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picard

Files of the artifact picard version 2.0.0 from the group com.github.broadinstitute.

Artifact picard
Group com.github.broadinstitute
Version 2.0.0
Last update 03. December 2015
Tags: picard
Organization com.github.broadinstitute
URL http://samtools.github.io/htsjdk/
License MIT License
Dependencies amount 2
Dependencies htsjdk, gatk-tools-java,
There are maybe transitive dependencies!
There is a newer version: 3.2.0
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picard
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Source code of picard version 2.0.0

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.CollectWgsMetricsFromQuerySorted
picard.analysis.picard.analysis.CollectWgsMetricsFromSampledSites
picard.analysis.picard.analysis.CompareMetrics
picard.analysis.picard.analysis.GcBiasDetailMetrics
picard.analysis.picard.analysis.GcBiasMetricsCollector
picard.analysis.picard.analysis.GcBiasSummaryMetrics
picard.analysis.picard.analysis.GcBiasUtils
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.GcBiasMetrics
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.ReadEndsForMarkDuplicatesWithBarcodes
picard.sam.markduplicates.util.picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
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.QuerySortedReadPairIteratorUtil
picard.util.picard.util.RExecutor
picard.util.picard.util.ScatterIntervalsByNs
picard.util.picard.util.TabbedInputParser
picard.util.picard.util.TabbedTextFileWithHeaderParser
picard.util.picard.util.TestNGUtil
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.GA4GHScheme
picard.vcf.picard.vcf.GA4GHSchemeWithMissingAsHomRef
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.GenotypeConcordanceSchemeFactory
picard.vcf.picard.vcf.GenotypeConcordanceStateCodes
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




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