MathUtil
LOG_4_BASE_E - Static variable in class picard.util.MathUtil
  Constant to convert between the natural base e and 4.0.
LOG_FAILED_INTERVALS - Variable in class picard.vcf.LiftoverVcf
LOG_ODDS_THRESHOLD - Variable in class picard.analysis.TheoreticalSensitivityMetrics
  Log-likelihood ratio is used as a threshold to distinguish a positive site with a given allele fraction from HOM_REF.
log10_1p(double) - Static method in class picard.util.MathUtil
  this function mimics the behavior of log_1p but resulting in log _base 10_ of (1+x) instead of natural log of 1+x
LOG10_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
  The log10 of the Chi-squared pvalue
LOG10_HET_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
  The log10 of the Chi-squared pvalue for the number of HETs and HOMs
LOG10_HOM_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
  The log10 of the Chi-squared pvalue for `FingerprintMetrics.NUM_HOM_ALLELE1` and `FingerprintMetrics.NUM_HOM_ALLELE2`
LOG10_PVAL - Variable in class picard.arrays.BafRegressMetrics
  The log p-value of the estimate
logLikelihoodsToProbs(double[]) - Static method in class picard.util.MathUtil
  Deprecated.
logMemoryStats(Log) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
logRRatio - Variable in class picard.arrays.illumina.InfiniumGTCRecord
LONG_HOMOPOLYMER - picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
LONG_HOMOPOLYMER - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
longLaneStr(int) - Static method in class picard.illumina.parser.IlluminaFileUtil
LOSS_OF_HET_RATE - Variable in class picard.fingerprint.CrosscheckFingerprints
LOW_DP - picard.vcf.GenotypeConcordanceStates.CallState
LOW_DP - picard.vcf.GenotypeConcordanceStates.TruthState
LOW_DP_CODE - picard.vcf.GenotypeConcordanceStateCodes
LOW_GQ - picard.vcf.GenotypeConcordanceStates.CallState
LOW_GQ - picard.vcf.GenotypeConcordanceStates.TruthState
LOW_GQ_CODE - picard.vcf.GenotypeConcordanceStateCodes
LOW_MQ_THRESHOLD - Variable in class picard.sam.util.SAMComparisonArgumentCollection
LRR - Static variable in class picard.arrays.illumina.InfiniumVcfFields

## M

M - picard.illumina.parser.ReadType
MACHINE_NAME - Variable in class picard.illumina.IlluminaBasecallsToFastq
MAD_COVERAGE - Variable in class picard.analysis.WgsMetrics
  The median absolute deviation of coverage of the genome after all filters are applied.
MAD_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
  The median absolute deviation of the distribution of all read lengths.
main(String[]) - Static method in class picard.cmdline.PicardCommandLine
  Override this if you want to include different java packages to search for classes that extend CommandLineProgram.
main(String[]) - Static method in class picard.sam.DuplicationMetrics
main(String[]) - Static method in class picard.Test
make() - Method in enum picard.util.IntervalList.IntervalListScatterMode
  Create the scatterer
makeAllReadCollector() - Method in class picard.analysis.directed.TargetMetricsCollector
makeAllReadCollector() - Method in class picard.metrics.MultiLevelCollector
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.GcBiasMetricsCollector
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordMultiLevelCollector
makeBarcodeRegex(int) - Static method in class picard.illumina.parser.ParameterizedFileUtil
makeChildCollector(String, String, String) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
makeChildCollector(String, String, String) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
  Make an InsertSizeCollector with the given arguments
makeChildCollector(String, String, String) - Method in class picard.analysis.directed.RnaSeqMetricsCollector
makeChildCollector(String, String, String) - Method in class picard.analysis.directed.TargetMetricsCollector
makeChildCollector(String, String, String) - Method in class picard.analysis.GcBiasMetricsCollector
makeChildCollector(String, String, String) - Method in class picard.analysis.RrbsMetricsCollector
makeChildCollector(String, String, String) - Method in class picard.metrics.MultiLevelCollector
  Construct a PerUnitMetricCollector with the given arguments.
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectHsMetrics
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectTargetedMetrics
  A factory method for the TargetMetricsCollector to use this time.
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
makeCycleFileParser(List<File>) - Method in class picard.illumina.parser.MultiTileBclParser
makeCycleFileParser(List<File>, PerTileCycleParser.CycleFilesParser<BclData>) - Method in class picard.illumina.parser.MultiTileBclParser
makeDataProvider() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
makeDataProvider(Integer) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
makeDataProvider(List<Integer>) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
  Call this method to create a ClusterData iterator over the specified tiles.
makeExceptionMsg() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
  Create a string that will be included in any NoSuchElementException thrown by the next() method
makeExceptionMsg() - Method in class picard.illumina.parser.readers.ClocsFileReader
makeExceptionMsg() - Method in class picard.illumina.parser.readers.LocsFileReader
makeExceptionMsg() - Method in class picard.illumina.parser.readers.PosFileReader
makeIgnoredSequenceIndicesSet(SAMFileHeader, Set<String>) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File, File, Set<String>) - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File, File, Set<String>, boolean) - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
  By default, this method calls the `CollectMultipleMetrics.ProgramInterface.makeInstance(String, String, File, File, Set, File, File, File, Set)` method without 'includeUnpaired' parameter.
makeIntervalArgumentCollection() - Method in class picard.analysis.CollectWgsMetrics
makeItSo(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
  Handles the FastqToSam execution on the FastqReader(s).
makeItSo(File, File, boolean, long, Collection<SinglePassSamProgram>) - Static method in class picard.analysis.SinglePassSamProgram
makeLaneTileRegex(String, int) - Static method in class picard.illumina.parser.ParameterizedFileUtil
  Return a regex string for finding Lane and Tile given a file extension pattern
makeLibraryCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
makeOverlapDetector(File, SAMFileHeader, File, Log) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
makePhredBinaryFromSolexaQualityAscii_1_3(String) - Static method in class picard.util.IlluminaUtil
  Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
makePhredBinaryFromSolexaQualityAscii_1_3(String, int, int) - Static method in class picard.util.IlluminaUtil
  Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
makeReadGroupCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
makeReferenceArgumentCollection() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
makeReferenceArgumentCollection() - Method in class picard.analysis.CollectRrbsMetrics
makeReferenceArgumentCollection() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
makeReferenceArgumentCollection() - Method in class picard.cmdline.CommandLineProgram
makeReferenceArgumentCollection() - Method in class picard.sam.CreateSequenceDictionary
makeReferenceArgumentCollection() - Method in class picard.sam.DownsampleSam
makeReferenceArgumentCollection() - Method in class picard.util.ScatterIntervalsByNs
makeReferenceArgumentCollection() - Method in class picard.vcf.LiftoverVcf
makeSampleCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
makeSeekable(List<File>, BclQualityEvaluationStrategy, int[]) - Static method in class picard.illumina.parser.readers.BclReader
makeSequenceDictionary(File) - Method in class picard.sam.CreateSequenceDictionary
  Read all the sequences from the given reference file, and convert into SAMSequenceRecords
MakeSitesOnlyVcf - Class in picard.vcf
  Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
MakeSitesOnlyVcf() - Constructor for class picard.vcf.MakeSitesOnlyVcf
makeSortingCollection() - Static method in class picard.util.SequenceDictionaryUtils
makeTileIterator(File) - Method in class picard.illumina.parser.PerTileParser
  Factory method for the iterator of each tile
makeTileIterator(File) - Method in class picard.illumina.parser.PosParser
  Make an CloseableIterator<PositionalData> based on the given file and fileType specified at construction.
MakeVcfSampleNameMap - Class in picard.vcf
  Creates a TSV from sample name to VCF/GVCF path, with one line per input.
MakeVcfSampleNameMap() - Constructor for class picard.vcf.MakeVcfSampleNameMap
Male - picard.pedigree.Sex
MALE_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
MANIFEST_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
MANIFEST_FILE_HEADER_NAMES - Static variable in class picard.arrays.illumina.IlluminaManifest
manifestFileParser - Variable in class picard.arrays.illumina.IlluminaManifest
manifestName - Variable in class picard.arrays.illumina.InfiniumEGTFile
MAP_FILE - Variable in class picard.arrays.MergePedIntoVcf
MAP_INFO_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
mappingQualityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies into the mapping-quality of the read under consideration
MAPPINGS_DIFFER - picard.sam.util.SamComparison.AlignmentComparison
MAPPINGS_DIFFER - Variable in class picard.sam.SamComparisonMetric
  The number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH.
MAPPINGS_MATCH - picard.sam.util.SamComparison.AlignmentComparison
MAPPINGS_MATCH - Variable in class picard.sam.SamComparisonMetric
  The number of primary records for which mappings match in files.
MarkDuplicates - Class in picard.sam.markduplicates
  A better duplication marking algorithm that handles all cases including clipped and gapped alignments.
MarkDuplicates() - Constructor for class picard.sam.markduplicates.MarkDuplicates
MarkDuplicates.DuplicateTaggingPolicy - Enum in picard.sam.markduplicates
  Enum used to control how duplicates are flagged in the DT optional tag on each read.
MarkDuplicates.DuplicateType - Enum in picard.sam.markduplicates
  Enum for the possible values that a duplicate read can be tagged with in the DT attribute.
MarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
  An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.
MarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
MarkDuplicatesWithMateCigarIterator - Class in picard.sam.markduplicates
  This will iterate through a coordinate sorted SAM file (iterator) and either mark or remove duplicates as appropriate.
MarkDuplicatesWithMateCigarIterator(SAMFileHeader, CloseableIterator<SAMRecord>, OpticalDuplicateFinder, DuplicateScoringStrategy.ScoringStrategy, int, boolean, boolean, int, int, List<File>) - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
  Initializes the mark duplicates iterator.
MarkIlluminaAdapters - Class in picard.illumina
  Command line program to mark the location of adapter sequences.
MarkIlluminaAdapters() - Constructor for class picard.illumina.MarkIlluminaAdapters
MarkQueue - Class in picard.sam.markduplicates.util
  This is the mark queue.
MarkQueue(DuplicateScoringStrategy.ScoringStrategy) - Constructor for class picard.sam.markduplicates.util.MarkQueue
MATCH_BARCODES_INLINE - Variable in class picard.illumina.IlluminaBasecallsToFastq
MATCH_BARCODES_INLINE - Variable in class picard.illumina.IlluminaBasecallsToSam
MATCHING_DICTIONARY_TAGS - Variable in class picard.sam.MergeBamAlignment
matchPattern - Variable in class picard.illumina.parser.ParameterizedFileUtil
  A pattern that will match files of this type for this lane
MatchResults - Class in picard.fingerprint
  Represents the results of a fingerprint comparison between one dataset and a specific fingerprint file.
MathUtil - Class in picard.util
  General math utilities
MathUtil.LogMath - Class in picard.util
  A collection of common math operations that work with log values.
MATRIX_OUTPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
MATRIX_OUTPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
max(double[]) - Static method in class picard.util.MathUtil
  Returns the largest value stored in the array.
max(long[]) - Static method in class picard.util.MathUtil
  Returns the largest value stored in the array.
MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH - Static variable in class picard.cmdline.CommandLineProgram
  CommandLineProgramProperties oneLineSummary attribute must be shorted than this in order to maintain reasonable help output formatting.
MAX_DIFF_RATE - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
MAX_DISCARD_FRACTION - Variable in class picard.sam.RevertSam
MAX_EDIT_DISTANCE_TO_JOIN - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK - Variable in class picard.fingerprint.CrosscheckFingerprints
MAX_ERROR_RATE - Static variable in class picard.util.ClippingUtility
  The default value used for the maximum error rate when matching read bases to clippable sequence.
MAX_ERROR_RATE_PE - Variable in class picard.illumina.MarkIlluminaAdapters
MAX_ERROR_RATE_SE - Variable in class picard.illumina.MarkIlluminaAdapters
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
MAX_FS - Variable in class picard.vcf.filter.FilterVcf
MAX_GROUP_RATIO - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
MAX_INSERT_SIZE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
MAX_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
  The maximum measure insert size by alignment.
MAX_INSERTIONS_OR_DELETIONS - Variable in class picard.sam.MergeBamAlignment
MAX_LOCI - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
MAX_MISMATCH_RATE - Variable in class picard.analysis.CollectRrbsMetrics
MAX_MISMATCHES - Variable in class picard.illumina.ExtractBarcodesProgram
MAX_NO_CALLS - Variable in class picard.illumina.ExtractBarcodesProgram
MAX_OPEN_TEMP_FILES - Variable in class picard.sam.ValidateSamFile
MAX_OPTICAL_DUPLICATE_SET_SIZE - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
MAX_OUTPUT - Variable in class picard.sam.ValidateSamFile
MAX_PE_ERROR_RATE - Static variable in class picard.util.ClippingUtility
  The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
MAX_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
MAX_PROB_BELOW_ONE - Static variable in class picard.util.MathUtil
  The double value closest to 1 while still being less than 1.
MAX_Q - Variable in class picard.sam.FastqToSam
MAX_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
  The maximum read length.
MAX_READ_LENGTH - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
  Deprecated.
MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
MAX_RECORDS_IN_RAM - Variable in class picard.cmdline.CommandLineProgram
MAX_RECORDS_IN_RAM - Static variable in class picard.sam.AbstractAlignmentMerger
MAX_RECORDS_TO_EXAMINE - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
  If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.
MAX_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
  The maximum coverage of reads that mapped to target regions of an experiment.
MAX_TO_MERGE - Variable in class picard.util.ScatterIntervalsByNs
MAX_UNSIGNED_SHORT - Static variable in class picard.arrays.illumina.InfiniumDataFile
maximalInterestingDistance - Variable in class picard.util.BarcodeEditDistanceQuery
  maximal edit distance between reads and barcodes to be considered
MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
maybeAdvance() - Method in class picard.illumina.parser.PerTileParser
maybeDemultiplex(ClusterData, Map<String, BarcodeMetric>, BarcodeMetric, ReadStructure) - Method in class picard.illumina.BasecallsConverter
  If we are demultiplexing and a barcodeExtractor is defined then this method will perform on-the-fly demuxing.
mean(double...) - Method in class picard.util.MathUtil.LogMath
  Computes the mean of the provided log values.
mean(double[]) - Static method in class picard.util.MathUtil
mean(double[], int, int) - Static method in class picard.util.MathUtil
  Calculated the mean of an array of doubles.
MEAN_AMPLICON_COVERAGE - Variable in class picard.analysis.directed.TargetedPcrMetrics
  The mean read coverage of all amplicon regions in the experiment.
MEAN_BAIT_COVERAGE - Variable in class picard.analysis.directed.HsMetrics
  The mean coverage of all baits in the experiment.
MEAN_BASE_QUALITY - Variable in class picard.analysis.GcBiasDetailMetrics
  The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
MEAN_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The mean number of clusters per tile.
MEAN_COVERAGE - Variable in class picard.analysis.WgsMetrics
  The mean coverage in bases of the genome territory, after all filters are applied.
MEAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
  Mean coverage of CpG sites
MEAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
  The mean insert size of the "core" of the distribution.
MEAN_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The mean percentage of pf clusters per tile.
MEAN_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The mean number of pf clusters per tile.
MEAN_PROBE_COVERAGE - Variable in class picard.analysis.directed.TargetMetrics
  The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
MEAN_R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
MEAN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
  The mean read length of the set of reads examined.
MEAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
  The mean coverage of targets.
MEAN_THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
MEAN_UMI_LENGTH - Variable in class picard.sam.markduplicates.UmiMetrics
  Number of bases in each UMI
MEAN_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
MEAN_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
MeanQualityByCycle - Class in picard.analysis
  Program to generate a data table and chart of mean quality by cycle from a BAM file.
MeanQualityByCycle - picard.analysis.CollectMultipleMetrics.Program
MeanQualityByCycle() - Constructor for class picard.analysis.MeanQualityByCycle
meanR - Variable in class picard.arrays.illumina.InfiniumEGTFile
meanTheta - Variable in class picard.arrays.illumina.InfiniumEGTFile
median(double...) - Static method in class picard.util.MathUtil
  Calculate the median of an array of doubles.
MEDIAN_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
  The median 3 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter, where 3 prime bias is calculated per transcript as: mean coverage of the 3 prime-most number of bases, divided by the mean coverage of the whole transcript.
MEDIAN_5PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
  The median 5 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
MEDIAN_5PRIME_TO_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
  The ratio of coverage at the 5 prime end to the 3 prime end based on the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
MEDIAN_ABSOLUTE_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
  The median absolute deviation of the distribution.
MEDIAN_COVERAGE - Variable in class picard.analysis.WgsMetrics
  The median coverage in bases of the genome territory, after all filters are applied.
MEDIAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
  Median coverage of CpG sites
MEDIAN_CV_COVERAGE - Variable in class picard.analysis.RnaSeqMetrics
  The median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
MEDIAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
  The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.
MEDIAN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
  The median read length.
MEDIAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
  The median coverage of targets.
MemoryBasedReadEndsForMarkDuplicatesMap - Class in picard.sam.markduplicates.util
  Map from String to ReadEnds object.
MemoryBasedReadEndsForMarkDuplicatesMap() - Constructor for class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
MendelianViolationMetrics - Class in picard.vcf.MendelianViolations
  Describes the type and number of mendelian violations found within a Trio.
MendelianViolationMetrics() - Constructor for class picard.vcf.MendelianViolations.MendelianViolationMetrics
MendelianViolationsByFamily - Class in picard.vcf.MendelianViolations
  Created by farjoun on 6/25/16.
MendelianViolationsByFamily() - Constructor for class picard.vcf.MendelianViolations.MendelianViolationsByFamily
merge(Collection<? extends MergeableMetricBase>) - Method in class picard.analysis.MergeableMetricBase
  for a collection of MergeableMetricBase, merge them all into "this" one.
merge(Collection<CallingMetricAccumulator.Result>) - Static method in class picard.vcf.CallingMetricAccumulator.Result
merge(Collection<RESULT>) - Method in interface picard.vcf.processor.VariantProcessor.ResultMerger
merge(List<VariantContext>) - Static method in class picard.arrays.CombineGenotypingArrayVcfs
  Merges multiple VariantContexts all for the same locus into a single hybrid.
merge(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
  Merge another metric into this one
merge(MergeableMetricBase) - Method in class picard.analysis.WgsMetrics
  Merges the various PCT_EXC_* metrics.
merge(Fingerprint) - Method in class picard.fingerprint.Fingerprint
  Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
merge(FingerprintIdDetails) - Method in class picard.fingerprint.FingerprintIdDetails
merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilities
  Merges in the likelihood information from the supplied haplotype probabilities object.
merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
  Merges information from another haplotype probabilities object for the same haplotype into this object.
merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
merge(BarcodeMetric) - Method in class picard.illumina.BarcodeMetric
  Adds the non-calculated
merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric) - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  Adds the non-calculated fields from the other metric to this one.
MERGE_NEARBY_TARGETS - Variable in class picard.util.BaitDesigner
MERGE_SEQUENCE_DICTIONARIES - Variable in class picard.sam.MergeSamFiles
MergeableMetricBase - Class in picard.analysis
  An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated (`MergeByAdding`).
MergeableMetricBase() - Constructor for class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding - Annotation Type in picard.analysis
  Metrics whose values can be merged by adding.
MergeableMetricBase.MergeByAssertEquals - Annotation Type in picard.analysis
  Metrics whose values should be equal when merging.
MergeableMetricBase.MergingIsManual - Annotation Type in picard.analysis
  Metrics that are merged manually in the `MergeableMetricBase.merge(MergeableMetricBase)` ()}.
MergeableMetricBase.NoMergingIsDerived - Annotation Type in picard.analysis
  Metrics that are not merged, but are subsequently derived from other metrics, for example by `MergeableMetricBase.calculateDerivedFields()`.
MergeableMetricBase.NoMergingKeepsValue - Annotation Type in picard.analysis
  Metrics that are not merged.
mergeAlignment(File) - Method in class picard.sam.AbstractAlignmentMerger
  Merges the alignment data with the non-aligned records from the source BAM file.
mergeAlignment(File) - Method in class picard.sam.SamAlignmentMerger
  Merges the alignment from the map file with the non-aligned records from the source BAM file.
MergeBamAlignment - Class in picard.sam
  Summary
MergeBamAlignment() - Constructor for class picard.sam.MergeBamAlignment
mergeFingerprintsBy(Map<FingerprintIdDetails, Fingerprint>, Function<FingerprintIdDetails, String>) - Static method in class picard.fingerprint.Fingerprint
mergeIfCan(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
  Merges another MergableMetricBase if possible
MergePedIntoVcf - Class in picard.arrays
  Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.
MergePedIntoVcf() - Constructor for class picard.arrays.MergePedIntoVcf
MergeSamFiles - Class in picard.sam
  This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similar to the \"merge\" function of Samtools (http://www.htslib.org/doc/samtools.html).
MergeSamFiles() - Constructor for class picard.sam.MergeSamFiles
MergeVcfs - Class in picard.vcf
  Combines multiple variant files into a single variant file.
MergeVcfs() - Constructor for class picard.vcf.MergeVcfs
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectGcBiasMetrics
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectInsertSizeMetrics
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectMultipleMetrics
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRnaSeqMetrics
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRrbsMetrics
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.directed.CollectTargetedMetrics
METRIC_ALLOWABLE_RELATIVE_CHANGE - Variable in class picard.analysis.CompareMetrics
MetricAccumulationLevel - Enum in picard.analysis
  For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.
metrics - Variable in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
METRICS - Variable in class picard.illumina.MarkIlluminaAdapters
METRICS_FILE - Variable in class picard.illumina.ExtractBarcodesProgram
METRICS_FILE - Variable in class picard.sam.DownsampleSam
METRICS_FILE - Variable in class picard.sam.markduplicates.CollectDuplicateMetrics
METRICS_FILE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
METRICS_FILE_PREFIX - Variable in class picard.analysis.CollectRrbsMetrics
METRICS_FILE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
METRICS_TO_IGNORE - Variable in class picard.analysis.CompareMetrics
MetricToAllowableRelativeChange - Variable in class picard.analysis.CompareMetrics
min(byte[]) - Static method in class picard.util.MathUtil
  Returns the smallest value stored in the array.
min(double[]) - Static method in class picard.util.MathUtil
  Returns the smallest value stored in the array.
min(int[]) - Static method in class picard.util.MathUtil
  Returns the smallest value stored in the array.
min(short[]) - Static method in class picard.util.MathUtil
  Returns the smallest value stored in the array.
MIN_AB - Variable in class picard.vcf.filter.FilterVcf
MIN_BASE_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
MIN_DP - Variable in class picard.vcf.filter.FilterVcf
MIN_DP - Variable in class picard.vcf.GenotypeConcordance
MIN_DP - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
MIN_GQ - Variable in class picard.vcf.filter.FilterVcf
MIN_GQ - Variable in class picard.vcf.GenotypeConcordance
MIN_GQ - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
MIN_GROUP_COUNT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
MIN_HET_FRACTION - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
MIN_HISTOGRAM_WIDTH - Variable in class picard.analysis.CollectInsertSizeMetrics
MIN_IDENTICAL_BASES - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
MIN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
  The minimum measured insert size.
MIN_LIFTOVER_PCT - Variable in class picard.util.LiftOverIntervalList
MIN_MAPPING_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
MIN_MATCH_BASES - Static variable in class picard.util.ClippingUtility
  The default value used for the minimum number of contiguous bases to match against.
MIN_MATCH_BASES_PE - Variable in class picard.illumina.MarkIlluminaAdapters
MIN_MATCH_BASES_SE - Variable in class picard.illumina.MarkIlluminaAdapters
MIN_MATCH_PE_BASES - Static variable in class picard.util.ClippingUtility
  The default value used for the minimum number of contiguous bases to match against in a paired end read
MIN_MEAN_QUALITY - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
MIN_MISMATCH_DELTA - Variable in class picard.illumina.ExtractBarcodesProgram
MIN_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
  At least one NextSeq run produced a small negative value for y coordinate (-5), so allow small negative values and see what happens.
MIN_Q - Variable in class picard.sam.FastqToSam
MIN_QD - Variable in class picard.vcf.filter.FilterVcf
MIN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
  The minimum read length.
MIN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
  The minimum coverage of reads that mapped to target regions of an experiment.
MIN_TRIMMED_LENGTH - Variable in class picard.illumina.IlluminaBasecallsToFastq
MIN_UNCLIPPED_BASES - Variable in class picard.sam.MergeBamAlignment
MINIMUM_BAITS_PER_TARGET - Variable in class picard.util.BaitDesigner
MINIMUM_BARCODE_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
MINIMUM_BASE_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
MINIMUM_BASE_QUALITY - Variable in class picard.analysis.directed.CollectTargetedMetrics
MINIMUM_BASE_QUALITY - Variable in class picard.illumina.ExtractBarcodesProgram
MINIMUM_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
MINIMUM_DISTANCE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
MINIMUM_GENOME_FRACTION - Variable in class picard.analysis.CollectGcBiasMetrics
MINIMUM_GQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
MINIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
MINIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
MINIMUM_LENGTH - Variable in class picard.analysis.CollectRnaSeqMetrics
MINIMUM_LOD_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectJumpingLibraryMetrics
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectOxoGMetrics
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.directed.CollectTargetedMetrics
MINIMUM_MAPPING_QUALITY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
MINIMUM_MQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
MINIMUM_PCT - Variable in class picard.analysis.CollectInsertSizeMetrics
MINIMUM_QUALITY - Variable in class picard.illumina.ExtractBarcodesProgram
MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.CollectOxoGMetrics
MINIMUM_READ_LENGTH - Variable in class picard.analysis.CollectRrbsMetrics
minimumBaseQuality - Variable in class picard.util.BarcodeEditDistanceQuery
  minimal base quality to condiser informative
MINUS - picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
MISALIGNED - picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
mismatchesInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies according to the overall mismatches (from NM) that the read has against the reference, NOT including the current base.
MismatchesInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
MISSING - picard.vcf.GenotypeConcordanceStates.CallState
MISSING - picard.vcf.GenotypeConcordanceStates.TruthState
MISSING_ALLELE_B_PROBESEQ - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Manifest contained no allele B probe sequence
MISSING_CODE - picard.vcf.GenotypeConcordanceStateCodes
  These codes allow for constants in the truth state enum and the call state enum to be compared.
MISSING_LEFT - Variable in class picard.sam.SamComparisonMetric
  The number of primary records which are found in right file but not found in left file
MISSING_RIGHT - Variable in class picard.sam.SamComparisonMetric
  The number of primary records which are found in left file but not found in right file
MISSING_SITES_HOM_REF - Variable in class picard.vcf.GenotypeConcordance
MMapBackedIteratorFactory - Class in picard.illumina.parser.readers
  MMapBackedIteratorFactory a file reader that takes a header size and a binary file, maps the file to a read-only byte buffer and provides methods to retrieve the header as it's own bytebuffer and create iterators of different data types over the values of file (starting after the end of the header).
MMapBackedIteratorFactory() - Constructor for class picard.illumina.parser.readers.MMapBackedIteratorFactory
MODE - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
MODE - Variable in class picard.sam.ValidateSamFile
MODE_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
  The MODE insert size of all paired end reads where both ends mapped to the same chromosome.
MOLECULAR_BARCODE_NAME - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The barcode name for which the metrics were calculated.
MOLECULAR_BARCODE_SEQUENCE_1 - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The barcode sequence for which the metrics were calculated.
MOLECULAR_IDENTIFIER_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
MOLECULAR_INDEX_BASE_QUALITY_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
MOLECULAR_INDEX_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
molecularBarcode - Variable in class picard.illumina.parser.ReadStructure
MolecularIndex - Static variable in enum picard.illumina.parser.ReadType
MostDistantPrimaryAlignmentSelectionStrategy - Class in picard.sam
  For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size.
MostDistantPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
MOTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The ID of the mother within the trio.
MOVE_TO_TAG - picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,​Histogram_KEY extends Comparable,​ARGTYPE> - Class in picard.metrics
  MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
MultiLevelCollector() - Constructor for class picard.metrics.MultiLevelCollector
MultilevelMetrics - Class in picard.metrics
MultilevelMetrics() - Constructor for class picard.metrics.MultilevelMetrics
MULTIPLEX_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToFastq
multiply(double[], double[]) - Static method in class picard.util.MathUtil
  Calculates the product of two arrays of the same length.
MultiThreadedChunkBased(int, VariantIteratorProducer, VariantProcessor.AccumulatorGenerator<A, R>) - Constructor for class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
multithreadingBy(int) - Method in class picard.vcf.processor.VariantProcessor.Builder
MultiTileBcl - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
MultiTileBclFileFaker - Class in picard.illumina.parser.fakers
  Created by jcarey on 3/13/14.
MultiTileBclFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileBclFileFaker
MultiTileBclFileUtil - Class in picard.illumina.parser
  NextSeq-style bcl's have all tiles for a cycle in a single file.
MultiTileBclParser - Class in picard.illumina.parser
  Parse .bcl.bgzf files that contain multiple tiles in a single file.
MultiTileBclParser(File, int, CycleIlluminaFileMap, OutputMapping, boolean, BclQualityEvaluationStrategy, TileIndex) - Constructor for class picard.illumina.parser.MultiTileBclParser
MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
  For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_<lane>.bci file can be used to figure out where each tile starts and ends.
MultiTileFilter - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
MultiTileFilterParser - Class in picard.illumina.parser
  Read filter file that contains multiple tiles in a single file.
MultiTileFilterParser(TileIndex, List<Integer>, File) - Constructor for class picard.illumina.parser.MultiTileFilterParser
MultiTileLocs - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
MultiTileLocsFileFaker - Class in picard.illumina.parser.fakers
  Created by jcarey on 3/13/14.
MultiTileLocsFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileLocsFileFaker
MultiTileLocsParser - Class in picard.illumina.parser
  Read locs file that contains multiple tiles in a single file.
MultiTileLocsParser(TileIndex, List<Integer>, File, int) - Constructor for class picard.illumina.parser.MultiTileLocsParser
MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
  Abstract class for files with fixed-length records for multiple tiles, e.g.
MultiTileParser(TileIndex, List<Integer>, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.MultiTileParser

