Download picard JAR 1.131 with all dependencies

Files of the artifact picard version 1.131 from the group com.github.broadinstitute.

Artifact picard
Group com.github.broadinstitute
Version 1.131

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picard

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Source code of picard version 1.131

META-INF

META-INF.META-INF.MANIFEST.MF

picard

picard.picard.PicardException

picard.picard.Test

picard.analysis

picard.analysis.picard.analysis.AlignmentSummaryMetrics

picard.analysis.picard.analysis.AlignmentSummaryMetricsCollector

picard.analysis.picard.analysis.BaseDistributionByCycleMetrics

picard.analysis.picard.analysis.CollectAlignmentSummaryMetrics

picard.analysis.picard.analysis.CollectBaseDistributionByCycle

picard.analysis.picard.analysis.CollectGcBiasMetrics

picard.analysis.picard.analysis.CollectInsertSizeMetrics

picard.analysis.picard.analysis.CollectJumpingLibraryMetrics

picard.analysis.picard.analysis.CollectMultipleMetrics

picard.analysis.picard.analysis.CollectOxoGMetrics

picard.analysis.picard.analysis.CollectQualityYieldMetrics

picard.analysis.picard.analysis.CollectRawWgsMetrics

picard.analysis.picard.analysis.CollectRnaSeqMetrics

picard.analysis.picard.analysis.CollectRrbsMetrics

picard.analysis.picard.analysis.CollectWgsMetrics

picard.analysis.picard.analysis.CompareMetrics

picard.analysis.picard.analysis.GcBiasDetailMetrics

picard.analysis.picard.analysis.GcBiasSummaryMetrics

picard.analysis.picard.analysis.InsertSizeMetrics

picard.analysis.picard.analysis.JumpingLibraryMetrics

picard.analysis.picard.analysis.MeanQualityByCycle

picard.analysis.picard.analysis.MetricAccumulationLevel

picard.analysis.picard.analysis.QualityScoreDistribution

picard.analysis.picard.analysis.RnaSeqMetrics

picard.analysis.picard.analysis.RrbsCpgDetailMetrics

picard.analysis.picard.analysis.RrbsMetrics

picard.analysis.picard.analysis.RrbsMetricsCollector

picard.analysis.picard.analysis.RrbsSummaryMetrics

picard.analysis.picard.analysis.SinglePassSamProgram

picard.analysis.artifacts

picard.analysis.artifacts.picard.analysis.artifacts.ArtifactCounter

picard.analysis.artifacts.picard.analysis.artifacts.CollectSequencingArtifactMetrics

picard.analysis.artifacts.picard.analysis.artifacts.ContextAccumulator

picard.analysis.artifacts.picard.analysis.artifacts.ConvertSequencingArtifactToOxoG