## N

n - Variable in class picard.arrays.illumina.InfiniumEGTFile
N - Static variable in class picard.arrays.illumina.InfiniumVcfFields
N_CYCLES - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
NA - picard.vcf.GenotypeConcordanceStates.ContingencyState
NA - Static variable in class picard.vcf.GenotypeConcordanceScheme
  These are convenience variables for defining a scheme.
nAlternateAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of doubletons where the two reads matched the alternate.
nAlternateAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of tripletons where the two reads matched the alternate.
nAlternateReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of alternate alleles in the reads.
name - Variable in class picard.annotation.Gene.Transcript
NAME - Variable in class picard.util.FifoBuffer
NAME_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
NATURAL_LOG_MATH - Static variable in class picard.util.MathUtil
nBadBarcodes - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of sets where the UMIs had poor quality bases and were not used for any comparisons.
NCBI_35 - Static variable in class picard.arrays.illumina.IlluminaManifest
NCBI_36 - Static variable in class picard.arrays.illumina.IlluminaManifest
NCBI_37 - Static variable in class picard.arrays.illumina.IlluminaManifest
nDeletedBases - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
  Total number of deleted bases
nDeletions - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
  Total number of deletions
nDifferentAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of doubletons where the two reads had different bases in the locus.
nDifferentAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of tripletons where at least one of the reads didn't match either allele of the het site.
nDuplicateSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of duplicate sets examined.
NEAR_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
  The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.
NEAR_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
  The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se.
NEAR_DISTANCE - Variable in class picard.analysis.directed.CollectTargetedMetrics
NEAR_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
  The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a probed region.
NEAR_PROBE_DISTANCE_DEFAULT - Static variable in class picard.analysis.directed.TargetMetricsCollector
  Default distance for a read to be considered "selected".
needsReferenceSequence() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
needsRefflatFile() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
NEGATIVE - picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
NEW_SAMPLE_NAME - Variable in class picard.vcf.RenameSampleInVcf
newCounter() - Method in class picard.analysis.CounterManager
  Creates a new Counter object and adds it to the list of managed Counters.
nExactlyDouble - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of sets of size exactly 2 found.
nExactlyTriple - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of sets of size exactly 3 found.
next() - Method in class picard.illumina.parser.MultiTileParser
next() - Method in class picard.illumina.parser.PerTileParser
next() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
  Return the next set of coordinates in a given file.
next() - Method in class picard.illumina.parser.readers.BarcodeFileReader
next() - Method in class picard.illumina.parser.readers.BclReader
next() - Method in class picard.illumina.parser.readers.CbclReader
next() - Method in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
next() - Method in class picard.illumina.parser.readers.FilterFileReader
next() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
next() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
next() - Method in class picard.util.AsyncIterator
next() - Method in interface picard.util.AtomicIterator
  Produces the next element from the iterator, if there is one; otherwise, produces `Optional.EMPTY`
next() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
next() - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
next() - Method in class picard.vcf.ByIntervalListVariantContextIterator
next() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
  Provides the next record from the underlying iterator after applying filter strings generated by the set of filters in use by the iterator.
next() - Method in class picard.vcf.PairedVariantSubContextIterator
next() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
NEXT_BASE_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
NEXTERA_V1 - picard.util.IlluminaUtil.IlluminaAdapterPair
NEXTERA_V2 - picard.util.IlluminaUtil.IlluminaAdapterPair
nextReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies bases into the following (uppercase) base as it was read from the sequencer (i.e.
nGoodBarcodes - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  the number of sets where the UMIs had good quality bases and were used for any comparisons.
NHOM - Variable in class picard.arrays.BafRegressMetrics
  The number of homozygous genotypes used to fit the model
nInsertedBases - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
  Total number of inserted bases
nInsertions - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
  Total number of inserts
nMatchingUMIsInDiffBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of UMIs that are match within Bi-sets that come from different alleles.
nMatchingUMIsInSameBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of UMIs that are match within Bi-sets that come from the same alleles.
nMismatchingAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of tripletons where the two reads had different bases in the locus.
nMismatchingAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of tripletons where at least one of the reads didn't match either allele of the het site.
nMismatchingBases - Variable in class picard.sam.SamErrorMetric.SimpleErrorCalculator
nMismatchingUMIsInContraOrientedBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of bi-sets with mismatching UMIs and opposite orientation.
nMismatchingUMIsInCoOrientedBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of bi-sets with mismatching UMIs and same orientation.
nMismatchingUMIsInDiffBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of UMIs that are different within Bi-sets that come from different alleles.
nMismatchingUMIsInSameBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of UMIs that are different within Bi-sets that come from the same alleles.
NN - picard.arrays.illumina.IlluminaGenotype
NO_CALL - picard.vcf.GenotypeConcordanceStates.CallState
NO_CALL - picard.vcf.GenotypeConcordanceStates.TruthState
NO_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
NO_CALL_BASE - Static variable in class picard.illumina.parser.readers.BaseBclReader
NO_CALL_CODE - picard.vcf.GenotypeConcordanceStateCodes
NO_LIBRARIES_SPECIFIED_IN_HEADER - Static variable in class picard.sam.SplitSamByLibrary
NO_MATCH - Static variable in class picard.util.ClippingUtility
  The value returned by methods returning int when no match is found.
NO_PHENO - Static variable in class picard.pedigree.PedFile
NO_VALUE - Static variable in interface picard.sam.util.PhysicalLocation
noMatchMetric - Variable in class picard.illumina.ExtractBarcodesProgram
NON_CPG_BASES - Variable in class picard.analysis.RrbsSummaryMetrics
  Number of times a non-CpG cytosine was encountered
NON_CPG_CONVERTED_BASES - Variable in class picard.analysis.RrbsSummaryMetrics
  Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)
NON_REF_GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The non-ref genotype concordance, ie for all var states only.
NON_ZERO_REGIONS - picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
NONE - picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
NONE - picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
NONJUMP_DUPLICATE_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
  The number of inward-facing pais that are duplicates
NONJUMP_DUPLICATE_PCT - Variable in class picard.analysis.JumpingLibraryMetrics
  The fraction of inward-facing pairs that are marked as duplicates
NONJUMP_LIBRARY_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
  The estimated library size for inward-facing pairs
NONJUMP_MEAN_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
  The mean insert size for inward-facing pairs
NONJUMP_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
  The number of inward-facing pairs in the SAM file
NONJUMP_STDEV_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
  The standard deviation on the insert size for inward-facing pairs
NonNFastaSize - Class in picard.reference
  A tool to count the number of non-N bases in a fasta file
NonNFastaSize() - Constructor for class picard.reference.NonNFastaSize
NonPF - picard.sam.ViewSam.PfStatus
nonSkips - Variable in class picard.illumina.parser.ReadStructure
nonStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  A constant stratifier which places all the reads into a single stratum.
normalizationVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
normalizeAlleles(VariantContext, String, VariantContext, String, Boolean) - Static method in class picard.vcf.GenotypeConcordance
  Gets the alleles for the truth and call genotypes.
NORMALIZED_COVERAGE - Variable in class picard.analysis.GcBiasDetailMetrics
  The ratio of "coverage" in this GC bin vs.
normalizedXIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
normalizedYIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
NormalizeFasta - Class in picard.reference
  Little program to "normalize" a fasta file to ensure that all line of sequence are the same length, and are a reasonable length!
NormalizeFasta() - Constructor for class picard.reference.NormalizeFasta
normalizeHistogram(Histogram<Integer>) - Static method in class picard.analysis.TheoreticalSensitivity
NORMX - Static variable in class picard.arrays.illumina.InfiniumVcfFields
NORMY - Static variable in class picard.arrays.illumina.InfiniumVcfFields
NOT_ALIGNED_ERROR - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
NotReported - picard.pedigree.Sex
NOVEL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of passing indels called that were not found in dbSNP
NOVEL_INS_DEL_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites
NOVEL_SNPS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The number of high confidence SNPS called that were not found in dbSNP
NOVEL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of passing bi-allelic SNPS called that were not found in dbSNP
NOVEL_TITV - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites
nReadsInBigSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of reads in duplicate of sizes greater than 3.
nRecordsInMemory - Variable in class picard.annotation.SortGff
nReferenceAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of doubletons where the two reads matched the reference.
nReferenceAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of tripletons where the two reads matched the reference.
nReferenceReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The number of reference alleles in the reads.
nsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratify by the number of Ns found in the read.
NsInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
nSites - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The count of sites used.
nThreeAllelesSites - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The count of sites in which a third allele was found.
nTotalReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  The total number of reads over the het sites.
NUM_ADAPTERS_TO_KEEP - Variable in class picard.illumina.MarkIlluminaAdapters
NUM_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The total number of assays (SNP and indels) in the VCF
NUM_AUTOCALL_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The number of passing autocall calls
NUM_BASES_WITH_OVERLAPPING_READS - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
  The number of bases for which an overlapping base from the mate read was found
NUM_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The number of passing calls
NUM_CHANNELS - Static variable in enum picard.illumina.parser.IntensityChannel
NUM_DELETED_BASES - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
  The number of deleted bases.
NUM_DELETIONS - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
  The number of deletions.
NUM_DIPLOID_DENOVO - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The number of diploid sites at which a potential de-novo mutation was observed (i.e.
NUM_DISAGREES_WITH_REF_AND_MATE - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
  The number of bases that disagree with both the reference and their mate (which agree with each other)
NUM_DISAGREES_WITH_REFERENCE_ONLY - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
  The number of bases that disagree with the reference, but agree with their mate
NUM_FILTERED_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The total number of filtered assays in the VCF
NUM_HAPLOID_DENOVO - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The number of sites at which the offspring is haploid, the parent is homozygous reference and the offspring is non-reference.
NUM_HAPLOID_OTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The number of sites at which the offspring is haploid and exhibits a reference allele that is not present in the parent.
NUM_HET - Variable in class picard.fingerprint.FingerprintMetrics
  Number of heterozygous calls
NUM_HOM_ALLELE1 - Variable in class picard.fingerprint.FingerprintMetrics
  Number of major allele homozygous calls
NUM_HOM_ALLELE2 - Variable in class picard.fingerprint.FingerprintMetrics
  Number of minor allele homozygous calls
NUM_HOM_ANY - Variable in class picard.fingerprint.FingerprintMetrics
  Number of homozygous calls of either allele (might not be the sum of `FingerprintMetrics.NUM_HOM_ALLELE1` and `FingerprintMetrics.NUM_HOM_ALLELE1` due to rounding
NUM_HOM_HET_HOM - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The number of sites at which one parent is homozygous, the other is heterozygous and the offspring is the alternative homozygote.
NUM_HOMREF_HOMVAR_HOM - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The number of sites at which the one parent is homozygous reference, the other homozygous variant and the offspring is homozygous.
NUM_HOMVAR_HOMVAR_HET - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The number of sites at which both parents are homozygous for a non-reference allele and the offspring is heterozygous.
NUM_IN_DB_SNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The number of high confidence SNPs found in dbSNP
NUM_IN_DB_SNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of passing bi-allelic SNPs found in dbSNP
NUM_IN_DB_SNP_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of passing complex indels found in dbSNP
NUM_IN_DB_SNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of passing indels found in dbSNP
NUM_IN_DB_SNP_MULTIALLELIC - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of passing multi-allelic SNPs found in dbSNP
NUM_INDELS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The number of indel calls
NUM_INSERTED_BASES - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
  The number of inserted bases.
NUM_INSERTIONS - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
  The number of insertions.
NUM_MARKERS_FILE - Variable in class picard.arrays.VcfToAdpc
NUM_N - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
  The number of Ns found in this read
NUM_NO_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The number of no-calls
NUM_NON_FILTERED_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The total number of NON-filtered assays in the VCF
NUM_OTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The number of otherwise unclassified events.
NUM_PROCESSORS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
NUM_PROCESSORS - Variable in class picard.illumina.ExtractIlluminaBarcodes
NUM_PROCESSORS - Variable in class picard.illumina.IlluminaBasecallsToFastq
NUM_PROCESSORS - Variable in class picard.illumina.IlluminaBasecallsToSam
NUM_PROCESSORS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
NUM_Q_GT_TWO - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
  The number of Quality scores greater than 2 found in this read
NUM_R1_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
  The number of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
NUM_R2_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
  The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
NUM_SEQUENCES - Variable in class picard.sam.CreateSequenceDictionary
NUM_SINGLETONS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  For summary metrics, the number of variants that appear in only one sample.
NUM_SINGLETONS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  For summary metrics, the number of variants that appear in only one sample.
NUM_SNPS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The number of bi-allelic SNP calls
NUM_THREADS - Variable in class picard.fingerprint.CrosscheckFingerprints
NUM_THREE_WAYS_DISAGREEMENT - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
  The number of bases that disagree with both the reference and their mate (which also disagree)
NUM_UNEXPLAINED_READS - Variable in class picard.analysis.RnaSeqMetrics
  The fraction of reads for which the transcription strand model could not be inferred.
NUM_VARIANT_SITES - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The number of biallelic, SNP sites at which all relevant samples exceeded the minimum genotype quality and depth and at least one of the samples was variant.
NUM_ZEROED_OUT_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The total number of zeroed-out (filtered out by Illumina in chip design) assays in the VCF
NUMBER_OF_SAMPLING - Variable in class picard.fingerprint.CalculateFingerprintMetrics
numClusters - Variable in class picard.illumina.parser.readers.FilterFileReader
  The number of cluster's pf values stored in this file
numCodes - Variable in class picard.arrays.illumina.InfiniumEGTFile
numOutputReads() - Method in class picard.illumina.parser.OutputMapping
numProcessors(int) - Method in class picard.illumina.BasecallsConverterBuilder
  Configures how many processors this converter will use.

## O

OBS_A - Variable in class picard.analysis.FingerprintingDetailMetrics
  The number of observations of the first, or A, allele of the SNP in the sequencing data.
OBS_B - Variable in class picard.analysis.FingerprintingDetailMetrics
  The number of observations of the second, or B, allele of the SNP in the sequencing data.
obsAllele1 - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
obsAllele2 - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
obsAlleleOther - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
OBSERVED_BASE_ERRORS - Variable in class picard.sam.markduplicates.UmiMetrics
  Number of errors inferred by comparing the observed and inferred UMIs
OBSERVED_GENOTYPE - Variable in class picard.analysis.FingerprintingDetailMetrics
  The most likely genotype given the observed evidence at the SNP locus in the sequencing data.
OBSERVED_SAMPLE_ALIAS - Variable in class picard.fingerprint.CheckFingerprint
OBSERVED_UMI_ENTROPY - Variable in class picard.sam.markduplicates.UmiMetrics
  Entropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs.
OBSERVED_UNIQUE_UMIS - Variable in class picard.sam.markduplicates.UmiMetrics
  Number of different UMI sequences observed
of(SAMRecord) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
of(SAMRecord) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
of(SAMRecord) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
of(SAMRecord) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
OFF_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
  The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.
OFF_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
  The number of PF_BASES_ALIGNED that are mapped away from any baited region.
OFF_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
  The number of PF aligned bases that mapped to neither on or near a probe.
OFFSPRING - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The ID of the offspring within the trio.
OFFSPRING_SEX - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The sex of the offspring.
OLD_SAMPLE_NAME - Variable in class picard.vcf.RenameSampleInVcf
ON_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
  The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.
ON_AMPLICON_VS_SELECTED - Variable in class picard.analysis.directed.TargetedPcrMetrics
  The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)
ON_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
  The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.
ON_BAIT_VS_SELECTED - Variable in class picard.analysis.directed.HsMetrics
  The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES).
ON_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
  The number of PF aligned probed bases that mapped to a baited region of the genome.
ON_PROBE_VS_SELECTED - Variable in class picard.analysis.directed.TargetMetrics
  The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).
ON_TARGET_BASES - Variable in class picard.analysis.directed.PanelMetricsBase
  The number of PF aligned bases that mapped to a targeted region of the genome.
ON_TARGET_FROM_PAIR_BASES - Variable in class picard.analysis.directed.TargetMetricsBase
  The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
ONE_MISMATCH_MATCHES - Variable in class picard.illumina.BarcodeMetric
  The number of all reads matching this barcode that matched with 1 error or no-call.
oneBasePaddedContextStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies into the one base context of the base, which includes one read-base on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
openInputs(boolean) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
  Since this may read its inputs more than once this method does all the opening and checking of the inputs.
OPTICAL_DUPLICATE_PIXEL_DISTANCE - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
opticalDuplicateFinder - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
OpticalDuplicateFinder - Class in picard.sam.markduplicates.util
  Contains methods for finding optical/co-localized/sequencing duplicates.
OpticalDuplicateFinder() - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
  Uses the default duplicate distance `OpticalDuplicateFinder.DEFAULT_OPTICAL_DUPLICATE_DISTANCE` (100) and the default read name regex `ReadNameParser.DEFAULT_READ_NAME_REGEX`.
OpticalDuplicateFinder(String, int, long, Log) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
OpticalDuplicateFinder(String, int, Log) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
opticalDuplicatePixelDistance - Variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
OpticalOnly - picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
OptionalReferenceArgumentCollection - Class in picard.cmdline.argumentcollections
  Picard default argument collection for an optional reference.
OptionalReferenceArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
orientation - Variable in class picard.sam.markduplicates.util.ReadEnds
orientationForOpticalDuplicates - Variable in class picard.sam.markduplicates.util.ReadEnds
  For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate
ORIGINAL_ALLELES - Static variable in class picard.vcf.LiftoverVcf
  Attribute used to store the list of original alleles (including REF), in the original order prior to liftover.
ORIGINAL_CONTIG - Static variable in class picard.vcf.LiftoverVcf
  Attribute used to store the name of the source contig/chromosome prior to liftover.
ORIGINAL_START - Static variable in class picard.vcf.LiftoverVcf
  Attribute used to store the position of the variant on the source contig prior to liftover.
ORIGINAL_VCF - Variable in class picard.arrays.MergePedIntoVcf
OtherProgramGroup - Class in picard.cmdline.programgroups
  Miscellaneous tools, e.g.
OtherProgramGroup() - Constructor for class picard.cmdline.programgroups.OtherProgramGroup
out - Variable in class picard.sam.FixMateInformation
out - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
out - Variable in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
OUT_PREFIX - Variable in class picard.sam.SplitSamByNumberOfReads
output - Variable in class picard.analysis.SinglePassSamProgram
OUTPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
OUTPUT - Variable in class picard.analysis.CollectMultipleMetrics
OUTPUT - Variable in class picard.analysis.CollectOxoGMetrics
OUTPUT - Variable in class picard.analysis.CollectWgsMetrics
OUTPUT - Variable in class picard.analysis.CompareMetrics
OUTPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
OUTPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
OUTPUT - Variable in class picard.analysis.SinglePassSamProgram
OUTPUT - Variable in class picard.annotation.SortGff
OUTPUT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
OUTPUT - Variable in class picard.arrays.CombineGenotypingArrayVcfs
OUTPUT - Variable in class picard.arrays.CreateBafRegressMetricsFile
OUTPUT - Variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
OUTPUT - Variable in class picard.arrays.GtcToVcf
OUTPUT - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
OUTPUT - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
OUTPUT - Variable in class picard.arrays.MergePedIntoVcf
OUTPUT - Variable in class picard.arrays.VcfToAdpc
OUTPUT - Variable in class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
OUTPUT - Variable in class picard.fingerprint.CalculateFingerprintMetrics
OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
OUTPUT - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
OUTPUT - Variable in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
OUTPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
OUTPUT - Variable in class picard.fingerprint.ExtractFingerprint
OUTPUT - Variable in class picard.fingerprint.IdentifyContaminant
OUTPUT - Variable in class picard.fingerprint.LiftOverHaplotypeMap
OUTPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
OUTPUT - Variable in class picard.illumina.IlluminaBasecallsToSam
OUTPUT - Variable in class picard.illumina.MarkIlluminaAdapters
OUTPUT - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
OUTPUT - Variable in class picard.reference.ExtractSequences
OUTPUT - Variable in class picard.reference.NonNFastaSize
OUTPUT - Variable in class picard.reference.NormalizeFasta
OUTPUT - Variable in class picard.sam.AddCommentsToBam
OUTPUT - Variable in class picard.sam.AddOATag
OUTPUT - Variable in class picard.sam.AddOrReplaceReadGroups
OUTPUT - Variable in class picard.sam.BuildBamIndex
OUTPUT - Variable in class picard.sam.CalculateReadGroupChecksum
OUTPUT - Variable in class picard.sam.CleanSam
OUTPUT - Variable in class picard.sam.CompareSAMs
OUTPUT - Variable in class picard.sam.CreateSequenceDictionary
OUTPUT - Variable in class picard.sam.DownsampleSam
OUTPUT - Variable in class picard.sam.FastqToSam
OUTPUT - Variable in class picard.sam.FilterSamReads
OUTPUT - Variable in class picard.sam.FixMateInformation
OUTPUT - Variable in class picard.sam.GatherBamFiles
OUTPUT - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
OUTPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
OUTPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
OUTPUT - Variable in class picard.sam.MergeBamAlignment
OUTPUT - Variable in class picard.sam.MergeSamFiles
OUTPUT - Variable in class picard.sam.PositionBasedDownsampleSam
OUTPUT - Variable in class picard.sam.ReorderSam
OUTPUT - Variable in class picard.sam.ReplaceSamHeader
OUTPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
OUTPUT - Variable in class picard.sam.RevertSam
OUTPUT - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
OUTPUT - Variable in class picard.sam.SamFormatConverter
OUTPUT - Variable in class picard.sam.SetNmMdAndUqTags
OUTPUT - Variable in class picard.sam.SortSam
OUTPUT - Variable in class picard.sam.SplitSamByLibrary
OUTPUT - Variable in class picard.sam.SplitSamByNumberOfReads
OUTPUT - Variable in class picard.sam.ValidateSamFile
OUTPUT - Variable in class picard.util.AccumulateQualityYieldMetrics
OUTPUT - Variable in class picard.util.BedToIntervalList
OUTPUT - Variable in class picard.util.IntervalListToBed
OUTPUT - Variable in class picard.util.IntervalListTools
OUTPUT - Variable in class picard.util.LiftOverIntervalList
OUTPUT - Variable in class picard.util.ScatterIntervalsByNs
OUTPUT - Variable in class picard.vcf.AccumulateVariantCallingMetrics
OUTPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
OUTPUT - Variable in class picard.vcf.filter.FilterVcf
OUTPUT - Variable in class picard.vcf.FixVcfHeader
OUTPUT - Variable in class picard.vcf.GatherVcfs
OUTPUT - Variable in class picard.vcf.GenotypeConcordance
OUTPUT - Variable in class picard.vcf.LiftoverVcf
OUTPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
OUTPUT - Variable in class picard.vcf.MakeVcfSampleNameMap
OUTPUT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
OUTPUT - Variable in class picard.vcf.MergeVcfs
OUTPUT - Variable in class picard.vcf.RenameSampleInVcf
OUTPUT - Variable in class picard.vcf.SortVcf
OUTPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
OUTPUT - Variable in class picard.vcf.VcfFormatConverter
OUTPUT - Variable in class picard.vcf.VcfToIntervalList
OUTPUT_AGILENT_FILES - Variable in class picard.util.BaitDesigner
OUTPUT_ALL_ROWS - Variable in class picard.vcf.GenotypeConcordance
OUTPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
OUTPUT_BY_READGROUP - Variable in class picard.sam.RevertSam
OUTPUT_BY_READGROUP_FILE_FORMAT - Variable in class picard.sam.RevertSam
OUTPUT_DIR - Variable in class picard.illumina.ExtractIlluminaBarcodes
OUTPUT_DIR - Variable in class picard.sam.SamToFastq
OUTPUT_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
OUTPUT_DIRECTORY - Variable in class picard.util.BaitDesigner
OUTPUT_ERRORS_ONLY - Variable in class picard.fingerprint.CrosscheckFingerprints
OUTPUT_FILE_PREFIX - Variable in class picard.fastq.BamToBfq
OUTPUT_MAP - Variable in class picard.sam.RevertSam
OUTPUT_PER_RG - Variable in class picard.sam.SamToFastq
OUTPUT_PREFIX - Variable in class picard.illumina.CollectIlluminaLaneMetrics
OUTPUT_PREFIX - Variable in class picard.illumina.IlluminaBasecallsToFastq
OUTPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
OUTPUT_TYPE - Variable in class picard.util.ScatterIntervalsByNs
OUTPUT_VALUE - Variable in class picard.util.IntervalListTools
OUTPUT_VCF - Variable in class picard.vcf.GenotypeConcordance
OUTPUT_VCF_CALL_SAMPLE_NAME - Static variable in class picard.vcf.GenotypeConcordance
OUTPUT_VCF_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
OUTPUT_VCF_TRUTH_SAMPLE_NAME - Static variable in class picard.vcf.GenotypeConcordance
OutputArgumentCollection - Interface in picard.cmdline.argumentcollections
  Base interface for an output argument collection.
outputDetailMetricsFile(VariantContext.Type, MetricsFile<GenotypeConcordanceDetailMetrics, ?>, GenotypeConcordanceCounts, String, String, boolean, boolean) - Static method in class picard.vcf.GenotypeConcordance
  Outputs the detailed statistics tables for SNP and Indel match categories.
OutputMapping - Class in picard.illumina.parser
  In multiple locations we need to know what cycles are output, as of now we output all non-skip cycles, but rather than sprinkle this knowledge throughout the parser code, instead OutputMapping provides all the data a client might want about the cycles to be output including what ReadType they are.
OutputMapping(ReadStructure) - Constructor for class picard.illumina.parser.OutputMapping
  Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips Substructure
outputMetrics() - Method in class picard.illumina.ExtractBarcodesProgram
OverlappingErrorMetric - Class in picard.sam.SamErrorMetric
  An error metric for the errors invovling bases in the overlapping region of a read-pair.
OverlappingErrorMetric() - Constructor for class picard.sam.SamErrorMetric.OverlappingErrorMetric
OverlappingErrorMetric(String, long, long, long, long, long) - Constructor for class picard.sam.SamErrorMetric.OverlappingErrorMetric
OverlappingReadsErrorCalculator - Class in picard.sam.SamErrorMetric
  A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
OverlappingReadsErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
OVERLAPS - picard.util.IntervalListTools.Action
OXIDATION_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES
OXIDATION_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  -10 * log10(OXIDATION_ERROR_RATE)
OXOG_METRICS_EXT - Static variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
OXOG_OUT - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG

## P

P_95_GREEN - Static variable in class picard.arrays.illumina.InfiniumVcfFields
P_95_RED - Static variable in class picard.arrays.illumina.InfiniumVcfFields
P95_GREEN - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The 95th Intensity Percentile for the green color channel for this sample
P95_RED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The 95th Intensity Percentile for the red color channel for this sample
PADDING - Variable in class picard.util.BaitDesigner
PADDING - Variable in class picard.util.IntervalListTools
Pair<X extends Comparable<X>,​Y extends Comparable<Y>> - Class in picard.sam.util
  Simple Pair class.
Pair(X, Y) - Constructor for class picard.sam.util.Pair
PAIR - picard.analysis.AlignmentSummaryMetrics.Category
PAIR_ORIENTATION - Variable in class picard.analysis.InsertSizeMetrics
  The pair orientation of the reads in this data category.
PAIRED_END - picard.util.IlluminaUtil.IlluminaAdapterPair
  The following sequences can be found in https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf and are protected by the following copyright notice: Oligonucleotide sequences (c) 2016 Illumina, Inc.
PAIRED_RUN - Variable in class picard.fastq.BamToBfq
PAIRED_RUN - Variable in class picard.illumina.MarkIlluminaAdapters
PAIRED_RUN - Variable in class picard.sam.MergeBamAlignment
  Deprecated.
PairedVariantSubContextIterator - Class in picard.vcf
  An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.
PairedVariantSubContextIterator(Iterator<VariantContext>, String, Iterator<VariantContext>, String, SAMSequenceDictionary) - Constructor for class picard.vcf.PairedVariantSubContextIterator
PairedVariantSubContextIterator.VcfTuple - Class in picard.vcf
  Little class to hold a pair of VariantContexts that are in sync with one another.
PairStratifier(ReadBaseStratification.RecordAndOffsetStratifier<T>, ReadBaseStratification.RecordAndOffsetStratifier<R>) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
PairStratifierFactory(ReadBaseStratification.RecordAndOffsetStratifier<T>, ReadBaseStratification.RecordAndOffsetStratifier<S>, String) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
  A factory for generating "pair" stratifier instances from two stratifiers and a string
PanelMetricsBase - Class in picard.analysis.directed
  A base class for Metrics for targeted panels.
PanelMetricsBase() - Constructor for class picard.analysis.directed.PanelMetricsBase
PARAMETER_DOC - Static variable in class picard.illumina.parser.ReadStructure
ParameterizedFileUtil - Class in picard.illumina.parser
ParameterizedFileUtil(boolean, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
ParameterizedFileUtil(boolean, String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
ParameterizedFileUtil(String, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
parseArgs(String[]) - Method in class picard.cmdline.CommandLineProgram
parseClusterRecordsFromTileMetrics(Collection<File>, Map<Integer, File>, ReadStructure) - Static method in class picard.illumina.parser.TileMetricsUtil
parseDirective(String) - Static method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
  Parses a "Directive" of the form "ERROR,STRATIFIER,STRATIFIER...etc." into a `BaseErrorAggregation` consisting of the appropriate `BaseCalculator` and the `CollectionStratifier` constructed from the various individual stratifiers.
parseInputFile(File, ReadStructure) - Static method in class picard.illumina.ExtractBarcodesProgram
  Parses any one of the following types of files: ExtractIlluminaBarcodes BARCODE_FILE IlluminaBasecallsToFastq MULTIPLEX_PARAMS IlluminaBasecallsToSam LIBRARY_PARAMS This will validate to file format as well as populate a Map of barcodes to metrics.
parseTileMetrics(File, ReadStructure, ValidationStringency) - Static method in class picard.illumina.parser.TileMetricsUtil
  Returns an unmodifiable collection of tile data read from the provided file.
PASS - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  The record in the manifest passes validation and will be used in VCF generation
PASS_FILTER - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
  The "PASS"ing filter String.
PathProvider - Enum in picard.nio
  A class whose purpose is to initialize the various plugins that provide Path support.
PCT_100X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
PCT_10X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
PCT_15X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
PCT_1X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
PCT_20X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
PCT_25X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
PCT_30X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
PCT_40X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
PCT_50X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
PCT_5X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
PCT_60X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
PCT_70X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
PCT_80X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
PCT_90X - Variable in class picard.analysis.WgsMetrics
  The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
PCT_A - Variable in class picard.analysis.BaseDistributionByCycleMetrics
PCT_ADAPTER - Variable in class picard.analysis.AlignmentSummaryMetrics
  The fraction of PF reads that are unaligned or aligned with MQ0 and match to a known adapter sequence right from the start of the read (indication of adapter-dimer pairs).
PCT_AMPLIFIED_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
  The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.
PCT_C - Variable in class picard.analysis.BaseDistributionByCycleMetrics
PCT_CHIMERAS - Variable in class picard.analysis.AlignmentSummaryMetrics
  The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.
PCT_CHIMERAS - Variable in class picard.analysis.JumpingLibraryMetrics
  The number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
PCT_CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Fraction of PF_ALIGNED_BASES that mapped to protein coding regions of genes, CODING_BASES/PF_ALIGNED_BASES
PCT_CONVERTED - Variable in class picard.analysis.RrbsCpgDetailMetrics
  CpG CONVERTED_BASES / CpG TOTAL_BASES (fraction)
PCT_CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
  Fraction of reads corresponding to mRNA transcripts which map to the correct strand of a reference genome = CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS).
PCT_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
  CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
PCT_DBSNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  The fraction of high confidence SNPs in dbSNP
PCT_DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The fraction of passing bi-allelic SNPs in dbSNP
PCT_DBSNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The fraction of passing indels in dbSNP
PCT_EXC_ADAPTER - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of aligned bases in reads that have MQ=0 and whose 5' end consists of adapter sequence.
PCT_EXC_ADAPTER - Variable in class picard.analysis.WgsMetrics
  The fraction of aligned bases that were filtered out because they were in reads with mapping quality 0 and the looked like adapter reads.
PCT_EXC_BASEQ - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of aligned bases that were filtered out because they were of low base quality.
PCT_EXC_BASEQ - Variable in class picard.analysis.WgsMetrics
  The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_BASE_QUALITY).
PCT_EXC_CAPPED - Variable in class picard.analysis.WgsMetrics
  The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP.
PCT_EXC_DUPE - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_DUPE - Variable in class picard.analysis.WgsMetrics
  The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_MAPQ - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
PCT_EXC_MAPQ - Variable in class picard.analysis.WgsMetrics
  The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (lower than MIN_MAPPING_QUALITY).
PCT_EXC_OFF_TARGET - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of aligned bases that were filtered out because they did not align over a target base.
PCT_EXC_OVERLAP - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
PCT_EXC_OVERLAP - Variable in class picard.analysis.WgsMetrics
  The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
PCT_EXC_TOTAL - Variable in class picard.analysis.WgsMetrics
  The total fraction of aligned bases excluded due to all filters.
PCT_EXC_UNPAIRED - Variable in class picard.analysis.WgsMetrics
  The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
PCT_G - Variable in class picard.analysis.BaseDistributionByCycleMetrics
PCT_GQ0_VARIANTS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
  The percentage of variants in a particular sample that have a GQ score of 0.
PCT_HARDCLIP - Variable in class picard.analysis.AlignmentSummaryMetrics
  The fraction of PF bases that are (on primary, aligned reads and) hard-clipped, as a fraction of the PF_ALIGNED_BASES (even though these are not aligned!)
PCT_INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Fraction of PF_ALIGNED_BASES that mapped to intergenic regions of genomic DNA, INTERGENIC_BASES/PF_ALIGNED_BASES
PCT_INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Fraction of PF_ALIGNED_BASES that correspond to gene introns, INTRONIC_BASES/PF_ALIGNED_BASES
PCT_JUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
  The number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
PCT_MATCHES - Variable in class picard.illumina.BarcodeMetric
  The fraction of all reads in the lane that matched to this barcode.
PCT_MIX - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
  The percent mixture (contamination) of the sample for ID
PCT_MRNA_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Sum of bases mapped to regions corresponding to UTRs and coding regions of mRNA transcripts, PCT_UTR_BASES + PCT_CODING_BASES
PCT_N - Variable in class picard.analysis.BaseDistributionByCycleMetrics
PCT_NON_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
  NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
PCT_NONJUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
  The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
PCT_OFF_AMPLICON - Variable in class picard.analysis.directed.TargetedPcrMetrics
  The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED
PCT_OFF_BAIT - Variable in class picard.analysis.directed.HsMetrics
  The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
PCT_OFF_PROBE - Variable in class picard.analysis.directed.TargetMetrics
  The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
PCT_PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).
PCT_PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).
PCT_PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).
PCT_PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The fraction of PF_READS
PCT_PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).
PCT_PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
  The fraction of reads that are PF (PF_READS / TOTAL_READS)
PCT_PF_READS - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of reads passing filter, PF_READS/TOTAL_READS.
PCT_PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
  The percentage of PF reads that aligned to the reference sequence.
PCT_PF_READS_IMPROPER_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
  The fraction of (primary) reads that are *not* "properly" aligned in pairs (as per SAM flag 0x2).
PCT_PF_UQ_READS - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
PCT_PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
PCT_R1_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
  The fraction of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
PCT_R2_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
  The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
PCT_READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
  The fraction of aligned reads whose mate pair was also aligned to the reference.
PCT_RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Fraction of PF_ALIGNED_BASES that mapped to regions encoding ribosomal RNA, RIBOSOMAL_BASES/PF_ALIGNED_BASES
PCT_SELECTED_BASES - Variable in class picard.analysis.directed.HsMetrics
  The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED.
PCT_SELECTED_BASES - Variable in class picard.analysis.directed.TargetMetrics
  The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
PCT_SOFTCLIP - Variable in class picard.analysis.AlignmentSummaryMetrics
  the fraction of PF bases that are on (primary) aligned reads and are soft-clipped, as a fraction of the PF_ALIGNED_BASES (even though these are not aligned!)
PCT_T - Variable in class picard.analysis.BaseDistributionByCycleMetrics
PCT_TARGET_BASES_100000X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 100000X or greater coverage.
PCT_TARGET_BASES_10000X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 10000X or greater coverage.
PCT_TARGET_BASES_1000X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 1000X or greater coverage.
PCT_TARGET_BASES_100X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 100X or greater coverage.
PCT_TARGET_BASES_10X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 10X or greater coverage.
PCT_TARGET_BASES_1X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 1X or greater coverage.
PCT_TARGET_BASES_20X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 20X or greater coverage.
PCT_TARGET_BASES_25000X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 25000X or greater coverage.
PCT_TARGET_BASES_2500X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 2500X or greater coverage.
PCT_TARGET_BASES_250X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 250X or greater coverage.
PCT_TARGET_BASES_2X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 2X or greater coverage.
PCT_TARGET_BASES_30X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 30X or greater coverage.
PCT_TARGET_BASES_40X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 40X or greater coverage.
PCT_TARGET_BASES_50000X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 50000X or greater coverage.
PCT_TARGET_BASES_5000X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 5000X or greater coverage.
PCT_TARGET_BASES_500X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 500X or greater coverage.
PCT_TARGET_BASES_50X - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of all target bases achieving 50X or greater coverage.
PCT_UMI_WITH_N - Variable in class picard.sam.markduplicates.UmiMetrics
  The percentage of reads that contain an UMI that contains at least one N
PCT_USABLE_BASES - Variable in class picard.analysis.RnaSeqMetrics
  The fraction of bases mapping to mRNA divided by the total number of PF bases, (CODING_BASES + UTR_BASES)/PF_BASES.
PCT_USABLE_BASES_ON_BAIT - Variable in class picard.analysis.directed.HsMetrics
  The number of aligned, de-duped, on-bait bases out of the PF bases available.
PCT_USABLE_BASES_ON_TARGET - Variable in class picard.analysis.directed.HsMetrics
  The number of aligned, de-duped, on-target bases out of all of the PF bases available.
PCT_UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Fraction of PF_ALIGNED_BASES that mapped to untranslated regions (UTR) of genes, UTR_BASES/PF_ALIGNED_BASES
PDF_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
PED_FILE - Variable in class picard.arrays.MergePedIntoVcf
PedFile - Class in picard.pedigree
  Represents a .ped file of family information as documented here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml Stores the information in memory as a map of individualId -> Pedigree information for that individual
PedFile(boolean) - Constructor for class picard.pedigree.PedFile
PedFile.PedTrio - Class in picard.pedigree
PedTrio(String, String, String, String, Sex, Number) - Constructor for class picard.pedigree.PedFile.PedTrio
  Constructs a TRIO that cannot be modified after the fact.
peek() - Method in class picard.sam.markduplicates.util.MarkQueue
  Returns the first element in this queue
PER_BASE_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
PER_TARGET_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
PER_TILE_PATTERN_STRING - Static variable in class picard.illumina.parser.ParameterizedFileUtil
PERCENT_DUPLICATION - Variable in class picard.sam.DuplicationMetrics
  The fraction of mapped sequence that is marked as duplicate.
percentageOrNull(Long, Long) - Static method in class picard.util.MathUtil
  Obtains percentage of two Longs
PERFECT_MATCHES - Variable in class picard.illumina.BarcodeMetric
  The number of all reads matching this barcode that matched with 0 errors or no-calls.
permute(double[], RandomDataGenerator) - Static method in class picard.util.MathUtil
  permute the input array randomly (using a RandomDataGenerator)
PerTileBarcodeExtractor(int, File, IlluminaDataProviderFactory, BarcodeExtractor) - Constructor for class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
  Constructor
PerTileFileUtil - Class in picard.illumina.parser
PerTileFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTileFileUtil
PerTileFileUtil(String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.PerTileFileUtil
PerTileOrPerRunFileUtil - Class in picard.illumina.parser
PerTileOrPerRunFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTileOrPerRunFileUtil
PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
  Abstract base class for Parsers that open a single tile file at a time and iterate through them.
PerTileParser(IlluminaFileMap) - Constructor for class picard.illumina.parser.PerTileParser
PerTileParser(IlluminaFileMap, int) - Constructor for class picard.illumina.parser.PerTileParser
PerTilePerCycleFileUtil - Class in picard.illumina.parser
PerTilePerCycleFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTilePerCycleFileUtil
PerUnitGcBiasMetricsCollector(String, String, String) - Constructor for class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
PerUnitInsertSizeMetricsCollector(String, String, String) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
PerUnitMetricCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,​HKEY extends Comparable,​ARGTYPE> - Interface in picard.metrics
  PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.
PerUnitRnaSeqMetricsCollector(String, String, String, Long) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
PerUnitRnaSeqMetricsCollector(RnaSeqMetrics, String, String, String, Long) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
  Derived classes that need to capture some additional metrics can use this ctor to supply a metrics instance that is a subclass of RnaSeqMetrics.
PerUnitTargetMetricCollector(String, Set<Interval>, String, String, String, long, long, long, Map<Interval, Double>, int, int, boolean, boolean) - Constructor for class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
  Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.
PF - picard.illumina.parser.IlluminaDataType
PF - picard.sam.ViewSam.PfStatus
PF_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
  The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.
PF_ALIGNED_BASES - Variable in class picard.analysis.RnaSeqMetrics
  The total number of aligned PF bases.
PF_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The total number of bases in all PF reads
PF_BASES - Variable in class picard.analysis.directed.PanelMetricsBase
  The number of bases in the PF_READS of a SAM or BAM file
PF_BASES - Variable in class picard.analysis.RnaSeqMetrics
  The total number of PF bases including non-aligned reads.
PF_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The total number of passing-filter bases assigned to the index.
PF_BASES_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
  The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
PF_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The total number of PF clusters assigned to the index.
PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The number of non-PF reads in this tile that are deemed empty.
PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The number of non-PF reads in this tile that are deemed "misaligned".
PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The number of non-PF reads in this tile that are deemed multiclonal.
PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The number of non-PF reads in this tile.
PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The number of non-PF reads in this tile that have not been classified.
PF_HQ_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
  The number of bases aligned to the reference sequence in reads that were mapped at high quality.
PF_HQ_ALIGNED_Q20_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
  The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.
PF_HQ_ALIGNED_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
  The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.
PF_HQ_ERROR_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
  The fraction of bases that mismatch the reference in PF HQ aligned reads.
PF_HQ_MEDIAN_MISMATCHES - Variable in class picard.analysis.AlignmentSummaryMetrics
  The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e.
PF_INDEL_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
  The number of insertion and deletion events per 100 aligned bases.
PF_MISMATCH_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
  The rate of bases mismatching the reference for all bases aligned to the reference sequence.
PF_NOISE_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
  The number of PF reads that are marked as noise reads.
PF_NORMALIZED_MATCHES - Variable in class picard.illumina.BarcodeMetric
  The "normalized" matches to each barcode.
PF_ONE_MISMATCH_MATCHES - Variable in class picard.illumina.BarcodeMetric
  The number of PF reads matching this barcode that matched with 1 error or no-call.
PF_PCT_MATCHES - Variable in class picard.illumina.BarcodeMetric
  The fraction of PF reads in the lane that matched to this barcode.
PF_PERFECT_MATCHES - Variable in class picard.illumina.BarcodeMetric
  The number of PF reads matching this barcode that matched with 0 errors or no-calls.
PF_Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The number of bases in PF reads that achieve quality score 20 or higher
PF_Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The sum of quality scores of all bases in PF reads divided by 20
PF_Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The number of bases in PF reads that achieve quality score 30 or higher
PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.BarcodeMetric
  The rate of PF reads matching this barcode to PF reads matching the most prevalent barcode.
PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
  The number of PF reads where PF is defined as passing Illumina's filter.
PF_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The number of reads that are PF - pass filter
PF_READS - Variable in class picard.analysis.directed.PanelMetricsBase
  The number of passing filter reads (PF).
PF_READS - Variable in class picard.illumina.BarcodeMetric
  The number of PF reads matching this barcode (always less than or equal to READS).
PF_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The total number of passing-filter reads assigned to the index.
PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
  The number of PF reads that were aligned to the reference sequence.
PF_READS_IMPROPER_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
  The number of (primary) aligned reads that are **not** "properly" aligned in pairs (as per SAM flag 0x2).
PF_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
PF_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
PF_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
PF_READS_ONLY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
PF_SELECTED_PAIRS - Variable in class picard.analysis.directed.TargetMetricsBase
  Tracks the number of read pairs that we see that are PF (used to calculate library size)
PF_SELECTED_UNIQUE_PAIRS - Variable in class picard.analysis.directed.TargetMetricsBase
  Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
PF_STATUS - Variable in class picard.sam.ViewSam
PF_UNIQUE_READS - Variable in class picard.analysis.directed.PanelMetricsBase
  The number of PF_READS that are not marked as duplicates.
PF_UQ_BASES_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
  The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
  The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.
PFFailDetailedMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
  This ctor is necessary for when reading metrics from file
PFFailDetailedMetric(Integer, int, int, int, int, CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
PFFailSummaryMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  This ctor is necessary for when reading metrics from file
PFFailSummaryMetric(String) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
PG_PROGRAM_NAME - Static variable in class picard.sam.PositionBasedDownsampleSam
pgIdsSeen - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
  The program groups that have been seen during the course of examining the input records.
pgTagArgumentCollection - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
pgTagArgumentCollection - Variable in class picard.sam.MergeBamAlignment
PGTagArgumentCollection - Class in picard.sam.util
  Argument Collection which holds parameters common to classes that want to add PG tags to reads in SAM/BAM files
PGTagArgumentCollection() - Constructor for class picard.sam.util.PGTagArgumentCollection
PHASESET_PREFIX - Static variable in class picard.fingerprint.HaplotypeMap
PHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
  Median phasing value across all tiles in a lane, applied to the first and second template reads
PHASING_BASE - picard.illumina.parser.IlluminaMetricsCode
phasingWeight - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
PhysicalLocation - Interface in picard.sam.util
  Small interface that provides access to the physical location information about a cluster.
PhysicalLocationForMateCigar - Class in picard.sam.markduplicates.util
  Stores the minimal information needed for optical duplicate detection.
PhysicalLocationForMateCigar(PhysicalLocation) - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
PhysicalLocationForMateCigarSet - Class in picard.sam.markduplicates.util
  This stores records that are comparable for detecting optical duplicates.
PhysicalLocationForMateCigarSet() - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
PhysicalLocationInt - Class in picard.sam.util
  Small class that provides access to the physical location information about a cluster.
PhysicalLocationInt() - Constructor for class picard.sam.util.PhysicalLocationInt
PhysicalLocationShort - Class in picard.sam.util
  Small class that provides access to the physical location information about a cluster.
PhysicalLocationShort() - Constructor for class picard.sam.util.PhysicalLocationShort
picard - package picard
picard.analysis - package picard.analysis
picard.analysis.artifacts - package picard.analysis.artifacts
picard.analysis.directed - package picard.analysis.directed
picard.analysis.replicates - package picard.analysis.replicates
picard.annotation - package picard.annotation
picard.arrays - package picard.arrays
picard.arrays.illumina - package picard.arrays.illumina
picard.cmdline - package picard.cmdline
picard.cmdline.argumentcollections - package picard.cmdline.argumentcollections
picard.cmdline.programgroups - package picard.cmdline.programgroups
picard.fastq - package picard.fastq
picard.filter - package picard.filter
picard.fingerprint - package picard.fingerprint
picard.illumina - package picard.illumina
picard.illumina.parser - package picard.illumina.parser
picard.illumina.parser.fakers - package picard.illumina.parser.fakers
picard.illumina.parser.readers - package picard.illumina.parser.readers
picard.illumina.quality - package picard.illumina.quality
picard.metrics - package picard.metrics
picard.nio - package picard.nio
picard.pedigree - package picard.pedigree
picard.reference - package picard.reference
picard.sam - package picard.sam
picard.sam.markduplicates - package picard.sam.markduplicates
picard.sam.markduplicates.util - package picard.sam.markduplicates.util
picard.sam.SamErrorMetric - package picard.sam.SamErrorMetric
picard.sam.util - package picard.sam.util
picard.util - package picard.util
picard.util.help - package picard.util.help
picard.util.IntervalList - package picard.util.IntervalList
picard.vcf - package picard.vcf
picard.vcf.filter - package picard.vcf.filter
picard.vcf.MendelianViolations - package picard.vcf.MendelianViolations
picard.vcf.processor - package picard.vcf.processor
picard.vcf.processor.util - package picard.vcf.processor.util
PicardCommandLine - Class in picard.cmdline
  This is the main class of Picard and is the way of executing individual command line programs.
PicardCommandLine() - Constructor for class picard.cmdline.PicardCommandLine
PicardException - Exception in picard
  Basic Picard runtime exception that, for now, does nothing much
PicardException(String) - Constructor for exception picard.PicardException
PicardException(String, Throwable) - Constructor for exception picard.PicardException
PicardHelpDoclet - Class in picard.util.help
  Custom Barclay-based Javadoc Doclet used for generating Picard help/documentation.
PicardHelpDoclet() - Constructor for class picard.util.help.PicardHelpDoclet
PicardHelpDocWorkUnitHandler - Class in picard.util.help
  The Picard Documentation work unit handler class that is the companion to PicardHelpDoclet.
PicardHelpDocWorkUnitHandler(HelpDoclet) - Constructor for class picard.util.help.PicardHelpDocWorkUnitHandler
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestEndMapqPrimaryAlignmentStrategy
  Primary alignment was filtered out.
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
  Primary alignment was filtered out.
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
pickPrimaryAlignment(HitsForInsert) - Method in interface picard.sam.PrimaryAlignmentSelectionStrategy
  When this method returns, one alignment has been marked as primary according to the implementation's strategy.
pickTranscripts(Map<Gene.Transcript, int[]>) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
  Picks the set of transcripts on which the coverage metrics are to be calculated.
PIPELINE_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The version of the pipeline used for this sample
PIPELINE_VERSION - Variable in class picard.arrays.GtcToVcf
PIPELINE_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
PLATFORM - Variable in class picard.illumina.IlluminaBasecallsToSam
PLATFORM - Variable in class picard.sam.FastqToSam
PLATFORM_MODEL - Variable in class picard.sam.FastqToSam
PLATFORM_UNIT - Variable in class picard.sam.FastqToSam
PLOIDY_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
PLUS - picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
pNormalizeLogProbability(double[]) - Static method in class picard.util.MathUtil
  Takes a complete set of mutually exclusive logPosteriors and converts them to probabilities that sum to 1 with as much fidelity as possible.
pNormalizeVector(double[]) - Static method in class picard.util.MathUtil
  Takes a vector of numbers and converts it to a vector of probabilities that sum to 1 with as much fidelity as possible.
poll(SamRecordTrackingBuffer, SAMFileHeader, OpticalDuplicateFinder, LibraryIdGenerator) - Method in class picard.sam.markduplicates.util.MarkQueue
  The poll method will return the read end that is *not* the duplicate of all comparable read ends that have been seen.
POLYCLONAL - picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
POOL_SIZE - Variable in class picard.util.BaitDesigner
Pos - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
PosFileFaker - Class in picard.illumina.parser.fakers
  Created by jcarey on 3/13/14.
PosFileFaker() - Constructor for class picard.illumina.parser.fakers.PosFileFaker
PosFileReader - Class in picard.illumina.parser.readers
  The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
PosFileReader(File) - Constructor for class picard.illumina.parser.readers.PosFileReader
Position - picard.illumina.parser.IlluminaDataType
POSITION - Variable in class picard.analysis.FingerprintingDetailMetrics
  The position of the SNP on the chromosome.
POSITION - Variable in class picard.analysis.RrbsCpgDetailMetrics
  Position within the sequence of the CpG site
PositionBasedDownsampleSam - Class in picard.sam
  Summary
PositionBasedDownsampleSam() - Constructor for class picard.sam.PositionBasedDownsampleSam
PositionInfo(float, float, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
POSITIVE - picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
PosParser - Class in picard.illumina.parser
  PosParser parses multiple files formatted as one of the three file formats that contain position information only (pos, locs, and clocs).
PosParser(IlluminaFileMap, int, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
PosParser(IlluminaFileMap, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
postDiNucleotideStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies a base onto the reference base that it covers and the following base, possibly reverse complemented if the read has been reversed by the aligner.
Ppv(GenotypeConcordanceScheme, GenotypeConcordanceStates.CallState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
  Returns the PPV defined by the scheme across the subset of call states.
PRE_ADAPTER_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
PRE_ADAPTER_IN - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
PRE_ADAPTER_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
PRE_INDEL_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
PreAdapterDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
PreAdapterSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
PredicateFilterDecoratingClosableIterator<T> - Class in picard.vcf.processor.util
  Performs on-the-fly filtering of the provided `VariantContext` `Iterator` such that only variants that satisfy all predicates are emitted.
PredicateFilterDecoratingClosableIterator(CloseableIterator<T>, Collection<Predicate<T>>) - Constructor for class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
PREDICTED_INSERT_SIZE - Variable in class picard.sam.FastqToSam
preDiNucleotideStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies a base onto the reference base that it covers and the preceding base, possibly reverse complemented if the read has been reversed by the aligner.
PREPHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
  Median pre-phasing value across all tiles in a lane, applied to the first and second template reads
PREPHASING_BASE - picard.illumina.parser.IlluminaMetricsCode
prephasingWeight - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
preprocessIntervalList(IntervalList) - Method in interface picard.util.IntervalList.IntervalListScatterer
  A function that will be called on an IntervalList prior to splitting it into sub-lists, and is a point where implementations can chose to impose some conditions on the lists, for example, merging overlapping/abutting intervals, removing duplicates, etc.
preprocessIntervalList(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererWithSubdivision
previousReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies bases into the previous (uppercase) base as it was read from the sequencer (i.e.
PRIMARY_ALIGNMENT_STRATEGY - Variable in class picard.sam.MergeBamAlignment
PRIMARY_MAPPED_ONLY - picard.sam.markduplicates.CheckDuplicateMarking.Mode
PRIMARY_ONLY - picard.sam.markduplicates.CheckDuplicateMarking.Mode
PRIMARY_PROPER_PAIR_ONLY - picard.sam.markduplicates.CheckDuplicateMarking.Mode
PrimaryAlignmentKey - Class in picard.sam.util
  It is useful to define a key such that the key will occur at most once among the primary alignments in a given file (assuming the file is valid).
PrimaryAlignmentKey(SAMRecord) - Constructor for class picard.sam.util.PrimaryAlignmentKey
PrimaryAlignmentSelectionStrategy - Interface in picard.sam
  Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate.
printUnknown(Set<Class<?>>, String) - Static method in class picard.cmdline.PicardCommandLine
  When a command does not match any known command, searches for similar commands, using the same method as GIT
PRIOR_ERROR - Static variable in class picard.sam.SamErrorMetric.ErrorMetric
PRIOR_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
PRO_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.
PRO_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.
PROB_EXPLICIT_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
PROBABILITY - Variable in class picard.sam.DownsampleSam
PROBABILITY - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
PROBE_A - Static variable in class picard.arrays.illumina.InfiniumVcfFields
PROBE_B - Static variable in class picard.arrays.illumina.InfiniumVcfFields
PROBE_SEQUENCE_MISMATCH - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Probe sequence not found in reference.
PROBE_SEQUENCE_STRAND_INVALID - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Deprecated.
  - but used in existing extended manifest files.
PROBE_SET - Variable in class picard.analysis.directed.TargetMetrics
  The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
PROBE_TERRITORY - Variable in class picard.analysis.directed.TargetMetrics
  The number of unique bases covered by the intervals of all probes in the probe set
process() - Method in class picard.vcf.processor.VariantProcessor
PROCESS_SINGLE_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
processAllCommandLinePrograms(List<String>, BiConsumer<Class<CommandLineProgram>, CommandLineProgramProperties>) - Static method in class picard.cmdline.PicardCommandLine
  Process each `CommandLineProgram`-derived class given a list of packages.
processDeletionLocus(SamLocusIterator.RecordAndOffset, SamLocusIterator.LocusInfo) - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
  Checks if the same record has been seen at the previous locus already, thereby determining whether or not a deletion has already been processed.
processFile() - Method in interface picard.analysis.WgsMetricsProcessor
  Method processes the input data and accumulates result data
processFile() - Method in class picard.analysis.WgsMetricsProcessorImpl
  Method gets the data from iterator for each locus and processes it with the help of collector.
processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.BasecallsConverter
  Abstract method for processing tiles of data and outputting records for each barcode.
processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.SortedBasecallsConverter
  Set up tile processing and record writing threads for this converter.
processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.UnsortedBasecallsConverter
  Set up tile processing and record writing threads for this converter.
product(double...) - Method in class picard.util.MathUtil.LogMath
  Computes the sum of the provided log values.
PROGRAM - Variable in class picard.analysis.CollectMultipleMetrics
PROGRAM_GROUP - Variable in class picard.sam.FastqToSam
PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.MergeBamAlignment
PROGRAM_GROUP_NAME - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_NAME - Variable in class picard.sam.MergeBamAlignment
PROGRAM_GROUP_VERSION - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
PROGRAM_GROUP_VERSION - Variable in class picard.sam.MergeBamAlignment
PROGRAM_RECORD_ID - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
PROGRAM_RECORD_ID - Variable in class picard.sam.MergeBamAlignment
PROGRAM_RECORD_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
PROGRESS_STEP_INTERVAL - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
PROGRESS_STEP_INTERVAL - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
promote(int[]) - Static method in class picard.util.MathUtil
  "Promotes" an int[] into a double array with the same values (or as close as precision allows).
PROPER - picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
PropertyUtils - Class in picard.util
  Utility for loading properties files from resources.
PropertyUtils() - Constructor for class picard.util.PropertyUtils
proportionsAboveThresholds(List<ArrayList<Integer>>, List<Double>) - Static method in class picard.analysis.TheoreticalSensitivity
PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Variable in class picard.illumina.MarkIlluminaAdapters
pSameAlleleWhenMismatchingUmi - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  When the UMIs mismatch, we expect about the same number of different alleles as the same (assuming that different UMI implies biological duplicate) thus, this value should be near 0.5
pSameUmiInIndependentBiDup - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  When the alleles are different, we know that this is a biological duplication, thus we expect nearly all the UMIs to be different (allowing for equality due to chance).
PSEUDO_AUTOSOMAL_REGIONS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
put(int, String, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
put(int, String, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
put(int, String, ReadEndsForMarkDuplicates) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
  Store the element in the map with the given key.
PVAL - Variable in class picard.arrays.BafRegressMetrics
  The p-value of the estimate

## Q

Q_SCORE - Variable in class picard.sam.SamErrorMetric.BaseErrorMetric
  The (phred) rate of bases that disagree with the reference
Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The number of bases in all reads that achieve quality score 20 or higher
Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The sum of quality scores of all bases divided by 20
Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The number of bases in all reads that achieve quality score 30 or higher
QdFilter - Class in picard.vcf.filter
  Filters out sites that have a QD annotation applied to them and where the QD value is lower than a lower limit.
QdFilter(double) - Constructor for class picard.vcf.filter.QdFilter
QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
qualities - Variable in class picard.illumina.parser.BclData
qualities - Variable in class picard.util.BarcodeEditDistanceQuery
  list of quality scores for reads
QUALITY - Variable in class picard.sam.SamToFastq
QUALITY_FORMAT - Variable in class picard.sam.FastqToSam
QUALITY_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
QualityScoreDistribution - Class in picard.analysis
  Charts quality score distribution within a BAM file.
QualityScoreDistribution - picard.analysis.CollectMultipleMetrics.Program
QualityScoreDistribution() - Constructor for class picard.analysis.QualityScoreDistribution
QualityScores - picard.illumina.parser.IlluminaDataType
QualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
QualityYieldMetricsCollector(boolean, boolean, boolean) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
QuerySortedReadPairIteratorUtil - Class in picard.util
  A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs
QuerySortedReadPairIteratorUtil() - Constructor for class picard.util.QuerySortedReadPairIteratorUtil
QuerySortedReadPairIteratorUtil.ReadPair - Class in picard.util
QUIET - Variable in class picard.cmdline.CommandLineProgram
QUINTILE_1 - picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
QUINTILE_2 - picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
QUINTILE_3 - picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
QUINTILE_4 - picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
QUINTILE_5 - picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin

## R

R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
R - Static variable in class picard.sam.markduplicates.util.ReadEnds
R1R2 - picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
RANDOM_SEED - Variable in class picard.sam.DownsampleSam
RANDOM_SEED_TAG - Static variable in class picard.sam.DownsampleSam
randomSublist(List<T>, int, Random) - Static method in class picard.util.MathUtil
  A small utility function to choose n random elements (un-shuffled) from a list
Range - Class in picard.illumina.parser
  While structurally identical to CompositeIndex, this class is maintained as it makes code more readable when the two are used together (see QSeqParser)
Range(int, int) - Constructor for class picard.illumina.parser.Range
rapidParseInt(String) - Static method in class picard.sam.util.ReadNameParser
  Very specialized method to rapidly parse a sequence of digits from a String up until the first non-digit character.
RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.BarcodeMetric
  The rate of all reads matching this barcode to all reads matching the most prevalent barcode.
RawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
RawWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
rawXIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
rawYIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
RE_REVERSE - Variable in class picard.sam.SamToFastq
read(byte[], int, int) - Method in class picard.util.CircularByteBuffer
  Read bytes from the buffer into the supplied array.
READ_CHUNK_SIZE - Variable in class picard.fastq.BamToBfq
READ_END - Variable in class picard.analysis.BaseDistributionByCycleMetrics
READ_GROUP - picard.analysis.MetricAccumulationLevel
READ_GROUP - Variable in class picard.analysis.FingerprintingDetailMetrics
  The sequencing read group from which sequence data was fingerprinted.
READ_GROUP - Variable in class picard.analysis.FingerprintingSummaryMetrics
  The read group from which sequence data was drawn for comparison.
READ_GROUP - Variable in class picard.metrics.MultilevelMetrics
  The read group to which these metrics apply.
READ_GROUP_ID - Variable in class picard.illumina.IlluminaBasecallsToSam
READ_GROUP_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
READ_GROUP_NAME - Variable in class picard.sam.FastqToSam
READ_LENGTH - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The average read length of all the reads (will be fixed for a lane)
READ_LENGTH - Variable in class picard.analysis.CollectWgsMetrics
READ_LIST_FILE - Variable in class picard.sam.FilterSamReads
READ_NAME_FORMAT - Variable in class picard.illumina.IlluminaBasecallsToFastq
READ_NAME_PREFIX - Variable in class picard.fastq.BamToBfq
READ_NAME_REGEX - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
READ_NAME_REGEX - Variable in class picard.sam.PositionBasedDownsampleSam
READ_ONE_BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
READ_ONE_BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
READ_PAIR_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
  The number of read pairs that were marked as duplicates.
READ_PAIR_OPTICAL_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
  The number of read pairs duplicates that were caused by optical duplication.
READ_PAIRS - Variable in class picard.analysis.InsertSizeMetrics
  The total number of read pairs that were examined in the entire distribution.
READ_PAIRS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
  The number of mapped read pairs examined.
READ_STARTS - Variable in class picard.analysis.GcBiasDetailMetrics
  The number of reads whose start position is at the start of a window of this GC.
READ_STRUCTURE - Variable in class picard.illumina.CheckIlluminaDirectory
READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaLaneMetrics
READ_STRUCTURE - Variable in class picard.illumina.ExtractBarcodesProgram
READ_TWO_BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
READ_TWO_BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
read1 - Variable in class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
READ1_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
READ1_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
READ1_TRIM - Variable in class picard.sam.MergeBamAlignment
READ1_TRIM - Variable in class picard.sam.SamToFastq
read1Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
read1IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
read1ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
read2 - Variable in class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
READ2_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
READ2_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
READ2_TRIM - Variable in class picard.sam.MergeBamAlignment
READ2_TRIM - Variable in class picard.sam.SamToFastq
read2Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
read2IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
read2ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
ReadBaseStratification - Class in picard.sam.SamErrorMetric
  Classes, methods, and enums that deal with the stratification of read bases and reference information.
ReadBaseStratification() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification
ReadBaseStratification.BinnedReadCycleStratifier - Class in picard.sam.SamErrorMetric
  Stratifies into quintiles of read cycle.
ReadBaseStratification.CigarOperatorsInReadStratifier - Class in picard.sam.SamErrorMetric
  Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.
ReadBaseStratification.CollectionStratifier - Class in picard.sam.SamErrorMetric
  A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.
ReadBaseStratification.Consensus - Enum in picard.sam.SamErrorMetric
  Types of consensus reads as determined by the number of duplicates used from first and second strands.
ReadBaseStratification.ConsensusStratifier - Class in picard.sam.SamErrorMetric
  Stratify by tags used during duplex and single index consensus calling.
ReadBaseStratification.CycleBin - Enum in picard.sam.SamErrorMetric
  An enum designed to hold a binned version of any probability-like number (between 0 and 1) in quintiles
ReadBaseStratification.FlowCellTileStratifier - Class in picard.sam.SamErrorMetric
  Stratifies base into their read's tile which is parsed from the read-name.
ReadBaseStratification.FlowCellXStratifier - Class in picard.sam.SamErrorMetric
  Stratifies base into their read's X coordinate which is parsed from the read-name.
ReadBaseStratification.FlowCellYStratifier - Class in picard.sam.SamErrorMetric
  Stratifies base into their read's Y coordinate which is parsed from the read-name.
ReadBaseStratification.GCContentStratifier - Class in picard.sam.SamErrorMetric
  A stratifier that uses GC (of the read) to stratify.
ReadBaseStratification.IndelLengthStratifier - Class in picard.sam.SamErrorMetric
  Stratifies according to the length of an insertion or deletion.
ReadBaseStratification.IndelsInReadStratifier - Class in picard.sam.SamErrorMetric
  Stratifies according to the number of indel bases (from CIGAR string) that the read has.
ReadBaseStratification.LongShortHomopolymer - Enum in picard.sam.SamErrorMetric
ReadBaseStratification.LongShortHomopolymerStratifier - Class in picard.sam.SamErrorMetric
  Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and whether the length is "long" or not).
ReadBaseStratification.MismatchesInReadStratifier - Class in picard.sam.SamErrorMetric
  Stratifies according to the overall mismatches (from `SAMTag.NM`) that the read has against the reference, NOT including the current base.
ReadBaseStratification.NsInReadStratifier - Class in picard.sam.SamErrorMetric
  Stratify by the number of Ns found in the read.
ReadBaseStratification.PairOrientation - Enum in picard.sam.SamErrorMetric
  An enum for holding a reads read-pair's Orientation (i.e.
ReadBaseStratification.PairStratifier<T extends Comparable<T>,​R extends Comparable<R>> - Class in picard.sam.SamErrorMetric
  A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.
ReadBaseStratification.ProperPaired - Enum in picard.sam.SamErrorMetric
  An enum to hold information about the "properness" of a read pair
ReadBaseStratification.ReadDirection - Enum in picard.sam.SamErrorMetric
  An enum for holding the direction for a read (positive strand or negative strand
ReadBaseStratification.ReadOrdinality - Enum in picard.sam.SamErrorMetric
  An enum to hold the ordinality of a read
ReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>> - Interface in picard.sam.SamErrorMetric
  The main interface for a stratifier.
ReadClassifier(ReadData) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier
  Heart of CLP.
readCount - Variable in class picard.analysis.directed.TargetMetricsCollector.Coverage
ReadData - Class in picard.illumina.parser
  Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
ReadData() - Constructor for class picard.illumina.parser.ReadData
ReadData(ReadType) - Constructor for class picard.illumina.parser.ReadData
ReadDataManipulationProgramGroup - Class in picard.cmdline.programgroups
  Tools that manipulate read data in SAM, BAM or CRAM format
ReadDataManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
ReadDescriptor - Class in picard.illumina.parser
  Represents one set of cycles in an ReadStructure (e.g.
ReadDescriptor(int, ReadType) - Constructor for class picard.illumina.parser.ReadDescriptor
readDirectionStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies bases into their read's Direction (i.e.
ReadEnds - Class in picard.sam.markduplicates.util
  Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
ReadEnds() - Constructor for class picard.sam.markduplicates.util.ReadEnds
ReadEndsForMarkDuplicates - Class in picard.sam.markduplicates.util
  Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
ReadEndsForMarkDuplicates() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
ReadEndsForMarkDuplicatesCodec - Class in picard.sam.markduplicates.util
  Codec for ReadEnds that just outputs the primitive fields and reads them back.
ReadEndsForMarkDuplicatesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
ReadEndsForMarkDuplicatesMap - Interface in picard.sam.markduplicates.util
  Interface for storing and retrieving ReadEnds objects.
ReadEndsForMarkDuplicatesWithBarcodes - Class in picard.sam.markduplicates.util
ReadEndsForMarkDuplicatesWithBarcodes() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodesCodec - Class in picard.sam.markduplicates.util
  Created by nhomer on 9/13/15.
ReadEndsForMarkDuplicatesWithBarcodesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
ReadEndsForMateCigar - Class in picard.sam.markduplicates.util
  A class to store individual records for MarkDuplicatesWithMateCigar.
ReadEndsForMateCigar(SAMFileHeader, SamRecordWithOrdinal, OpticalDuplicateFinder, short) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
  Builds a read ends object that represents a single read.
ReadEndsForMateCigar(ReadEndsForMateCigar, SamRecordWithOrdinal) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
  Creates a shallow copy from the "other"
readGroup - Variable in class picard.sam.markduplicates.util.ReadEnds
READGROUP - picard.fingerprint.CrosscheckMetric.DataType
READGROUP_ID_REGEX - Static variable in class picard.sam.AddOrReplaceReadGroups
readgroupStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies to the readgroup id of the read.
readHeader(int) - Method in class picard.illumina.parser.readers.CbclReader
  Reads the Cbcl header and sets up the data streams.
readIndexInFile - Variable in class picard.sam.util.RepresentativeReadIndexer
readLaneTiles(File, ReadStructure, ValidationStringency, int) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
  Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
readLengths - Variable in class picard.illumina.parser.ReadStructure
ReadNameEncoder - Interface in picard.fastq
ReadNameParser - Class in picard.sam.util
  Provides access to the physical location information about a cluster.
ReadNameParser() - Constructor for class picard.sam.util.ReadNameParser
  Creates are read name parser using the default read name regex and optical duplicate distance.
ReadNameParser(String) - Constructor for class picard.sam.util.ReadNameParser
  Creates are read name parser using the given read name regex.
ReadNameParser(String, Log) - Constructor for class picard.sam.util.ReadNameParser
  Creates are read name parser using the given read name regex.
readNameRegex - Variable in class picard.sam.util.ReadNameParser
readNextLine() - Method in class picard.util.AbstractInputParser
readNextLine() - Method in class picard.util.BasicInputParser
  Workhorse method that reads the next line from the underlying reader
readOneBarcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
readOrdinalityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies bases into their read's Ordinality (i.e.
readOrientationStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies bases into their read-pair's Orientation (i.e.
ReadPair() - Constructor for class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
readPairednessStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies bases into their read's Proper-pairedness
READS - Variable in class picard.illumina.BarcodeMetric
  The total number of reads matching the barcode.
READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The total number of reads examined
READS_ALIGNED - Variable in class picard.analysis.RrbsSummaryMetrics
  Number of mapped reads processed
READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
  The number of aligned reads whose mate pair was also aligned to the reference.
READS_IGNORED_MISMATCHES - Variable in class picard.analysis.RrbsSummaryMetrics
  Number of reads discarded for exceeding the mismatch threshold
READS_IGNORED_SHORT - Variable in class picard.analysis.RrbsSummaryMetrics
  Number of reads discarded due to being too short
READS_TO_ALIGN - Variable in class picard.fastq.BamToBfq
READS_USED - Variable in class picard.analysis.GcBiasDetailMetrics
  This option is used to mark including or excluding duplicates.
READS_USED - Variable in class picard.analysis.GcBiasSummaryMetrics
  This option is used to mark including or excluding duplicates.
READS_WITH_NO_CPG - Variable in class picard.analysis.RrbsSummaryMetrics
  Number of reads discarded for having no CpG sites
ReadStructure - Class in picard.illumina.parser
  Describes the intended logical output structure of clusters of an Illumina run.
ReadStructure(String) - Constructor for class picard.illumina.parser.ReadStructure
  Converts readStructureString into a List<ReadDescriptor> and calls the primary constructor using this List as it's argument.
ReadStructure(List<ReadDescriptor>) - Constructor for class picard.illumina.parser.ReadStructure
  Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.
ReadStructure.Substructure - Class in picard.illumina.parser
  Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous in the containing ReadStructure but they ARE in the order they appear in the containing ReadStructure
readSubsequence - Variable in class picard.util.BarcodeEditDistanceQuery
  list of barcode reads
readTwoBarcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
ReadType - Enum in picard.illumina.parser
  A read type describes a stretch of cycles in an ReadStructure (e.g.
reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingAdapterFilter
reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingDuplicateFilter
reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingFilter
  Return true if we are to filter this record out, false otherwise.
reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingMapQFilter
reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingPairedFilter
Record(int, int, Float, Float, float, IlluminaGenotype) - Constructor for class picard.arrays.illumina.IlluminaAdpcFileWriter.Record
RECORDS_ONLY - Variable in class picard.sam.ViewSam
RECOVER_SWAPPED_REF_ALT - Variable in class picard.vcf.LiftoverVcf
RED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
  The red intensity value for the control.
ref() - Method in enum picard.analysis.artifacts.Transition
  Gets the reference for the transition.
REF_BASE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
  The reference base (or it's complement).
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The (upper-case) original base on the reference strand.
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The (upper-case) original base on the reference strand.
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The (upper-case) original base on the reference strand.
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The (upper-case) original base on the reference strand.
REF_COUNT - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
  The number of reference bases observed.
REF_FLAT - Variable in class picard.analysis.CollectMultipleMetrics
REF_FLAT - Variable in class picard.analysis.CollectRnaSeqMetrics
REF_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The number of reference alleles observed as C in read 1 and G in read 2.
REF_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The number of reference alleles observed as G in read 1 and C in read 2.
REF_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
REF_TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The total number of reference alleles observed
REFERENCE - Variable in class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
REFERENCE - Variable in class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
REFERENCE - Variable in class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
REFERENCE_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
REFERENCE_SEQUENCE - Variable in class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
REFERENCE_SEQUENCE - Variable in class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
REFERENCE_SEQUENCE - Variable in class picard.cmdline.CommandLineProgram
REFERENCE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
ReferenceArgumentCollection - Interface in picard.cmdline.argumentcollections
  Base interface for a reference argument collection.
referenceBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies a base onto the reference base that it covers, possibly reverse complemented if the read has been reversed by the aligner.
referenceFasta - Variable in class picard.sam.AbstractAlignmentMerger
ReferenceProgramGroup - Class in picard.cmdline.programgroups
  Tools that analyze and manipulate FASTA format references
ReferenceProgramGroup() - Constructor for class picard.cmdline.programgroups.ReferenceProgramGroup
referenceSequence - Variable in class picard.cmdline.CommandLineProgram
RefFlatReader - Class in picard.annotation
  Loads gene annotations from a refFlat file into an OverlapDetector<Gene>.
RefFlatReader.RefFlatColumns - Enum in picard.annotation
ReflectionUtil - Class in picard.util
  Class which contains utility functions that use reflection.
ReflectionUtil() - Constructor for class picard.util.ReflectionUtil
reflectiveCopy(TargetMetrics, MT, String[], String[]) - Static method in class picard.analysis.directed.TargetMetricsCollector
  Since the targeted metrics (HsMetrics, TargetedPcrMetrics,...) share many of the same values as TargetMetrics, this copy will copy all public attributes in targetMetrics to the outputMetrics' attributes of the same name.
REJECT - Variable in class picard.util.LiftOverIntervalList
REJECT - Variable in class picard.vcf.LiftoverVcf
remove() - Method in class picard.illumina.parser.MultiTileParser
remove() - Method in class picard.illumina.parser.PerTileParser
remove() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
remove() - Method in class picard.illumina.parser.readers.BarcodeFileReader
remove() - Method in class picard.illumina.parser.readers.BclReader
remove() - Method in class picard.illumina.parser.readers.FilterFileReader
remove() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
remove() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
remove() - Method in class picard.util.AsyncIterator
remove() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
remove() - Method in class picard.vcf.ByIntervalListVariantContextIterator
remove() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
remove() - Method in class picard.vcf.PairedVariantSubContextIterator
remove() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
remove(int, String) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
remove(int, String) - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
remove(int, String) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
  Remove element with given key from the map.
remove(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
  Removes the end from this set, if present
REMOVE_ALIGNMENT_INFORMATION - Variable in class picard.sam.RevertSam
REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.PositionBasedDownsampleSam
REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.RevertSam
REMOVE_DUPLICATES - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
REMOVE_SEQUENCING_DUPLICATES - Variable in class picard.sam.markduplicates.MarkDuplicates
removeIncompleteTrios() - Method in class picard.pedigree.PedFile
  Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
removeLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
RenameSampleInVcf - Class in picard.vcf
  Renames a sample within a VCF or BCF.
RenameSampleInVcf() - Constructor for class picard.vcf.RenameSampleInVcf
renderPhasingMetricsFilesFromBasecallingDirectory(File) - Static method in class picard.illumina.parser.TileMetricsUtil
REORDER_INPUT_BY_FIRST_VARIANT - Variable in class picard.vcf.GatherVcfs
ReorderSam - Class in picard.sam
  Reorders a SAM/BAM input file according to the order of contigs in a second reference file.
ReorderSam() - Constructor for class picard.sam.ReorderSam
REPEAT_TOLERANCE - Variable in class picard.util.BaitDesigner
replace(ReadEndsForMateCigar, ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
  Replaces a given end with the other end.
ReplaceSamHeader - Class in picard.sam
ReplaceSamHeader() - Constructor for class picard.sam.ReplaceSamHeader
replicationRateFromReplicateSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  An estimate of the duplication rate that is based on the duplicate sets we observed.
REPORT_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
REPORTED_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The sex, as reported by the collaborator
RepresentativeReadIndexer - Class in picard.sam.util
  Little struct-like class to hold a record index, the index of the corresponding representative read, and duplicate set size information.
RepresentativeReadIndexer() - Constructor for class picard.sam.util.RepresentativeReadIndexer
RepresentativeReadIndexerCodec - Class in picard.sam.markduplicates.util
  Codec for read names and integers that outputs the primitive fields and reads them back.
RepresentativeReadIndexerCodec() - Constructor for class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
representativeReadIndexInFile - Variable in class picard.sam.util.RepresentativeReadIndexer
REQUIRE_INDEX - Variable in class picard.vcf.VcfFormatConverter
RequiredOutputArgumentCollection - Class in picard.cmdline.argumentcollections
RequiredOutputArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
RequiredOutputArgumentCollection(File) - Constructor for class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
RequiredReferenceArgumentCollection - Class in picard.cmdline.argumentcollections
  Argument collection for references that are required (and not common).
RequiredReferenceArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
requiresReference() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
requiresReference() - Method in class picard.analysis.CollectOxoGMetrics
requiresReference() - Method in class picard.analysis.CollectWgsMetrics
requiresReference() - Method in class picard.arrays.GtcToVcf
requiresReference() - Method in class picard.cmdline.CommandLineProgram
requiresReference() - Method in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
requiresReference() - Method in class picard.fingerprint.ExtractFingerprint
requiresReference() - Method in class picard.fingerprint.IdentifyContaminant
requiresReference() - Method in class picard.reference.ExtractSequences
requiresReference() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
requiresReference() - Method in class picard.sam.MergeBamAlignment
requiresReference() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
requiresReference() - Method in class picard.sam.SetNmMdAndUqTags
requiresReference() - Method in class picard.util.BaitDesigner
resetRefSeqFileWalker() - Method in class picard.sam.AbstractAlignmentMerger
RESTORE_HARDCLIPS - Variable in class picard.sam.RevertSam
RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertSam
result() - Method in class picard.vcf.CallingMetricAccumulator
result() - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
RESULT - Variable in class picard.fingerprint.CrosscheckMetric
REV_COMPED_ALLELES - Static variable in class picard.util.LiftoverUtils
REV_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.
REV_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.
REV_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).
reverseComplementVariantContext(VariantContext, Interval, ReferenceSequence) - Static method in class picard.util.LiftoverUtils
RevertOriginalBaseQualitiesAndAddMateCigar - Class in picard.sam
  This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped SAM, BAM or CRAM files.
RevertOriginalBaseQualitiesAndAddMateCigar() - Constructor for class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile - Enum in picard.sam
  Used as a return for the canSkipSAMFile function.
RevertSam - Class in picard.sam
  Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.
RevertSam() - Constructor for class picard.sam.RevertSam
RevertSam.FileType - Enum in picard.sam
revertSamRecord(SAMRecord) - Method in class picard.sam.RevertSam
  Takes an individual SAMRecord and applies the set of changes/reversions to it that have been requested by program level options.
reviseAndConditionallyLogQuality(byte) - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
  Accepts a quality read from a BCL file and (1) returns a 1 if the value was 0 and (2) makes a note of the provided quality if it is low.
RExecutor - Class in picard.util
  Util class for executing R scripts.
RExecutor() - Constructor for class picard.util.RExecutor
RF - Static variable in class picard.sam.markduplicates.util.ReadEnds
RG_TAG - Variable in class picard.sam.SamToFastq
RGCN - Variable in class picard.sam.AddOrReplaceReadGroups
RGDS - Variable in class picard.sam.AddOrReplaceReadGroups
RGDT - Variable in class picard.sam.AddOrReplaceReadGroups
RGFO - Variable in class picard.sam.AddOrReplaceReadGroups
RGID - Variable in class picard.sam.AddOrReplaceReadGroups
RGKS - Variable in class picard.sam.AddOrReplaceReadGroups
RGLB - Variable in class picard.sam.AddOrReplaceReadGroups
RGPG - Variable in class picard.sam.AddOrReplaceReadGroups
RGPI - Variable in class picard.sam.AddOrReplaceReadGroups
RGPL - Variable in class picard.sam.AddOrReplaceReadGroups
RGPM - Variable in class picard.sam.AddOrReplaceReadGroups
RGPU - Variable in class picard.sam.AddOrReplaceReadGroups
RGSM - Variable in class picard.sam.AddOrReplaceReadGroups
RIBOSOMAL - picard.annotation.LocusFunction
RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Number of bases in primary alignments that align to ribosomal sequence.
RIBOSOMAL_INTERVALS - Variable in class picard.analysis.CollectRnaSeqMetrics
ribosomalInitialValue - Variable in class picard.analysis.directed.RnaSeqMetricsCollector
RIGHT_FILE - Variable in class picard.fingerprint.CrosscheckMetric
RIGHT_FILE - Variable in class picard.sam.SamComparisonMetric
  Right file used in comparison
RIGHT_GROUP_VALUE - Variable in class picard.fingerprint.CrosscheckMetric
RIGHT_LANE - Variable in class picard.fingerprint.CrosscheckMetric
RIGHT_LIBRARY - Variable in class picard.fingerprint.CrosscheckMetric
RIGHT_MOLECULAR_BARCODE_SEQUENCE - Variable in class picard.fingerprint.CrosscheckMetric
RIGHT_PRIMER - Variable in class picard.util.BaitDesigner
RIGHT_RUN_BARCODE - Variable in class picard.fingerprint.CrosscheckMetric
RIGHT_SAMPLE - Variable in class picard.fingerprint.CrosscheckMetric
rightVariantContext - Variable in class picard.vcf.PairedVariantSubContextIterator.VcfTuple
RIlmn - Variable in class picard.arrays.illumina.InfiniumGTCRecord
RnaSeqMetrics - Class in picard.analysis
  Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
RnaSeqMetrics - picard.analysis.CollectMultipleMetrics.Program
RnaSeqMetrics() - Constructor for class picard.analysis.RnaSeqMetrics
RnaSeqMetricsCollector - Class in picard.analysis.directed
RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector
RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean, int) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector
RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector - Class in picard.analysis.directed
RnaSeqMetricsCollector.StrandSpecificity - Enum in picard.analysis.directed
round(double...) - Static method in class picard.util.MathUtil
  returns a long array containing the rounded values of the input array
round(double, int) - Static method in class picard.util.MathUtil
  Round off the value to the specified precision.
RR - Static variable in class picard.sam.markduplicates.util.ReadEnds
RrbsCpgDetailMetrics - Class in picard.analysis
  Holds information about CpG sites encountered for RRBS processing QC
RrbsCpgDetailMetrics() - Constructor for class picard.analysis.RrbsCpgDetailMetrics
RrbsMetricsCollector - Class in picard.analysis
RrbsMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, int, int, int, double) - Constructor for class picard.analysis.RrbsMetricsCollector
RrbsSummaryMetrics - Class in picard.analysis
  Holds summary statistics from RRBS processing QC
RrbsSummaryMetrics() - Constructor for class picard.analysis.RrbsSummaryMetrics
RRNA_FRAGMENT_PERCENTAGE - Variable in class picard.analysis.CollectRnaSeqMetrics
RS_ID - Static variable in class picard.arrays.illumina.InfiniumVcfFields
rsNames - Variable in class picard.arrays.illumina.InfiniumEGTFile
rsNameToIndex - Variable in class picard.arrays.illumina.InfiniumEGTFile
run() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
  run method which extracts barcodes and accumulates metrics for an entire tile
run() - Method in class picard.Test
RUN_BARCODE - Variable in class picard.fastq.BamToBfq
RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToSam
RUN_DATE - Variable in class picard.sam.FastqToSam
RUN_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
RUN_START_DATE - Variable in class picard.illumina.IlluminaBasecallsToSam

## S

S - picard.illumina.parser.ReadType
S_LOCS_FILE - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
sam - picard.sam.RevertSam.FileType
SAM_FILES - Variable in class picard.sam.CompareSAMs
SamAlignmentMerger - Class in picard.sam
  Class that takes in a set of alignment information in SAM format and merges it with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, int) - Constructor for class picard.sam.SamAlignmentMerger
  Constructor with a default value for unmappingReadStrategy
SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, int, AbstractAlignmentMerger.UnmappingReadStrategy, List<String>) - Constructor for class picard.sam.SamAlignmentMerger
  Constructor
SamComparison - Class in picard.sam.util
  Compare two SAM/BAM files.
SamComparison(SamReader, SamReader) - Constructor for class picard.sam.util.SamComparison
  Note: the caller must make sure the SamReaders are closed properly.
SamComparison(SamReader, SamReader, String, String, SAMComparisonArgumentCollection) - Constructor for class picard.sam.util.SamComparison
SamComparison.AlignmentComparison - Enum in picard.sam.util
samComparisonArgumentCollection - Variable in class picard.sam.CompareSAMs
SAMComparisonArgumentCollection - Class in picard.sam.util
  Argument collection for SAM comparison
SAMComparisonArgumentCollection() - Constructor for class picard.sam.util.SAMComparisonArgumentCollection
SamComparisonMetric - Class in picard.sam
  Metric for results of SamComparison.
SamComparisonMetric() - Constructor for class picard.sam.SamComparisonMetric
SamFormatConverter - Class in picard.sam
  Converts a BAM file to human-readable SAM output or vice versa
SamFormatConverter() - Constructor for class picard.sam.SamFormatConverter
SamHeaderAndIterator(SAMFileHeader, CloseableIterator<SAMRecord>) - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
SAMPLE - picard.analysis.MetricAccumulationLevel
SAMPLE - picard.fingerprint.CrosscheckMetric.DataType
SAMPLE - Variable in class picard.analysis.FingerprintingDetailMetrics
  The name of the sample who's genotypes the sequence data was compared to.
SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
  The sample whose known genotypes the sequence data was compared to.
SAMPLE - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
SAMPLE - Variable in class picard.arrays.BafRegressMetrics
  The sample name
SAMPLE - Variable in class picard.metrics.MultilevelMetrics
  The sample to which these metrics apply.
SAMPLE - Variable in class picard.vcf.MakeSitesOnlyVcf
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The name of the sample
SAMPLE_ALIAS - Variable in class picard.arrays.GtcToVcf
SAMPLE_ALIAS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
SAMPLE_ALIAS - Variable in class picard.fingerprint.ExtractFingerprint
SAMPLE_ALIAS - Variable in class picard.fingerprint.FingerprintMetrics
  The Sample alias taken from RG header or #CHROME line
SAMPLE_ALIAS - Variable in class picard.fingerprint.IdentifyContaminant
SAMPLE_ALIAS - Variable in class picard.illumina.IlluminaBasecallsToSam
SAMPLE_ALIAS - Variable in class picard.sam.RevertSam
SAMPLE_ALIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
  The name of the sample being assayed
SAMPLE_ALIAS_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
SAMPLE_INDIVIDUAL_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
SAMPLE_NAME - Variable in class picard.sam.FastqToSam
SAMPLE_SIZE - Variable in class picard.analysis.CollectWgsMetrics
SAMPLE_SIZE - Variable in class picard.analysis.directed.CollectTargetedMetrics
SAMPLE_SIZE - Variable in class picard.analysis.TheoreticalSensitivityMetrics
  Number of samples drawn at each depth in the depth distribution.
sampleBarcodes - Variable in class picard.illumina.parser.ReadStructure
sampleCumulativeSums(int, int, boolean) - Method in class picard.analysis.TheoreticalSensitivity.RouletteWheel
SAMPLES_FILE - Variable in class picard.arrays.VcfToAdpc
SAMRecordAndReference - Class in picard.metrics
SAMRecordAndReference(SAMRecord, ReferenceSequence) - Constructor for class picard.metrics.SAMRecordAndReference
SAMRecordAndReferenceMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,​HKEY extends Comparable> - Class in picard.metrics
SAMRecordAndReferenceMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
SAMRecordMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,​HKEY extends Comparable> - Class in picard.metrics
  Defines a MultilevelPerRecordCollector using the argument type of SAMRecord so that this doesn't have to be redefined for each subclass of MultilevelPerRecordCollector
SAMRecordMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordMultiLevelCollector
samRecordWithOrdinal - Variable in class picard.sam.markduplicates.util.ReadEndsForMateCigar
SamRecordWithOrdinalAndSetDuplicateReadFlag - Class in picard.sam.markduplicates.util
  This class sets the duplicate read flag as the result state when examining sets of records.
SamRecordWithOrdinalAndSetDuplicateReadFlag() - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
SamRecordWithOrdinalAndSetDuplicateReadFlag(SAMRecord, long) - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
SamSequenceRecordsIterator(File, boolean) - Constructor for class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
SamToBfqWriter - Class in picard.fastq
  Class to take unmapped reads in SAM/BAM/CRAM file format and create Maq binary fastq format file(s) -- one or two of them, depending on whether it's a paired-end read.
SamToBfqWriter(File, File, String, Integer, Integer, boolean, String, boolean, boolean, Integer) - Constructor for class picard.fastq.SamToBfqWriter
  Constructor
SamToBfqWriter(File, String, boolean, String, boolean) - Constructor for class picard.fastq.SamToBfqWriter
  Constructor
SamToFastq - Class in picard.sam
  Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger FASTQ format.
SamToFastq() - Constructor for class picard.sam.SamToFastq
SamToFastqWithTags - Class in picard.sam
  Extracts read sequences and qualities from the input SAM/BAM file and SAM/BAM tags and writes them into output files in Sanger FASTQ format.
SamToFastqWithTags() - Constructor for class picard.sam.SamToFastqWithTags
SANITIZE - Variable in class picard.sam.RevertSam
scaledEvidenceProbabilityUsingGenotypeFrequencies(double[]) - Method in class picard.fingerprint.HaplotypeProbabilities
  This function returns the scaled probability of the evidence collected given a vector of priors on the haplotype using the internal likelihood, which may be scaled by an unknown factor.
SCAN_WINDOW_SIZE - Variable in class picard.analysis.CollectGcBiasMetrics
scanDir(File, String) - Method in class picard.cmdline.ClassFinder
  Scans a directory on the filesystem for classes.
scanJar(File, String) - Method in class picard.cmdline.ClassFinder
  Scans the entries in a ZIP/JAR file for classes under the parent package.
SCANNER_NAME - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The name of the scanner used for this sample
SCANNER_NAME - Static variable in class picard.arrays.illumina.InfiniumVcfFields
scatter(IntervalList, int) - Method in interface picard.util.IntervalList.IntervalListScatterer
  Scatter an `IntervalList` into several IntervalLists.
SCATTER_CONTENT - Variable in class picard.util.IntervalListTools
SCATTER_COUNT - Variable in class picard.util.IntervalListTools
ScatterIntervalsByNReferenceArgumentCollection() - Constructor for class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
ScatterIntervalsByNs - Class in picard.util
  A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
ScatterIntervalsByNs() - Constructor for class picard.util.ScatterIntervalsByNs
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection - Class in picard.util
scheme - Variable in class picard.vcf.GenotypeConcordanceScheme
  The underlying scheme
score - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
SCORE - Variable in class picard.util.IntervalListToBed
SD_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The standard deviation of clusters per tile.
SD_COVERAGE - Variable in class picard.analysis.WgsMetrics
  The standard deviation of coverage of the genome after all filters are applied.
SD_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The standard deviation in percentage of pf clusters per tile.
SD_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The standard deviation in number of pf clusters per tile.
SD_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
  The standard deviation of the read lengths.
SECOND - picard.illumina.parser.TileTemplateRead
SECOND - picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
SECOND_END_FASTQ - Variable in class picard.sam.SamToFastq
SECOND_INPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
SECOND_INPUT - Variable in class picard.util.IntervalListTools
SECOND_INPUT_SAMPLE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
SECOND_OF_PAIR - picard.analysis.AlignmentSummaryMetrics.Category
SECOND_READ_TRANSCRIPTION_STRAND - picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
SECONDARY_OR_SUPPLEMENTARY_RDS - Variable in class picard.sam.DuplicationMetrics
  The number of reads that were either secondary or supplementary
seek(List<File>, TileIndex, int) - Method in class picard.illumina.parser.readers.BclReader
seekToTile(int) - Method in class picard.illumina.parser.MultiTileParser
seekToTile(int) - Method in class picard.illumina.parser.PerTileParser
sensitivityAtConstantDepth(int, Histogram<Integer>, double, int, double, long) - Static method in class picard.analysis.TheoreticalSensitivity
  Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution at a constant depth.
seq(double, double, double) - Static method in class picard.util.MathUtil
  Mimic's R's seq() function to produce a sequence of equally spaced numbers.
SEQUENCE_DICTIONARY - Variable in class picard.annotation.SortGff
SEQUENCE_DICTIONARY - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
SEQUENCE_DICTIONARY - Variable in class picard.fingerprint.LiftOverHaplotypeMap
SEQUENCE_DICTIONARY - Variable in class picard.sam.ReorderSam
SEQUENCE_DICTIONARY - Variable in class picard.util.BedToIntervalList
SEQUENCE_DICTIONARY - Variable in class picard.util.LiftOverIntervalList
SEQUENCE_DICTIONARY - Variable in class picard.vcf.CollectVariantCallingMetrics
SEQUENCE_DICTIONARY - Variable in class picard.vcf.MergeVcfs
SEQUENCE_DICTIONARY - Variable in class picard.vcf.SortVcf
SEQUENCE_DICTIONARY - Variable in class picard.vcf.SplitVcfs
SEQUENCE_DICTIONARY - Variable in class picard.vcf.UpdateVcfSequenceDictionary
SEQUENCE_DICTIONARY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
SEQUENCE_MISMATCH - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Deprecated.
  - but used in existing extended manifest files.
SEQUENCE_NAME - Variable in class picard.analysis.RrbsCpgDetailMetrics
  Sequence the CpG is seen in
SEQUENCE_NAMES - Variable in class picard.analysis.CollectRrbsMetrics
SEQUENCE_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
SequenceDictionaryUtils - Class in picard.util
  Class with helper methods for generating and writing SequenceDictionary objects.
SequenceDictionaryUtils() - Constructor for class picard.util.SequenceDictionaryUtils
SequenceDictionaryUtils.SamSequenceRecordsIterator - Class in picard.util
SEQUENCING - picard.sam.markduplicates.MarkDuplicates.DuplicateType
SEQUENCING_CENTER - Variable in class picard.illumina.IlluminaBasecallsToSam
SEQUENCING_CENTER - Variable in class picard.sam.FastqToSam
SequencingArtifactMetrics - Class in picard.analysis.artifacts
SequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics
SequencingArtifactMetrics.BaitBiasDetailMetrics - Class in picard.analysis.artifacts
  Bait bias artifacts broken down by context.
SequencingArtifactMetrics.BaitBiasSummaryMetrics - Class in picard.analysis.artifacts
  Summary analysis of a single bait bias artifact, also known as a reference bias artifact.
SequencingArtifactMetrics.PreAdapterDetailMetrics - Class in picard.analysis.artifacts
  Pre-adapter artifacts broken down by context.
SequencingArtifactMetrics.PreAdapterSummaryMetrics - Class in picard.analysis.artifacts
  Summary analysis of a single pre-adapter artifact.
SET_ONLY_UQ - Variable in class picard.sam.SetNmMdAndUqTags
setAddPGTagToReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
  Set addPGTagToReads.
setAllowDuplicateReads(boolean) - Method in class picard.fingerprint.FingerprintChecker
  Sets whether duplicate reads should be allowed when calling genotypes from SAM files.
setApplyEamssFiltering(boolean) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
  Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores.
setAssayFormat(String) - Method in class picard.arrays.illumina.IlluminaManifest
setAttributesToReverse(Set<String>) - Method in class picard.sam.AbstractAlignmentMerger
  Sets the set of attributes to be reversed on reads marked as negative strand.
setAttributesToReverseComplement(Set<String>) - Method in class picard.sam.AbstractAlignmentMerger
  Sets the set of attributes to be reverse complemented on reads marked as negative strand.
setBaitSetName(String) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
  Sets the name of the bait set explicitly instead of inferring it from the bait file.
setBases(byte[]) - Method in class picard.illumina.parser.ReadData
setBigDuplicateSetSize(int) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
  Sets the size of a set that is big enough to log progress about.
setClipOverlappingReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
setConverter(BasecallsConverter.ClusterDataConverter<CLUSTER_OUTPUT_RECORD>) - Method in class picard.illumina.BasecallsConverter
  Must be called before doTileProcessing.
setCounter(long) - Method in class picard.analysis.AbstractWgsMetricsCollector
  Sets the counter to the current number of processed loci.
setDateManufactured(String) - Method in class picard.arrays.illumina.IlluminaManifest
setDefaultHeaders(List<Header>) - Method in class picard.cmdline.CommandLineProgram
setDefaultSampleID(String) - Method in class picard.fingerprint.FingerprintChecker
setDescriptorFileName(String) - Method in class picard.arrays.illumina.IlluminaManifest
setDupe(boolean) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
setGcCacheSize(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
setGenomeAssembly(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
setGenotypingErrorRate(double) - Method in class picard.fingerprint.FingerprintChecker
  Sets the assumed genotyping error rate used when accurate error rates are not available.
setHardClipOverlappingReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
setHgGenomeBuild(String) - Method in class picard.arrays.illumina.IlluminaManifestRecord
setIdentifier(String) - Method in class picard.arrays.illumina.InfiniumDataFile
setIncludeSecondaryAlignments(boolean) - Method in class picard.sam.AbstractAlignmentMerger
setInputStream(InputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
setInputStream(InputStream) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
setKeepAlignerProperPairFlags(boolean) - Method in class picard.sam.AbstractAlignmentMerger
  If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.
setLane(int) - Method in class picard.illumina.parser.ClusterData
setLibraryId(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
setLibraryId(short) - Method in class picard.sam.markduplicates.util.ReadEnds
setLibraryId(short) - Method in interface picard.sam.util.PhysicalLocation
setLibraryId(short) - Method in class picard.sam.util.PhysicalLocationInt
setLocationBinSize(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
  defaults to 2500
setLocationSet(PhysicalLocationForMateCigarSet) - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
setLociCount(int) - Method in class picard.arrays.illumina.IlluminaManifest
setLocusMaxReads(int) - Method in class picard.fingerprint.FingerprintChecker
setLongHomopolymer(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
  defaults to 6
setManifestFileParser(CsvInputParser) - Method in class picard.arrays.illumina.IlluminaManifest
setMatchedBarcode(String) - Method in class picard.illumina.parser.ClusterData
setMaxDuplicateSetSize(long) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
  Sets the size of a set that is too big to process.
setMaxPairErrorRate(double) - Method in class picard.util.AdapterMarker
setMaxRecordsInRam(int) - Method in class picard.sam.AbstractAlignmentMerger
  Allows the caller to override the maximum records in RAM.
setMaxSingleEndErrorRate(double) - Method in class picard.util.AdapterMarker
setMinimumBaseQuality(int) - Method in class picard.fingerprint.FingerprintChecker
  Sets the minimum base quality for bases used when computing a fingerprint from sequence data.
setMinimumMappingQuality(int) - Method in class picard.fingerprint.FingerprintChecker
  Sets the minimum mapping quality for reads used when computing fingerprints from sequence data.
setMinPairMatchBases(int) - Method in class picard.util.AdapterMarker
setMinSingleEndMatchBases(int) - Method in class picard.util.AdapterMarker
setNearProbeDistance(int) - Method in class picard.analysis.directed.TargetMetricsCollector
  Sets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
SetNmAndUqTags - Class in picard.sam
  Deprecated.
SetNmAndUqTags() - Constructor for class picard.sam.SetNmAndUqTags
  Deprecated.
SetNmMdAndUqTags - Class in picard.sam
  Fixes the NM, MD, and UQ tags in a SAM or BAM file.
SetNmMdAndUqTags() - Constructor for class picard.sam.SetNmMdAndUqTags
setNoSideEffects(boolean) - Method in class picard.analysis.directed.TargetMetricsCollector
  In the case of ignoring bases in overlapping reads from the same template, we choose to internally modify the SAM record's CIGAR to clip overlapping bases.
setNumAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
  After seeing the thresholdForSelectingAdapters number of adapters, keep up to this many of the original adapters.
setNumAssays(int) - Method in class picard.arrays.illumina.IlluminaManifest
setOffset(int) - Method in class picard.arrays.illumina.InfiniumFileTOC
setOffsetX(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setOffsetY(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setOrCheckLane(int) - Method in class picard.illumina.parser.ClusterData
  Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckPf(boolean) - Method in class picard.illumina.parser.ClusterData
  Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckTile(int) - Method in class picard.illumina.parser.ClusterData
  Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckX(int) - Method in class picard.illumina.parser.ClusterData
  Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckY(int) - Method in class picard.illumina.parser.ClusterData
  Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOutputStream(OutputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
setOutputStream(OutputStream) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
setPerBaseOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
  Sets the (optional) File to write per-base coverage information to.
setPerTargetOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
  Sets the (optional) File to write per-target coverage information to.
setPf(boolean) - Method in class picard.illumina.parser.ClusterData
setpLossofHet(double) - Method in class picard.fingerprint.FingerprintChecker
setPositionInfo(AbstractIlluminaPositionFileReader.PositionInfo) - Method in class picard.illumina.parser.CbclData
setPriorError(double) - Static method in class picard.sam.SamErrorMetric.ErrorMetric
setProgramRecord(SAMProgramRecord) - Method in class picard.sam.AbstractAlignmentMerger
setProgramsToRun(Collection<CollectMultipleMetrics.ProgramInterface>) - Method in class picard.analysis.CollectMultipleMetrics
  Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones available via enum.
setQualities(byte[]) - Method in class picard.illumina.parser.ReadData
setReadGroup(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
setReadGroup(short) - Method in class picard.sam.markduplicates.util.ReadEnds
setReadGroup(short) - Method in interface picard.sam.util.PhysicalLocation
setReadGroup(short) - Method in class picard.sam.util.PhysicalLocationInt
setReadType(ReadType) - Method in class picard.illumina.parser.ReadData
setReferenceFasta(File) - Method in class picard.fingerprint.FingerprintChecker
setReferenceSequence(File) - Method in class picard.analysis.SinglePassSamProgram
  Set the reference File.
setReserved1(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setReserved2(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setReserved3(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setReserved4(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setReserved5(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setReserved6(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setResultState(boolean) - Method in class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
setRsId(String) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
setScaleX(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setScaleY(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setShear(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setSize - Variable in class picard.sam.util.RepresentativeReadIndexer
setSkipBlankLines(boolean) - Method in class picard.util.AbstractInputParser
setSpecies(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
setTheta(float) - Method in class picard.arrays.illumina.InfiniumTransformation
setThresholdForSelectingAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
  When this number of adapters have been matched, discard the least-frequently matching ones.
setTile(int) - Method in class picard.illumina.parser.ClusterData
setTile(short) - Method in interface picard.sam.util.PhysicalLocation
setTile(short) - Method in class picard.sam.util.PhysicalLocationInt
setTileLimits(Integer, Integer) - Method in class picard.illumina.BasecallsConverter
  Uses the firstTile and tileLimit parameters to set which tiles will be processed.
setTiles(List<Integer>) - Method in class picard.illumina.parser.ParameterizedFileUtil
setTilesForPerRunFile(List<Integer>) - Method in class picard.illumina.parser.ParameterizedFileUtil
setTilesForPerRunFile(List<Integer>) - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
setToMarkQueueMinimumDistance(int) - Method in class picard.sam.markduplicates.util.MarkQueue
  Sets the minimum genomic distance such that we can be assured that all duplicates have been considered.
setTreatGroupedDelimitersAsOne(boolean) - Method in class picard.util.AbstractInputParser
setup(SAMFileHeader, File) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectBaseDistributionByCycle
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectGcBiasMetrics
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectInsertSizeMetrics
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectQualityYieldMetrics
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectRnaSeqMetrics
setup(SAMFileHeader, File) - Method in class picard.analysis.MeanQualityByCycle
setup(SAMFileHeader, File) - Method in class picard.analysis.QualityScoreDistribution
setup(SAMFileHeader, File) - Method in class picard.analysis.SinglePassSamProgram
  Should be implemented by subclasses to do one-time initialization work.
setup(SAMFileHeader, File) - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
setup(VCFHeader) - Method in class picard.vcf.CallingMetricAccumulator
setup(VCFHeader) - Method in class picard.vcf.GvcfMetricAccumulator
setup(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>) - Method in class picard.metrics.MultiLevelCollector
  Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
setupOpticalDuplicateFinder() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
setUri(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
setValidationStringency(ValidationStringency) - Method in class picard.fingerprint.FingerprintChecker
setValuesFromAlignment(SAMRecord, SAMRecord, boolean) - Method in class picard.sam.AbstractAlignmentMerger
  Sets the values from the alignment record on the unaligned BAM record.
setVersion(int) - Method in class picard.arrays.illumina.InfiniumTransformation
setWordCount(int) - Method in class picard.util.AbstractInputParser
setX(int) - Method in class picard.illumina.parser.ClusterData
setX(int) - Method in interface picard.sam.util.PhysicalLocation
setX(int) - Method in class picard.sam.util.PhysicalLocationInt
setX(int) - Method in class picard.sam.util.PhysicalLocationShort
setY(int) - Method in class picard.illumina.parser.ClusterData
setY(int) - Method in interface picard.sam.util.PhysicalLocation
setY(int) - Method in class picard.sam.util.PhysicalLocationInt
setY(int) - Method in class picard.sam.util.PhysicalLocationShort
Sex - Enum in picard.pedigree
  Represents the sex of an individual.
shiftedLogEvidenceProbability() - Method in class picard.fingerprint.HaplotypeProbabilities
  Returns log (p(evidence)) + c assuming that the prior on haplotypes is given by the internal haplotypeFrequencies
shiftedLogEvidenceProbabilityGivenOtherEvidence(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilities
  returns the log-probability the evidence, using as priors the posteriors of another object
shiftedLogEvidenceProbabilityUsingGenotypeFrequencies(double[]) - Method in class picard.fingerprint.HaplotypeProbabilities
SHORT_HOMOPOLYMER - picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
shortToByteArray(short) - Static method in class picard.arrays.illumina.InfiniumDataFile
  Utility method to convert a short to a byte array
shouldBeInLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
  Returns true if we should track this for optical duplicate detection, false otherwise
shouldIncludeInterval(long, double, long) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
shouldIncludeInterval(long, double, long) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivisionWithOverflow
Simple - picard.util.BaitDesigner.DesignStrategy
  Ultra simple bait design algorithm that just lays down baits starting at the target start position until either the bait start runs off the end of the target or the bait would run off the sequence
SimpleErrorCalculator - Class in picard.sam.SamErrorMetric
  A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
SimpleErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.SimpleErrorCalculator
SimpleMarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
  This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.
SimpleMarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
SIMPLEX_CONSENSUS - picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
  Read which had multiple observations, but all from the same strand (or the strand could not be determined).
SIMPLEX_SINGLETON - picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
  Read which only one observation is made.
SINGLE_END - picard.util.IlluminaUtil.IlluminaAdapterPair
SingleBarcodeDistanceMetric - Class in picard.util
  A class for finding the distance between a single barcode and a barcode-read (with base qualities)
SingleBarcodeDistanceMetric(byte[], byte[], byte[], int, int) - Constructor for class picard.util.SingleBarcodeDistanceMetric
SinglePassSamProgram - Class in picard.analysis
  Super class that is designed to provide some consistent structure between subclasses that simply iterate once over a coordinate sorted BAM and collect information from the records as the go in order to produce some kind of output.
SinglePassSamProgram() - Constructor for class picard.analysis.SinglePassSamProgram
size() - Method in class picard.fingerprint.HaplotypeBlock
  Returns the number of SNPs within the haplotype block.
size() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
size() - Method in class picard.sam.markduplicates.util.MarkQueue
  The number of records currently in this queue.
size() - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
size() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
  The number of records in this set
size() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
SIZE_OF - Static variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
sizeInRam() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
sizeInRam() - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
sizeInRam() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
Skip - Static variable in enum picard.illumina.parser.ReadType
SKIP_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
SKIP_MATE_VALIDATION - Variable in class picard.sam.ValidateSamFile
skipEmptyFiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
skipRecords(int) - Method in class picard.illumina.parser.readers.FilterFileReader
skipRecords(int) - Method in class picard.illumina.parser.readers.LocsFileReader
skips - Variable in class picard.illumina.parser.ReadStructure
Snp - Class in picard.fingerprint
  Class to represent a SNP in context of a haplotype block that is used in fingerprinting.
Snp(String, String, int, byte, byte, double, List<String>) - Constructor for class picard.fingerprint.Snp
SNP - picard.util.VariantType
SNP - Variable in class picard.analysis.FingerprintingDetailMetrics
  The name of a representative SNP within the haplotype that was compared.
SNP_ALLELES - Variable in class picard.analysis.FingerprintingDetailMetrics
  The possible alleles for the SNP.
SNP_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
SNP_OUTPUT - Variable in class picard.vcf.SplitVcfs
SNP_REFERENCE_BIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
snpCounter - Variable in class picard.vcf.GenotypeConcordance
snps - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
softClipsLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies into the number of soft-clipped bases that the read has in its alignment, or -1 if not aligned.
SORT - Variable in class picard.illumina.IlluminaBasecallsToFastq
SORT - Variable in class picard.illumina.IlluminaBasecallsToSam
SORT - Variable in class picard.util.BedToIntervalList
SORT - Variable in class picard.util.IntervalListToBed
SORT - Variable in class picard.util.IntervalListTools
SORT_ORDER - Variable in class picard.sam.AddOrReplaceReadGroups
SORT_ORDER - Variable in class picard.sam.FastqToSam
SORT_ORDER - Variable in class picard.sam.FilterSamReads
SORT_ORDER - Variable in class picard.sam.FixMateInformation
SORT_ORDER - Variable in class picard.sam.MergeBamAlignment
SORT_ORDER - Variable in class picard.sam.MergeSamFiles
SORT_ORDER - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
SORT_ORDER - Variable in class picard.sam.RevertSam
SORT_ORDER - Variable in class picard.sam.SortSam
SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
SortedBasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
  SortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
SortedBasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, int, List<File>, int, Integer, Integer, Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor) - Constructor for class picard.illumina.SortedBasecallsConverter
  Constructs a new SortedBaseCallsConverter.
SortGff - Class in picard.annotation
  Summary
SortGff() - Constructor for class picard.annotation.SortGff
SORTING_COLLECTION_SIZE_RATIO - Variable in class picard.sam.markduplicates.MarkDuplicates
SortSam - Class in picard.sam
  Sorts a SAM or BAM file.
SortSam() - Constructor for class picard.sam.SortSam
SortVcf - Class in picard.vcf
  Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate.
SortVcf() - Constructor for class picard.vcf.SortVcf
SOURCE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
SOURCE - Variable in class picard.fingerprint.FingerprintMetrics
  The originating file (if available) for this fingerprint
SOURCE_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
SOURCE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
SOURCE_SEQUENCE_INVALID - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Source sequence is invalid (contains invalid character).
SOURCE_SEQUENCE_MISMATCH - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Deprecated.
  - but used in existing extended manifest files.
SOURCE_SEQUENCE_STRAND_INVALID - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Deprecated.
  - but used in existing extended manifest files.
SOURCE_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
SOURCE_VERSION_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
specialArgumentsCollection - Variable in class picard.cmdline.CommandLineProgram
SPECIES - Variable in class picard.sam.CreateSequenceDictionary
SPECIES_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
split(String, String[], String) - Method in class picard.Test
SPLIT_TO_N_FILES - Variable in class picard.sam.SplitSamByNumberOfReads
SPLIT_TO_N_READS - Variable in class picard.sam.SplitSamByNumberOfReads
SplitSamByLibrary - Class in picard.sam
  Command-line program to split a SAM/BAM/CRAM file into separate files based on library name.
SplitSamByLibrary() - Constructor for class picard.sam.SplitSamByLibrary
SplitSamByNumberOfReads - Class in picard.sam
  Splits the input queryname sorted or query-grouped SAM/BAM/CRAM file and writes it into multiple BAM files, each with an approximately equal number of reads.
SplitSamByNumberOfReads() - Constructor for class picard.sam.SplitSamByNumberOfReads
SplitVcfs - Class in picard.vcf
  Splits the input VCF file into two, one for indels and one for SNPs.
SplitVcfs() - Constructor for class picard.vcf.SplitVcfs
STANDARD_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
  Standard deviation of insert sizes over the "core" of the distribution.
StandardOptionDefinitions - Class in picard.cmdline
  A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.
StandardOptionDefinitions() - Constructor for class picard.cmdline.StandardOptionDefinitions
start - Variable in class picard.annotation.Gene.Transcript.Exon
start - Variable in class picard.illumina.parser.Range
start() - Method in class picard.annotation.Gene.Transcript
start() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
start() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
  Starts the work of the executor, returning immediately.
start() - Method in class picard.vcf.processor.VcfFileSegment
start(RootDoc) - Static method in class picard.util.help.PicardHelpDoclet
  Create a doclet of the appropriate type and generate the FreeMarker templates properties.
stddev(double[], double) - Static method in class picard.util.MathUtil
  Calculated the standard deviation of an array of doubles.
stddev(double[], int, int) - Static method in class picard.util.MathUtil
  Calculated the standard deviation of an array of doubles.
stddev(double[], int, int, double) - Static method in class picard.util.MathUtil
  Calculated the standard deviation of an array of doubles.
STDERR - Variable in class picard.arrays.BafRegressMetrics
  The standard error of the estimate
stop() - Method in class picard.vcf.processor.VcfFileSegment
STOP_AFTER - Variable in class picard.analysis.CollectMultipleMetrics
STOP_AFTER - Variable in class picard.analysis.CollectOxoGMetrics
STOP_AFTER - Variable in class picard.analysis.CollectWgsMetrics
STOP_AFTER - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
STOP_AFTER - Variable in class picard.analysis.SinglePassSamProgram
STOP_AFTER - Variable in class picard.sam.PositionBasedDownsampleSam
STRAND - picard.annotation.RefFlatReader.RefFlatColumns
STRAND_BALANCE - Variable in class picard.analysis.AlignmentSummaryMetrics
  The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.
STRAND_SPECIFICITY - Variable in class picard.analysis.CollectRnaSeqMetrics
STRATEGY - Variable in class picard.sam.DownsampleSam
STRATIFIER_VALUE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
  Returns the number of bases associated with I and D CIGAR elements.
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in interface picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier
STRICT - Variable in class picard.vcf.SplitVcfs
stringSeqsToString(String[], String) - Static method in class picard.util.IlluminaUtil
STRIP_UNPAIRED_MATE_NUMBER - Variable in class picard.sam.FastqToSam
  Deprecated.
SUBDIVISION_MODE - Variable in class picard.util.IntervalListTools
subsetAlleles(GenotypesContext, List<Allele>, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
  Create the new GenotypesContext with the subsetted PLs and ADs Expects allelesToKeep to be in the same order in which they are in originalAlleles.
subsetAlleles(VariantContext, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
subsettedPLIndices(List<Allele>, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
  Given a list of original alleles and a subset of new alleles to retain, find the array of old PL indices that correspond to new PL indices i.e.
subsetVCToMatchSnp(VariantContext, Snp) - Static method in class picard.util.AlleleSubsettingUtils
  Method to subset the alleles in the VariantContext to those in the input snp.
SUBSTITUTION - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
  A single string representing the substition from REF_BASE to ALT_BASE for convenience.
SUBSTITUTION_RATE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
  The rate of the substitution in question.
Substructure(List<Integer>, List<Range>) - Constructor for class picard.illumina.parser.ReadStructure.Substructure
  Indices into the ReadStructure.descriptors for this specific substructure, indices must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous)
SUBTRACT - picard.util.IntervalListTools.Action
subtractMax(double[]) - Static method in class picard.util.MathUtil
sum(double...) - Method in class picard.util.MathUtil.LogMath
  Computes the sum of the provided log values.
sum(double[]) - Static method in class picard.util.MathUtil
  Returns the sum of the elements in the array.
sum(double[], double) - Static method in class picard.util.MathUtil
  calculates the sum of an array and a double.
sum(double[], double[]) - Static method in class picard.util.MathUtil
  calculates the sum of the arrays as a third array.
sum(long[], int, int) - Static method in class picard.util.MathUtil
  Returns the sum of the elements in the array starting with start and ending before stop.
SUMMARY - picard.sam.ValidateSamFile.Mode
SUMMARY - Variable in class picard.metrics.GcBiasMetrics
SUMMARY_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
SUMMARY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
SUMMARY_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
SUMMARY_OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
summaryMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
SUPPORTED_BUILD - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
SUPPORTED_CHAIN_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
SUPPORTED_REFERENCE_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
supportedTypes() - Method in class picard.illumina.parser.MultiTileParser
supportedTypes() - Method in class picard.illumina.parser.PosParser
supportsMetricAccumulationLevel() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
swapAlleles(VariantContext, Allele, Allele) - Static method in class picard.util.AlleleSubsettingUtils
  Swaps one of the alleles in a VC (and its genotypes) with another.
SWAPPED_ALLELES - Static variable in class picard.util.LiftoverUtils
  Attribute used to store the fact that the alt and ref alleles of the variant have been swapped, while all the INFO annotations have not.
swapRefAlt(VariantContext, Collection<String>, Collection<String>) - Static method in class picard.util.LiftoverUtils
  method to swap the reference and alt alleles of a bi-allelic, SNP
SYMDIFF - picard.util.IntervalListTools.Action
SYNTHETIC_PHASESET_PREFIX - Static variable in class picard.fingerprint.HaplotypeMap

## T

T - picard.analysis.artifacts.Transition.Base
T - picard.illumina.parser.IntensityChannel
T - picard.illumina.parser.ReadType
TAB_MODE - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
TabbedInputParser - Class in picard.util
  Parser for tab-delimited files
TabbedInputParser(boolean, File...) - Constructor for class picard.util.TabbedInputParser
  Constructor
TabbedInputParser(boolean, InputStream...) - Constructor for class picard.util.TabbedInputParser
  Constructor
TabbedTextFileWithHeaderParser - Class in picard.util
  Parse a tabbed text file in which columns are found by looking at a header line rather than by position.
TabbedTextFileWithHeaderParser(File) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
TabbedTextFileWithHeaderParser(File, String[]) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
TabbedTextFileWithHeaderParser(TabbedInputParser) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
TabbedTextFileWithHeaderParser.Row - Class in picard.util
TAG - Variable in class picard.sam.FilterSamReads
TAG_DUPLICATE_SET_MEMBERS - Variable in class picard.sam.markduplicates.MarkDuplicates
TAG_GROUP_SEPERATOR - Variable in class picard.sam.SamToFastqWithTags
TAG_PER_MOLECULAR_INDEX - Variable in class picard.illumina.IlluminaBasecallsToSam
TAG_VALUE - Variable in class picard.sam.FilterSamReads
TAGGING_POLICY - Variable in class picard.sam.markduplicates.MarkDuplicates
TAGS_TO_DROP - Variable in class picard.vcf.LiftoverVcf
TAGS_TO_REVERSE - Variable in class picard.vcf.LiftoverVcf
TAIL_LIMIT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
takeSome(Interval, long, long, double) - Method in interface picard.util.IntervalList.IntervalListScatterer
  Figure out how much of the input interval to put into current list and how much to leave for the next interval list.
takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererWithSubdivision
TANDEM_READS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
TARGET_BUILD - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
TARGET_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedMetrics
TARGET_INTERVALS - Variable in class picard.vcf.CollectVariantCallingMetrics
TARGET_TERRITORY - Variable in class picard.analysis.directed.PanelMetricsBase
  The number of unique bases covered by the intervals of all targets that should be covered
TargetedPcrMetrics - Class in picard.analysis.directed
  Metrics class for the analysis of reads obtained from targeted pcr experiments e.g.
TargetedPcrMetrics() - Constructor for class picard.analysis.directed.TargetedPcrMetrics
TargetedPcrMetricsCollector - Class in picard.analysis.directed
  Calculates HS metrics for a given SAM or BAM file.
TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
TargetMetrics - Class in picard.analysis.directed
  TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
TargetMetrics() - Constructor for class picard.analysis.directed.TargetMetrics
TargetMetricsBase - Class in picard.analysis.directed
  TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
TargetMetricsBase() - Constructor for class picard.analysis.directed.TargetMetricsBase
TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics> - Class in picard.analysis.directed
  TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector
TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector
TargetMetricsCollector.Coverage - Class in picard.analysis.directed
  A simple class that is used to store the coverage information about an interval.
TargetMetricsCollector.PerUnitTargetMetricCollector - Class in picard.analysis.directed
  Collect the Target Metrics for one unit of "accumulation" (i.e.
TARGETS - Variable in class picard.util.BaitDesigner
Template - Static variable in enum picard.illumina.parser.ReadType
templates - Variable in class picard.illumina.parser.ReadStructure
Test - Class in picard
Test() - Constructor for class picard.Test
TEST_INPUT_READABILITY - Variable in class picard.fingerprint.CalculateFingerprintMetrics
TEST_INPUT_READABILITY - Variable in class picard.fingerprint.CrosscheckFingerprints
TEST_INPUT_READABILITY - Variable in class picard.fingerprint.ExtractFingerprint
TEST_INPUT_READABILITY - Variable in class picard.fingerprint.IdentifyContaminant
Testing - Class in picard.cmdline.programgroups
  For internal test purposes only.
Testing() - Constructor for class picard.cmdline.programgroups.Testing
THEORETICAL_SENSITIVITY - Variable in class picard.analysis.TheoreticalSensitivityMetrics
  Estimation of sensitivity at a particular allele fraction.
THEORETICAL_SENSITIVITY_OUTPUT - Variable in class picard.analysis.CollectWgsMetrics
THEORETICAL_SENSITIVITY_OUTPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
THEORETICAL_SENSITIVITY_Q - Variable in class picard.analysis.TheoreticalSensitivityMetrics
  Phred-scaled value of 1-THEORETICAL_SENSITIVITY.
theoreticalHetSensitivitySampleSize - Variable in class picard.analysis.WgsMetrics
  The sample size used for theoretical het sensitivity.
theoreticalSensitivity(Histogram<Integer>, Histogram<Integer>, int, double, double) - Static method in class picard.analysis.TheoreticalSensitivity
  Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution and depth distribution.
TheoreticalSensitivity - Class in picard.analysis
  Created by David Benjamin on 5/13/15.
TheoreticalSensitivity() - Constructor for class picard.analysis.TheoreticalSensitivity
TheoreticalSensitivity.RouletteWheel - Class in picard.analysis
TheoreticalSensitivityMetrics - Class in picard.analysis
  TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in the calculation.
TheoreticalSensitivityMetrics() - Constructor for class picard.analysis.TheoreticalSensitivityMetrics
THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
thetaIlmn - Variable in class picard.arrays.illumina.InfiniumGTCRecord
THREAD_COUNT - Variable in class picard.vcf.CollectVariantCallingMetrics
THREAD_COUNT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
ThreadPoolExecutorUtil - Class in picard.util
ThreadPoolExecutorUtil() - Constructor for class picard.util.ThreadPoolExecutorUtil
ThreadPoolExecutorWithExceptions - Class in picard.util
  This version of the thread pool executor will throw an exception if any of the internal jobs have throw exceptions while executing
ThreadPoolExecutorWithExceptions(int) - Constructor for class picard.util.ThreadPoolExecutorWithExceptions
  Creates a fixed size thread pool executor that will rethrow exceptions from submitted jobs.
THREE - picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
THREE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
THREE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToSam
THREE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
THREE_PRIME_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
THREE_WAYS_DISAGREEMENT_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
  The (phred) rate of bases that disagree with both the reference and their mate (which also disagree)
tile - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
  The tile, which is determined from the file name
tile - Variable in class picard.sam.util.PhysicalLocationInt
Tile - Class in picard.illumina.parser
  Represents a tile from TileMetricsOut.bin.
Tile(int, int, float, float, TilePhasingValue...) - Constructor for class picard.illumina.parser.Tile
TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
  The Tile that is described by this metric
TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  The Tile that is described by this metric.
TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToFastq
TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToSam
TILE_METRICS_OUT_FILE_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
  The expected name of the tile metrics output file.
TILE_NUMBER_COMPARATOR - Static variable in class picard.illumina.BasecallsConverter
  A comparator used to sort Illumina tiles in their proper order.
TILE_NUMBERS - Variable in class picard.illumina.CheckIlluminaDirectory
tileIndex - Variable in class picard.illumina.parser.MultiTileFileUtil
TileIndex - Class in picard.illumina.parser
  Load a file containing 8-byte records like this: tile number: 4-byte int number of clusters in tile: 4-byte int Number of records to read is determined by reaching EOF.
TileIndex.TileIndexRecord - Class in picard.illumina.parser
tileIsSet() - Method in class picard.illumina.parser.ClusterData
tileLimit(Integer) - Method in class picard.illumina.BasecallsConverterBuilder
  Configures the total number of tiles that the converter will process.
tileMetricsOut() - Method in class picard.illumina.parser.IlluminaFileUtil
TileMetricsOutReader - Class in picard.illumina.parser.readers
  Reads a TileMetricsOut file commonly found in the InterOp directory of an Illumina Run Folder.
TileMetricsOutReader(File) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader
  Return a TileMetricsOutReader for the specified file
TileMetricsOutReader.IlluminaLaneTileCode - Class in picard.illumina.parser.readers
  Helper class which captures the combination of a lane, tile & metric code
TileMetricsOutReader.IlluminaTileMetrics - Class in picard.illumina.parser.readers
  IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut file
TileMetricsOutReader.TileMetricsVersion - Enum in picard.illumina.parser.readers
TileMetricsUtil - Class in picard.illumina.parser
  Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
TileMetricsUtil() - Constructor for class picard.illumina.parser.TileMetricsUtil
TilePhasingValue - Class in picard.illumina.parser
  Captures information about a phasing value - Which read it corresponds to, which phasing type and a median value
TilePhasingValue(TileTemplateRead, float, float) - Constructor for class picard.illumina.parser.TilePhasingValue
tiles - Variable in class picard.illumina.BasecallsConverter
tiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
TileTemplateRead - Enum in picard.illumina.parser
  Defines the first or second template read for a tile
TMP_DIR - Variable in class picard.cmdline.CommandLineProgram
TN - picard.vcf.GenotypeConcordanceStates.ContingencyState
TN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
  The TN (true negative) count across all variants
TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
TN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
toClassName(String) - Method in class picard.cmdline.ClassFinder
  Convert a filename to a class name by removing '.class' and converting '/'s to '.'s.
toCode() - Method in enum picard.pedigree.Sex
  Returns the code used to encode this sex in a ped/fam file.
TOP - picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
TOP_GENOMIC_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
toReadStructure() - Method in class picard.illumina.parser.ReadStructure.Substructure
  Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g.
toString() - Method in enum picard.analysis.artifacts.Transition
toString() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
toString() - Method in class picard.arrays.illumina.ArraysControlInfo
toString() - Method in class picard.arrays.illumina.IlluminaManifestRecord
toString() - Method in class picard.fingerprint.HaplotypeBlock
toString() - Method in class picard.fingerprint.Snp
toString() - Method in class picard.illumina.IlluminaBasecallingMetrics
toString() - Method in class picard.illumina.parser.ClusterData
toString() - Method in class picard.illumina.parser.Range
toString() - Method in class picard.illumina.parser.ReadDescriptor
toString() - Method in class picard.illumina.parser.ReadStructure
  Converts this object into a String using rules complementary to the single string constructor above.
toString() - Method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
toString() - Method in class picard.sam.util.Pair
toString() - Method in class picard.vcf.processor.VcfFileSegment
toSymbol() - Method in enum picard.pedigree.Sex
  Returns the single-character symbol used to encode sex in a VCF file
TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The total number of basecalls observed at all sites.
TOTAL_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The total number of bases in all reads
TOTAL_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The total number of bases assigned to the index.
TOTAL_BASES - Variable in class picard.sam.SamErrorMetric.ErrorMetric
  The total number of bases included in the calculation of this metric
TOTAL_CLUSTERS - Variable in class picard.analysis.GcBiasSummaryMetrics
  The total number of clusters that were seen in the gc bias calculation.
TOTAL_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The total number of clusters assigned to the index.
TOTAL_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of passing complex indel calls that were examined
TOTAL_GQ0_VARIANTS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
  The total number of variants in a particular sample that have a GQ score of 0.
TOTAL_HET_DEPTH - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
  total number of reads (from AD field) for passing bi-allelic SNP hets for this sample
TOTAL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of passing indel calls that were examined
TOTAL_MENDELIAN_VIOLATIONS - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
  The total of all mendelian violations observed.
TOTAL_MULTIALLELIC_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of passing multi-allelic SNP calls that were examined
TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The total Phred-scaled Q-score for this artifact.
TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The total Phred-scaled Q-score for this artifact.
TOTAL_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
  The total number of reads including all PF and non-PF reads.
TOTAL_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  The total number of reads in the input file
TOTAL_READS - Variable in class picard.analysis.directed.PanelMetricsBase
  The total number of reads in the SAM or BAM file examined.
TOTAL_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
  The total number of reads assigned to the index.
TOTAL_READS_IN_INPUT - Variable in class picard.sam.SplitSamByNumberOfReads
TOTAL_SITES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
  The total number of sites that had at least one base covering them.
TOTAL_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
  Number of times this CpG site was encountered
TOTAL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  The number of passing bi-allelic SNPs calls (i.e.
totalCycles - Variable in class picard.illumina.parser.ReadStructure
totalScore - Variable in class picard.arrays.illumina.InfiniumEGTFile
TP - picard.vcf.GenotypeConcordanceStates.ContingencyState
TP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
  The TP (true positive) count across all variants
TP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
TP_FP - Static variable in class picard.vcf.GenotypeConcordanceScheme
TP_FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
TP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
TP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
trackOpticalDuplicates(List<? extends ReadEnds>, ReadEnds, OpticalDuplicateFinder, LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
  Looks through the set of reads and identifies how many of the duplicates are in fact optical duplicates, and stores the data in the instance level histogram.
Transcript(String, int, int, int, int, int) - Constructor for class picard.annotation.Gene.Transcript
TRANSCRIPT_NAME - picard.annotation.RefFlatReader.RefFlatColumns
transcriptionEnd - Variable in class picard.annotation.Gene.Transcript
transcriptionStart - Variable in class picard.annotation.Gene.Transcript
Transition - Enum in picard.analysis.artifacts
  Enum representation of a transition from one base to any other.
Transition.Base - Enum in picard.analysis.artifacts
transitionOf(char, char) - Static method in enum picard.analysis.artifacts.Transition
  Gets a the enum representing the transition from a 'reference' to a 'call' base.
TRIALLELIC - Static variable in class picard.arrays.illumina.InfiniumVcfFields
TRIMMING_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToFastq
TRIOS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
triSiteHeterogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  the rate of heterogeneity within tripleton sets
triSiteHomogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
  the rate of homogeneity within tripleton sets.
TRUNCATE_NAMES_AT_WHITESPACE - Variable in class picard.sam.CreateSequenceDictionary
TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE - Variable in class picard.reference.NormalizeFasta
TRUSEQ_SMALLRNA - picard.util.IlluminaUtil.IlluminaAdapterPair
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
  The name of the 'truth' sample
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
  The name of the 'truth' sample
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The name of the 'truth' sample
TRUTH_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
  The state of the 'truth' sample (i.e.
TRUTH_VCF - Variable in class picard.vcf.GenotypeConcordance
truthAllele1 - Variable in class picard.vcf.GenotypeConcordance.Alleles
truthAllele2 - Variable in class picard.vcf.GenotypeConcordance.Alleles
truthAlleles() - Method in class picard.vcf.GenotypeConcordance.Alleles
TruthAndCallStates(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Constructor for class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
truthState - Variable in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
TT - picard.fingerprint.DiploidGenotype
TtoA - picard.analysis.artifacts.Transition
TtoC - picard.analysis.artifacts.Transition
TtoG - picard.analysis.artifacts.Transition
TtoT - picard.analysis.artifacts.Transition
TVAL - Variable in class picard.arrays.BafRegressMetrics
  The test statistic for the estimate
TWO - picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
twoBasePaddedContextStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
  Stratifies into the two base context of the base, which includes two read-bases on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
TX_END - picard.annotation.RefFlatReader.RefFlatColumns
TX_START - picard.annotation.RefFlatReader.RefFlatColumns
type - Variable in class picard.illumina.parser.ReadDescriptor
TYPE_NAME - Variable in class picard.illumina.IlluminaPhasingMetrics
  Defines an Illumina template read number (first or second)

## U

uByteToInt(byte) - Static method in class picard.util.UnsignedTypeUtil
  Convert an unsigned byte to a signed int
uByteToShort(byte) - Static method in class picard.util.UnsignedTypeUtil
  Convert an unsigned byte to a signed short
uIntToFloat(int) - Static method in class picard.util.UnsignedTypeUtil
uIntToLong(int) - Static method in class picard.util.UnsignedTypeUtil
  Convert an unsigned int to a long
UMI_BASE_QUALITIES - Variable in class picard.sam.markduplicates.UmiMetrics
  Estimation of Phred scaled quality scores for UMIs
UMI_METRICS_FILE - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
UMI_TAG_NAME - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
UmiAwareMarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
  This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
UmiAwareMarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
UmiGraph - Class in picard.sam.markduplicates
  UmiGraph is used to identify UMIs that come from the same original source molecule.
UmiMetrics - Class in picard.sam.markduplicates
  Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.
UmiMetrics() - Constructor for class picard.sam.markduplicates.UmiMetrics
UmiMetrics(String) - Constructor for class picard.sam.markduplicates.UmiMetrics
UmiMetrics(String, double, int, int, int, int, int, double, double, double, double) - Constructor for class picard.sam.markduplicates.UmiMetrics
Unaligned - picard.sam.ViewSam.AlignmentStatus
UNEXPECTED_MATCH - picard.fingerprint.CrosscheckMetric.FingerprintResult
UNEXPECTED_MISMATCH - picard.fingerprint.CrosscheckMetric.FingerprintResult
unfilteredBaseQHistogram - Variable in class picard.analysis.WgsMetrics
  The count of bases observed with a given base quality.
unfilteredBaseQHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
  Count of bases observed with a given base quality.
unfilteredDepthHistogram - Variable in class picard.analysis.WgsMetrics
  Count of sites with a given depth of coverage.
unfilteredDepthHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
  Count of sites with a given depth of coverage.
UNION - picard.util.IntervalListTools.Action
UNIQUE - Variable in class picard.util.BedToIntervalList
UNIQUE - Variable in class picard.util.IntervalListTools
Unknown - picard.pedigree.Sex
UNKNOWN - picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
UNKNOWN - picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
  Read whose consensus status cannot be determined.
UNKNOWN - picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
UNKNOWN - Static variable in class picard.metrics.MultiLevelCollector
UNKNOWN_SEX - Static variable in class picard.pedigree.PedFile
UNMAP_CONTAMINANT_READS - Variable in class picard.sam.MergeBamAlignment
UNMAPPED_BAM - Variable in class picard.sam.MergeBamAlignment
UNMAPPED_BOTH - picard.sam.util.SamComparison.AlignmentComparison
UNMAPPED_BOTH - Variable in class picard.sam.SamComparisonMetric
  The number of primary records which are not mapped in either file.
UNMAPPED_LEFT - picard.sam.util.SamComparison.AlignmentComparison
UNMAPPED_LEFT - Variable in class picard.sam.SamComparisonMetric
  The number of primary records which are mapped in right file and found but not mapped in left file
UNMAPPED_READ_STRATEGY - Variable in class picard.sam.MergeBamAlignment
UNMAPPED_READS - Variable in class picard.sam.DuplicationMetrics
  The total number of unmapped reads examined.
UNMAPPED_RIGHT - picard.sam.util.SamComparison.AlignmentComparison
UNMAPPED_RIGHT - Variable in class picard.sam.SamComparisonMetric
  The number of primary records which are mapped in left file and found but not mapped in right file
UNPAIRED - picard.analysis.AlignmentSummaryMetrics.Category
UNPAIRED_FASTQ - Variable in class picard.sam.SamToFastq
UNPAIRED_READ_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
  The number of fragments that were marked as duplicates.
UNPAIRED_READS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
  The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate.
unsafeNextInfo() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
  Returns the next position info.
unsafeNextInfo() - Method in class picard.illumina.parser.readers.ClocsFileReader
  Grab the next set of offset values, decompress them.
unsafeNextInfo() - Method in class picard.illumina.parser.readers.LocsFileReader
unsafeNextInfo() - Method in class picard.illumina.parser.readers.PosFileReader
  Read a line of text and parse it into two float values, create a PositionInfo and return it
UnsignedTypeUtil - Class in picard.util
  A utility class for dealing with unsigned types.
UnsignedTypeUtil() - Constructor for class picard.util.UnsignedTypeUtil
UnsortedBasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
  UnortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
UnsortedBasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, Integer, Integer, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor, Integer) - Constructor for class picard.illumina.UnsortedBasecallsConverter
  Constructs a new BasecallsConverter object.
UNSUPPORTED_GENOME_BUILD - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
updateCigarForTrimmedOrClippedBases(SAMRecord, SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
updateMetric(SamComparison.AlignmentComparison) - Method in class picard.sam.SamComparisonMetric
updateMetrics(Map<String, BarcodeMetric>, BarcodeMetric) - Method in class picard.illumina.BasecallsConverter
UpdateVcfSequenceDictionary - Class in picard.vcf
  Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
UpdateVcfSequenceDictionary() - Constructor for class picard.vcf.UpdateVcfSequenceDictionary
URI - Variable in class picard.sam.CreateSequenceDictionary
USAGE - Static variable in class picard.illumina.IlluminaBasecallsToSam
USAGE - Variable in class picard.sam.ViewSam
USAGE_SUMMARY - Static variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
USE_FAST_ALGORITHM - Variable in class picard.analysis.CollectWgsMetrics
USE_FIRST - picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
USE_JDK_DEFLATER - Variable in class picard.cmdline.CommandLineProgram
USE_JDK_INFLATER - Variable in class picard.cmdline.CommandLineProgram
USE_OQ - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
USE_OQ - Variable in class picard.analysis.CollectOxoGMetrics
USE_ORIGINAL_QUALITIES - Variable in class picard.analysis.CollectQualityYieldMetrics
USE_ORIGINAL_QUALITIES_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
USE_SEQUENTIAL_FASTQS - Variable in class picard.sam.FastqToSam
USE_THREADING - Variable in class picard.sam.MergeSamFiles
USE_VCF_INDEX - Variable in class picard.vcf.GenotypeConcordance
useLegacyParser() - Static method in class picard.cmdline.CommandLineProgram
  Return true if the legacy Picard command line parser should be used in place of the Barclay command line parser, otherwise, false.
usesNoRefReads() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
usesNoRefReads() - Method in class picard.analysis.CollectInsertSizeMetrics
usesNoRefReads() - Method in class picard.analysis.CollectQualityYieldMetrics
  Ensure that we get all reads regardless of alignment status.
usesNoRefReads() - Method in class picard.analysis.SinglePassSamProgram
  Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.
usesNoRefReads() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
uShortToInt(short) - Static method in class picard.util.UnsignedTypeUtil
  Convert an unsigned short to an Int
UTR - picard.annotation.LocusFunction
UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
  Number of bases in primary alignments that align to a UTR base for some gene, and not a coding base.

## V

VALID_ALLELES - Static variable in class picard.arrays.illumina.IlluminaManifest
VALIDATE_INDEX - Variable in class picard.sam.ValidateSamFile
validateCountsAgainstScheme(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
  Validates that there are no counts for NA states in the underlying scheme
ValidateSamFile - Class in picard.sam
  This tool reports on the validity of a SAM or BAM file relative to the SAM format specification.
ValidateSamFile() - Constructor for class picard.sam.ValidateSamFile
ValidateSamFile.Mode - Enum in picard.sam
validateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
  Check that all cells in the scheme exist.
VALIDATION_STRINGENCY - Variable in class picard.cmdline.CommandLineProgram
value - Variable in enum picard.arrays.illumina.IlluminaGenotype
valueOf(String) - Static method in enum picard.analysis.AlignmentSummaryMetrics.Category
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.artifacts.Transition.Base
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.artifacts.Transition
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.CollectMultipleMetrics.Program
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.MetricAccumulationLevel
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.annotation.LocusFunction
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.annotation.RefFlatReader.RefFlatColumns
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.arrays.illumina.IlluminaGenotype
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.fingerprint.CrosscheckMetric.DataType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.fingerprint.CrosscheckMetric.FingerprintResult
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.fingerprint.DiploidGenotype
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.fingerprint.DiploidHaplotype
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.fingerprint.HaplotypeProbabilities.Genotype
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.DistanceMetric
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IlluminaDataType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IntensityChannel
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.ReadType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.TileTemplateRead
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.nio.PathProvider
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.pedigree.Sex
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.FilterSamReads.Filter
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.markduplicates.CheckDuplicateMarking.Mode
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.RevertSam.FileType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.util.SamComparison.AlignmentComparison
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.ValidateSamFile.Mode
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.ViewSam.AlignmentStatus
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.ViewSam.PfStatus
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.BaitDesigner.DesignStrategy
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.IntervalList.IntervalListScatterMode
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.IntervalListTools.Action
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.VariantType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStateCodes
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStates.ContingencyState
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
  Returns the enum constant of this type with the specified name.
values() - Static method in enum picard.analysis.AlignmentSummaryMetrics.Category
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.artifacts.Transition.Base
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.artifacts.Transition
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.CollectMultipleMetrics.Program
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.MetricAccumulationLevel
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.annotation.LocusFunction
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.annotation.RefFlatReader.RefFlatColumns
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.arrays.illumina.IlluminaGenotype
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.fingerprint.CrosscheckMetric.DataType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.fingerprint.CrosscheckMetric.FingerprintResult
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.fingerprint.DiploidGenotype
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.fingerprint.DiploidHaplotype
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.fingerprint.HaplotypeProbabilities.Genotype
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.DistanceMetric
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IlluminaDataType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IlluminaMetricsCode
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IntensityChannel
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.ReadType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.TileTemplateRead
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.nio.PathProvider
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.pedigree.Sex
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.FilterSamReads.Filter
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.markduplicates.CheckDuplicateMarking.Mode
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.RevertSam.FileType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.util.SamComparison.AlignmentComparison
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.ValidateSamFile.Mode
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.ViewSam.AlignmentStatus
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.ViewSam.PfStatus
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.BaitDesigner.DesignStrategy
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.IntervalList.IntervalListScatterMode
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.IntervalListTools.Action
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.VariantType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.GenotypeConcordanceStateCodes
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.GenotypeConcordanceStates.ContingencyState
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
  Returns an array containing the constants of this enum type, in the order they are declared.
VAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))
VAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))
VAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))
VARIANT_ID_METHOD - Static variable in class picard.vcf.VcfToIntervalList
VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
  The type of the event (i.e.
VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
  The type of the event (i.e.
VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
  The type of the event (i.e.
VariantAccumulatorExecutor<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,​RESULT> - Interface in picard.vcf.processor
  Describes the functionality for an executor that manages the delegation of work to `VariantProcessor.Accumulator`s.
VariantAccumulatorExecutor.MultiThreadedChunkBased<A extends VariantProcessor.Accumulator<R>,​R> - Class in picard.vcf.processor
  A `VariantAccumulatorExecutor` that breaks down work into chunks described by the provided `VariantIteratorProducer` and spreads them over the indicated number of threads.
VariantCallingDetailMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
VariantCallingSummaryMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
VariantEvaluationProgramGroup - Class in picard.cmdline.programgroups
  Tools that evaluate and refine variant calls, e.g.
VariantEvaluationProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantEvaluationProgramGroup
VariantFilter - Interface in picard.vcf.filter
  Interface for classes that can generate filters for VariantContexts.
VariantFilteringProgramGroup - Class in picard.cmdline.programgroups
  Tools that filter variants
VariantFilteringProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantFilteringProgramGroup
VariantIteratorProducer - Class in picard.vcf.processor
  A mechanism for iterating over `CloseableIterator` of `VariantContext`s in in some fashion, given VCF files and optionally an interval list.
VariantIteratorProducer() - Constructor for class picard.vcf.processor.VariantIteratorProducer
VariantManipulationProgramGroup - Class in picard.cmdline.programgroups
  Tools that manipulate variant call format (VCF) data
VariantManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantManipulationProgramGroup
VariantProcessor<RESULT,​ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>> - Class in picard.vcf.processor
  Describes an object that processes variants and produces a result.
VariantProcessor.Accumulator<RESULT> - Interface in picard.vcf.processor
  Handles `VariantContext`s, and accumulates their data in some fashion internally.
VariantProcessor.AccumulatorGenerator<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,​RESULT> - Interface in picard.vcf.processor
  Generates instances of `VariantProcessor.Accumulator`s.
VariantProcessor.Builder<A extends VariantProcessor.Accumulator<R>,​R> - Class in picard.vcf.processor
  Simple builder of `VariantProcessor`s.
VariantProcessor.ResultMerger<RESULT> - Interface in picard.vcf.processor
  Takes a collection of results produced by `VariantProcessor.Accumulator.result()` and merges them into a single RESULT.
VariantType - Enum in picard.util
  Enum to hold the possible types of dbSnps.
VC_FILTERED - picard.vcf.GenotypeConcordanceStates.CallState
VC_FILTERED - picard.vcf.GenotypeConcordanceStates.TruthState
VC_FILTERED_CODE - picard.vcf.GenotypeConcordanceStateCodes
vcf() - Method in class picard.vcf.processor.VcfFileSegment
VCF - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
VCF - Variable in class picard.arrays.VcfToAdpc
VCF - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
VCF_DIR - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
VcfFileSegment - Class in picard.vcf.processor
  Describes a segment of a particular VCF file.
VcfFileSegment() - Constructor for class picard.vcf.processor.VcfFileSegment
VcfFileSegmentGenerator - Class in picard.vcf.processor
  Describes a mechanism for producing `VcfFileSegment`s from a VCF file.
VcfFileSegmentGenerator() - Constructor for class picard.vcf.processor.VcfFileSegmentGenerator
VcfFormatConverter - Class in picard.vcf
  Converts an ASCII VCF file to a binary BCF or vice versa.
VcfFormatConverter() - Constructor for class picard.vcf.VcfFormatConverter
VcfToAdpc - Class in picard.arrays
  A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).
VcfToAdpc() - Constructor for class picard.arrays.VcfToAdpc
VcfToIntervalList - Class in picard.vcf
  Converts a VCF or BCF file to a Picard Interval List.
VcfToIntervalList() - Constructor for class picard.vcf.VcfToIntervalList
VcfToIntervalList.VARIANT_ID_TYPES - Enum in picard.vcf
VcfUtils - Class in picard.vcf
  Created by farjoun on 4/1/17.
VcfUtils() - Constructor for class picard.vcf.VcfUtils
VERBOSE - picard.sam.ValidateSamFile.Mode
VERBOSITY - Variable in class picard.cmdline.CommandLineProgram
verify(List<Integer>) - Method in class picard.illumina.parser.TileIndex
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileFileUtil
  expectedCycles are not checked in this implementation.
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.ParameterizedFileUtil
  Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileFileUtil
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileParser
verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileParser
VerifyIDIntensityContaminationMetrics - Class in picard.arrays
VerifyIDIntensityContaminationMetrics() - Constructor for class picard.arrays.VerifyIDIntensityContaminationMetrics
version - Variable in class picard.illumina.parser.readers.FilterFileReader
  Version number found in the FilterFile, this should equal 3
version - Variable in enum picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
ViewSam - Class in picard.sam
  Prints a SAM or BAM file to the screen.
ViewSam() - Constructor for class picard.sam.ViewSam
ViewSam.AlignmentStatus - Enum in picard.sam
ViewSam.PfStatus - Enum in picard.sam

## W

WARN_ON_MISSING_CONTIG - Variable in class picard.vcf.LiftoverVcf
WgsMetrics - Class in picard.analysis
  Metrics for evaluating the performance of whole genome sequencing experiments.
WgsMetrics() - Constructor for class picard.analysis.WgsMetrics
  Create an instance of this metric that is not mergeable.
WgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.WgsMetrics
  Create an instance of this metric that is mergeable.
WgsMetricsCollector(CollectWgsMetrics, int, IntervalList) - Constructor for class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
WgsMetricsProcessor - Interface in picard.analysis
  Interface for processing data and generate result for CollectWgsMetrics
WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset> - Class in picard.analysis
  Implementation of `WgsMetricsProcessor` that gets input data from a given iterator and processes it with a help of collector
WgsMetricsProcessorImpl(AbstractLocusIterator<T, AbstractLocusInfo<T>>, ReferenceSequenceFileWalker, AbstractWgsMetricsCollector<T>, ProgressLogger) - Constructor for class picard.analysis.WgsMetricsProcessorImpl
WgsMetricsWithNonZeroCoverage() - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
WgsMetricsWithNonZeroCoverage(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage, int, IntervalList) - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
WHOLE_GENOME - picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
WIDTH_OF_10_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 10% of all read pairs.
WIDTH_OF_20_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 20% of all read pairs.
WIDTH_OF_30_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 30% of all read pairs.
WIDTH_OF_40_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 40% of all read pairs.
WIDTH_OF_50_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 50% of all read pairs.
WIDTH_OF_60_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 60% of all read pairs.
WIDTH_OF_70_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 70% of all read pairs.
WIDTH_OF_80_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 80% of all read pairs.
WIDTH_OF_90_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 90% of all read pairs.
WIDTH_OF_95_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 95% of all read pairs.
WIDTH_OF_99_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
  The "width" of the bins, centered around the median, that encompass 100% of all read pairs.
WINDOW_SIZE - Variable in class picard.analysis.GcBiasSummaryMetrics
  The window size on the genome used to calculate the GC of the sequence.
WINDOWS - Variable in class picard.analysis.GcBiasDetailMetrics
  The number of windows on the reference genome that have this G+C content.
withApplyEamssFiltering(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
  Configures whether or not the converter will apply EAMSS filtering.
withAsyncWriterPool(AsyncWriterPool) - Method in class picard.illumina.BasecallsConverterBuilder
withBarcodeExtractor(BarcodeExtractor) - Method in class picard.illumina.BasecallsConverterBuilder
withBarcodesDir(File) - Method in class picard.illumina.BasecallsConverterBuilder
  Configure the director used to find barcode files created by ExtractIlluminaBarcodes.
withBclQualityEvaluationStrategy(BclQualityEvaluationStrategy) - Method in class picard.illumina.BasecallsConverterBuilder
  Configures the bcl quality evaluation strategy that the converter will apply.
withDemultiplex(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
  Configures whether or not the converter will demultiplex reads by barcode.
withIgnoreUnexpectedBarcodes(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
  Configures whether or not the converter will ignore unexpected barcodes or throw an exception if one is found.
withIncludeNonPfReads(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
  Configures whether or not the converter will ignore non-PF reads.
withInput(File...) - Method in class picard.vcf.processor.VariantProcessor.Builder
withMaxRecordsInRam(int) - Method in class picard.illumina.BasecallsConverterBuilder
  Specify the max number of records in RAM.
withMolecularIndexQualityTag(String) - Method in class picard.illumina.ClusterDataToSamConverter
  Sets the SAM tag to use to store the molecular index base qualities.
withMolecularIndexTag(String) - Method in class picard.illumina.ClusterDataToSamConverter
  Sets the SAM tag to use to store the molecular index bases.
withoutChromosomes(Set<String>) - Method in class picard.fingerprint.HaplotypeMap
  Returns a copy of this haplotype map that excludes haplotypes on the chromosomes provided.
withSorting(Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, List<File>) - Method in class picard.illumina.BasecallsConverterBuilder
  Builds a new sorting basecalls converter.
withTagPerMolecularIndex(List<String>) - Method in class picard.illumina.ClusterDataToSamConverter
  Sets the SAM tags to use to store the bases each molecular index.
WORST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
WORST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
WORST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The Q-score for the worst context.
WORST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The Q-score for the worst context.
WORST_POST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
WORST_POST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
WORST_POST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The Q-score for the worst post-context.
WORST_POST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The Q-score for the worst post-context.
WORST_PRE_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
WORST_PRE_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
WORST_PRE_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  The Q-score for the worst pre-context.
WORST_PRE_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  The Q-score for the worst pre-context.
write(byte[], int, int) - Method in class picard.util.CircularByteBuffer
  Write bytes into the buffer from the supplied array.
write(DataOutputStream) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter.Record
write(File) - Method in class picard.pedigree.PedFile
  Writes a set of pedigrees out to disk.
write(Iterable<IlluminaAdpcFileWriter.Record>) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
write(OUTPUT_RECORD) - Method in interface picard.illumina.BasecallsConverter.ConvertedClusterDataWriter
  Write out a single record of type OUTPUT_RECORD.
write(IlluminaAdpcFileWriter.Record) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
WRITE_ORIGINAL_ALLELES - Variable in class picard.vcf.LiftoverVcf
WRITE_ORIGINAL_POSITION - Variable in class picard.vcf.LiftoverVcf
WRITE_READS_FILES - Variable in class picard.sam.FilterSamReads
writeAlignment(SAMRecord) - Method in class picard.sam.FixMateInformation
writeAsVcf(File, File) - Method in class picard.fingerprint.HaplotypeMap
writeBfqFiles() - Method in class picard.fastq.SamToBfqWriter
  Writes the binary fastq file(s) to the output directory
writeFingerPrint(Fingerprint, File, File, String, String) - Static method in class picard.fingerprint.FingerprintUtils
  A function that takes a Fingerprint and writes it as a VCF to a file
writeReport(File) - Method in class picard.sam.util.SamComparison
writeReport(File, List<Header>) - Method in class picard.sam.util.SamComparison
writerPool - Variable in class picard.illumina.BasecallsConverter
writeToFile(File) - Method in class picard.fingerprint.HaplotypeMap
  Writes out a HaplotypeMap file with the contents of this map.

## X

x - Variable in class picard.sam.util.PhysicalLocationInt
X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
X - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
  The X coordinate of the read within the tile
xIsSet() - Method in class picard.illumina.parser.ClusterData
xPos - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
  The x-position as it occurs in the file being read
xQseqCoord - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
  The QSeq style x-coordinat, an integer = Math.round(xPos*10 + 1000)

## Y

y - Variable in class picard.sam.util.PhysicalLocationInt
Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
Y - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
  The Y coordinate of the read within the tile
yIsSet() - Method in class picard.illumina.parser.ClusterData
yPos - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
  The y-position as it occurs in the file being read
yQseqCoord - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
  The QSeq style y-coordinates, an integer = Math.round(yPos*10 + 1000)

## Z

ZCALL_THRESHOLDS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ZCALL_THRESHOLDS_FILE - Variable in class picard.arrays.MergePedIntoVcf
ZCALL_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
  The version of ZCall used for calling this sample
ZCALL_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ZCALL_VERSION - Variable in class picard.arrays.MergePedIntoVcf
ZERO_CVG_TARGETS_PCT - Variable in class picard.analysis.directed.PanelMetricsBase
  The fraction of targets that did not reach coverage=1 over any base.
ZEROED_OUT_ASSAY - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ZTHRESH_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
ZTHRESH_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields

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