picard.analysis.artifacts.picard.analysis.artifacts.SequencingArtifactMetrics

picard.analysis.artifacts.picard.analysis.artifacts.Transition

picard.analysis.directed

picard.analysis.directed.picard.analysis.directed.CalculateHsMetrics

picard.analysis.directed.picard.analysis.directed.CollectTargetedMetrics

picard.analysis.directed.picard.analysis.directed.CollectTargetedPcrMetrics

picard.analysis.directed.picard.analysis.directed.HsMetricCollector

picard.analysis.directed.picard.analysis.directed.HsMetrics

picard.analysis.directed.picard.analysis.directed.InsertSizeMetricsCollector

picard.analysis.directed.picard.analysis.directed.RnaSeqMetricsCollector

picard.analysis.directed.picard.analysis.directed.TargetMetricsCollector

picard.analysis.directed.picard.analysis.directed.TargetedPcrMetrics

picard.analysis.directed.picard.analysis.directed.TargetedPcrMetricsCollector

picard.annotation

picard.annotation.picard.annotation.AnnotationException

picard.annotation.picard.annotation.Gene

picard.annotation.picard.annotation.GeneAnnotationReader

picard.annotation.picard.annotation.LocusFunction

picard.annotation.picard.annotation.RefFlatReader

picard.cmdline

picard.cmdline.picard.cmdline.ClassFinder

picard.cmdline.picard.cmdline.CommandLineDefaults

picard.cmdline.picard.cmdline.CommandLineParseException

picard.cmdline.picard.cmdline.CommandLineParser

picard.cmdline.picard.cmdline.CommandLineParserDefinitionException

picard.cmdline.picard.cmdline.CommandLineProgram

picard.cmdline.picard.cmdline.CommandLineProgramGroup

picard.cmdline.picard.cmdline.CommandLineProgramProperties

picard.cmdline.picard.cmdline.CreateHtmlDocForProgram

picard.cmdline.picard.cmdline.CreateHtmlDocForStandardOptions

picard.cmdline.picard.cmdline.NestedOptions

picard.cmdline.picard.cmdline.Option

picard.cmdline.picard.cmdline.PicardCommandLine

picard.cmdline.picard.cmdline.PositionalArguments

picard.cmdline.picard.cmdline.StandardOptionDefinitions

picard.cmdline.programgroups

picard.cmdline.programgroups.picard.cmdline.programgroups.Fasta

picard.cmdline.programgroups.picard.cmdline.programgroups.Illumina

picard.cmdline.programgroups.picard.cmdline.programgroups.Intervals

picard.cmdline.programgroups.picard.cmdline.programgroups.Metrics

picard.cmdline.programgroups.picard.cmdline.programgroups.None

picard.cmdline.programgroups.picard.cmdline.programgroups.SamOrBam

picard.cmdline.programgroups.picard.cmdline.programgroups.Testing

picard.cmdline.programgroups.picard.cmdline.programgroups.VcfOrBcf

picard.fastq

picard.fastq.picard.fastq.BamToBfq

picard.fastq.picard.fastq.BamToBfqWriter

picard.fastq.picard.fastq.Casava18ReadNameEncoder

picard.fastq.picard.fastq.IlluminaReadNameEncoder

picard.fastq.picard.fastq.ReadNameEncoder

picard.illumina

picard.illumina.picard.illumina.CheckIlluminaDirectory

picard.illumina.picard.illumina.ClusterDataToSamConverter

picard.illumina.picard.illumina.CollectIlluminaBasecallingMetrics

picard.illumina.picard.illumina.CollectIlluminaLaneMetrics

picard.illumina.picard.illumina.ExtractIlluminaBarcodes

picard.illumina.picard.illumina.IlluminaBasecallingMetrics

picard.illumina.picard.illumina.IlluminaBasecallsConverter

picard.illumina.picard.illumina.IlluminaBasecallsToFastq

picard.illumina.picard.illumina.IlluminaBasecallsToSam

picard.illumina.picard.illumina.IlluminaLaneMetrics

picard.illumina.picard.illumina.IlluminaPhasingMetrics

picard.illumina.picard.illumina.LanePhasingMetricsCollector

picard.illumina.picard.illumina.MarkIlluminaAdapters

picard.illumina.parser

picard.illumina.parser.picard.illumina.parser.BarcodeParser

picard.illumina.parser.picard.illumina.parser.BclData

picard.illumina.parser.picard.illumina.parser.BclParser

picard.illumina.parser.picard.illumina.parser.ClusterData

picard.illumina.parser.picard.illumina.parser.ClusterIntensityFileReader

picard.illumina.parser.picard.illumina.parser.CycleIlluminaFileMap

picard.illumina.parser.picard.illumina.parser.FilterParser

picard.illumina.parser.picard.illumina.parser.FourChannelIntensityData

picard.illumina.parser.picard.illumina.parser.IlluminaData

picard.illumina.parser.picard.illumina.parser.IlluminaDataProvider

picard.illumina.parser.picard.illumina.parser.IlluminaDataProviderFactory

picard.illumina.parser.picard.illumina.parser.IlluminaDataType

picard.illumina.parser.picard.illumina.parser.IlluminaFileMap

picard.illumina.parser.picard.illumina.parser.IlluminaFileNotFoundException

picard.illumina.parser.picard.illumina.parser.IlluminaFileUtil

picard.illumina.parser.picard.illumina.parser.IlluminaMetricsCode

picard.illumina.parser.picard.illumina.parser.IlluminaParser

picard.illumina.parser.picard.illumina.parser.IlluminaTextIterator

picard.illumina.parser.picard.illumina.parser.IntensityChannel

picard.illumina.parser.picard.illumina.parser.MultiTileBclFileUtil

picard.illumina.parser.picard.illumina.parser.MultiTileBclParser

picard.illumina.parser.picard.illumina.parser.MultiTileFileUtil

picard.illumina.parser.picard.illumina.parser.MultiTileFilterParser

picard.illumina.parser.picard.illumina.parser.MultiTileLocsParser

picard.illumina.parser.picard.illumina.parser.MultiTileParser

picard.illumina.parser.picard.illumina.parser.OutputMapping

picard.illumina.parser.picard.illumina.parser.ParameterizedFileUtil

picard.illumina.parser.picard.illumina.parser.PerTileCycleParser

picard.illumina.parser.picard.illumina.parser.PerTileFileUtil

picard.illumina.parser.picard.illumina.parser.PerTileParser

picard.illumina.parser.picard.illumina.parser.PerTilePerCycleFileUtil

picard.illumina.parser.picard.illumina.parser.PosParser

picard.illumina.parser.picard.illumina.parser.Range

picard.illumina.parser.picard.illumina.parser.ReadData

picard.illumina.parser.picard.illumina.parser.ReadDescriptor

picard.illumina.parser.picard.illumina.parser.ReadStructure

picard.illumina.parser.picard.illumina.parser.ReadType

picard.illumina.parser.picard.illumina.parser.Tile

picard.illumina.parser.picard.illumina.parser.TileIndex

picard.illumina.parser.picard.illumina.parser.TileMetricsUtil

picard.illumina.parser.picard.illumina.parser.TilePhasingValue

picard.illumina.parser.picard.illumina.parser.TileTemplateRead

picard.illumina.parser.fakers

picard.illumina.parser.fakers.picard.illumina.parser.fakers.BarcodeFileFaker

picard.illumina.parser.fakers.picard.illumina.parser.fakers.BciFileFaker

picard.illumina.parser.fakers.picard.illumina.parser.fakers.BclFileFaker

picard.illumina.parser.fakers.picard.illumina.parser.fakers.ClocsFileFaker

picard.illumina.parser.fakers.picard.illumina.parser.fakers.FileFaker

picard.illumina.parser.fakers.picard.illumina.parser.fakers.FilterFileFaker

picard.illumina.parser.fakers.picard.illumina.parser.fakers.LocsFileFaker

picard.illumina.parser.fakers.picard.illumina.parser.fakers.MultiTileBclFileFaker

picard.illumina.parser.fakers.picard.illumina.parser.fakers.MultiTileLocsFileFaker

picard.illumina.parser.fakers.picard.illumina.parser.fakers.PosFileFaker

picard.illumina.parser.readers

picard.illumina.parser.readers.picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

picard.illumina.parser.readers.picard.illumina.parser.readers.BarcodeFileReader

picard.illumina.parser.readers.picard.illumina.parser.readers.BclIndexReader

picard.illumina.parser.readers.picard.illumina.parser.readers.BclQualityEvaluationStrategy

picard.illumina.parser.readers.picard.illumina.parser.readers.BclReader

picard.illumina.parser.readers.picard.illumina.parser.readers.ClocsFileReader

picard.illumina.parser.readers.picard.illumina.parser.readers.FilterFileReader

picard.illumina.parser.readers.picard.illumina.parser.readers.LocsFileReader

picard.illumina.parser.readers.picard.illumina.parser.readers.MMapBackedIteratorFactory

picard.illumina.parser.readers.picard.illumina.parser.readers.PosFileReader

picard.illumina.parser.readers.picard.illumina.parser.readers.TileMetricsOutReader

picard.illumina.quality

picard.illumina.quality.picard.illumina.quality.CollectHiSeqXPfFailMetrics

picard.metrics

picard.metrics.picard.metrics.MultiLevelCollector

picard.metrics.picard.metrics.MultilevelMetrics

picard.metrics.picard.metrics.PerUnitMetricCollector

picard.metrics.picard.metrics.SAMRecordAndReference

picard.metrics.picard.metrics.SAMRecordAndReferenceMultiLevelCollector

picard.metrics.picard.metrics.SAMRecordMultiLevelCollector

picard.pedigree

picard.pedigree.picard.pedigree.PedFile

picard.pedigree.picard.pedigree.Sex

picard.reference

picard.reference.picard.reference.ExtractSequences

picard.reference.picard.reference.NormalizeFasta

picard.sam

picard.sam.picard.sam.AbstractAlignmentMerger

picard.sam.picard.sam.AddCommentsToBam

picard.sam.picard.sam.AddOrReplaceReadGroups

picard.sam.picard.sam.BamIndexStats

picard.sam.picard.sam.BestEndMapqPrimaryAlignmentStrategy

picard.sam.picard.sam.BestMapqPrimaryAlignmentSelectionStrategy

picard.sam.picard.sam.BuildBamIndex

picard.sam.picard.sam.CalculateReadGroupChecksum

picard.sam.picard.sam.CheckTerminatorBlock

picard.sam.picard.sam.CleanSam

picard.sam.picard.sam.CompareSAMs

picard.sam.picard.sam.CreateSequenceDictionary

picard.sam.picard.sam.DownsampleSam

picard.sam.picard.sam.DuplicationMetrics

picard.sam.picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy

picard.sam.picard.sam.FastqToSam

picard.sam.picard.sam.FilterSamReads

picard.sam.picard.sam.FixMateInformation

picard.sam.picard.sam.GatherBamFiles

picard.sam.picard.sam.HitsForInsert

picard.sam.picard.sam.MergeBamAlignment

picard.sam.picard.sam.MergeSamFiles

picard.sam.picard.sam.MostDistantPrimaryAlignmentSelectionStrategy

picard.sam.picard.sam.MultiHitAlignedReadIterator

picard.sam.picard.sam.PositionBasedDownsampleSam

picard.sam.picard.sam.PrimaryAlignmentSelectionStrategy

picard.sam.picard.sam.ReorderSam

picard.sam.picard.sam.ReplaceSamHeader

picard.sam.picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar

picard.sam.picard.sam.RevertSam

picard.sam.picard.sam.SamAlignmentMerger

picard.sam.picard.sam.SamFormatConverter

picard.sam.picard.sam.SamToFastq

picard.sam.picard.sam.SortSam

picard.sam.picard.sam.SplitSamByLibrary

picard.sam.picard.sam.ValidateSamFile

picard.sam.picard.sam.ViewSam

picard.sam.markduplicates

picard.sam.markduplicates.picard.sam.markduplicates.EstimateLibraryComplexity

picard.sam.markduplicates.picard.sam.markduplicates.MarkDuplicates

picard.sam.markduplicates.picard.sam.markduplicates.MarkDuplicatesWithMateCigar

picard.sam.markduplicates.picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator

picard.sam.markduplicates.util

picard.sam.markduplicates.util.picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

picard.sam.markduplicates.util.picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

picard.sam.markduplicates.util.picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap

picard.sam.markduplicates.util.picard.sam.markduplicates.util.LibraryIdGenerator

picard.sam.markduplicates.util.picard.sam.markduplicates.util.MarkQueue

picard.sam.markduplicates.util.picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap

picard.sam.markduplicates.util.picard.sam.markduplicates.util.OpticalDuplicateFinder

picard.sam.markduplicates.util.picard.sam.markduplicates.util.PhysicalLocationForMateCigar

picard.sam.markduplicates.util.picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet

picard.sam.markduplicates.util.picard.sam.markduplicates.util.ReadEnds

picard.sam.markduplicates.util.picard.sam.markduplicates.util.ReadEndsForMarkDuplicates

picard.sam.markduplicates.util.picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec

picard.sam.markduplicates.util.picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap

picard.sam.markduplicates.util.picard.sam.markduplicates.util.ReadEndsForMateCigar

picard.sam.markduplicates.util.picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag

picard.sam.util

picard.sam.util.picard.sam.util.PhysicalLocation

picard.sam.util.picard.sam.util.ReadNameParsingUtils

picard.util

picard.util.picard.util.AbstractInputParser

picard.util.picard.util.AdapterMarker

picard.util.picard.util.AdapterPair

picard.util.picard.util.AsyncIterator

picard.util.picard.util.AtomicIterator

picard.util.picard.util.BaitDesigner

picard.util.picard.util.BasicInputParser

picard.util.picard.util.BedToIntervalList

picard.util.picard.util.CircularByteBuffer

picard.util.picard.util.ClippingUtility

picard.util.picard.util.CsvInputParser

picard.util.picard.util.DbSnpBitSetUtil

picard.util.picard.util.DelimitedTextFileWithHeaderIterator

picard.util.picard.util.FifoBuffer

picard.util.picard.util.FileChannelJDKBugWorkAround

picard.util.picard.util.IlluminaUtil

picard.util.picard.util.IntervalListScatterer

picard.util.picard.util.IntervalListTools

picard.util.picard.util.Iterators

picard.util.picard.util.LiftOverIntervalList

picard.util.picard.util.MathUtil

picard.util.picard.util.MetricsDoclet

picard.util.picard.util.RExecutor

picard.util.picard.util.ScatterIntervalsByNs

picard.util.picard.util.TabbedInputParser

picard.util.picard.util.TabbedTextFileWithHeaderParser

picard.util.picard.util.UnsignedTypeUtil

picard.util.picard.util.VariantType

picard.vcf

picard.vcf.picard.vcf.ByIntervalListVariantContextIterator

picard.vcf.picard.vcf.CallingMetricAccumulator

picard.vcf.picard.vcf.CollectVariantCallingMetrics

picard.vcf.picard.vcf.GatherVcfs

picard.vcf.picard.vcf.GenotypeConcordance

picard.vcf.picard.vcf.GenotypeConcordanceContingencyMetrics

picard.vcf.picard.vcf.GenotypeConcordanceCounts

picard.vcf.picard.vcf.GenotypeConcordanceDetailMetrics

picard.vcf.picard.vcf.GenotypeConcordanceScheme

picard.vcf.picard.vcf.GenotypeConcordanceStates

picard.vcf.picard.vcf.GenotypeConcordanceSummaryMetrics

picard.vcf.picard.vcf.LiftoverVcf

picard.vcf.picard.vcf.MakeSitesOnlyVcf

picard.vcf.picard.vcf.MergeVcfs

picard.vcf.picard.vcf.RenameSampleInVcf

picard.vcf.picard.vcf.SortVcf

picard.vcf.picard.vcf.SplitVcfs

picard.vcf.picard.vcf.UpdateVcfSequenceDictionary

picard.vcf.picard.vcf.VcfFormatConverter

picard.vcf.picard.vcf.VcfToIntervalList

picard.vcf.filter

picard.vcf.filter.picard.vcf.filter.AlleleBalanceFilter

picard.vcf.filter.picard.vcf.filter.DepthFilter

picard.vcf.filter.picard.vcf.filter.FilterApplyingVariantIterator

picard.vcf.filter.picard.vcf.filter.FilterVcf

picard.vcf.filter.picard.vcf.filter.FisherStrandFilter

picard.vcf.filter.picard.vcf.filter.GenotypeFilter

picard.vcf.filter.picard.vcf.filter.GenotypeQualityFilter

picard.vcf.filter.picard.vcf.filter.QdFilter

picard.vcf.filter.picard.vcf.filter.VariantFilter

picard.vcf.processor

picard.vcf.processor.picard.vcf.processor.VariantAccumulatorExecutor

picard.vcf.processor.picard.vcf.processor.VariantIteratorProducer

picard.vcf.processor.picard.vcf.processor.VariantProcessor

picard.vcf.processor.picard.vcf.processor.VcfFileSegment

picard.vcf.processor.picard.vcf.processor.VcfFileSegmentGenerator

picard.vcf.processor.util

picard.vcf.processor.util.picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator