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picard-tools package

picard-tools 2.26.6+dfsg-2 source package in Ubuntu

Changelog

picard-tools (2.26.6+dfsg-2) unstable; urgency=medium

  * Removing now useless versioned dependencies
  * Deleting the main class name in the jar invocation by PicardCommandLine

 -- Pierre Gruet <email address hidden>  Sat, 04 Dec 2021 10:21:59 +0100

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Uploaded by:
Debian Med
Uploaded to:
Sid
Original maintainer:
Debian Med
Architectures:
all
Section:
science
Urgency:
Medium Urgency

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Series Pocket Published Component Section

Builds

Jammy: [FULLYBUILT] amd64

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File Size SHA-256 Checksum
picard-tools_2.26.6+dfsg-2.dsc 2.7 KiB 86a81cdfab0292e9b70e5837f782445a7bd85504ab778b81fe90f42c1110c5a4
picard-tools_2.26.6+dfsg.orig.tar.xz 20.2 MiB 8e93e4f5995bec467e4a061e5c8a4a3b4258c3266b19ffa45ff6638bed8c4420
picard-tools_2.26.6+dfsg-2.debian.tar.xz 19.6 KiB 103331d01ba58e7c0ea89d4e604bd0e5bf29d14e0042e236c0682de2e0d62037

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Binary packages built by this source

libpicard-java: Java library to manipulate SAM and BAM files

 SAM (Sequence Alignment/Map) format is a generic format for storing
 large nucleotide sequence alignments. This library provides classes to
 manipulate SAM and BAM files.
 .
 A command line wrapper for this library is provided in the picard-tools
 package.

libpicard-java-doc: Documentation for the java picard library

 SAM (Sequence Alignment/Map) format is a generic format for storing
 large nucleotide sequence alignments. The picard java library provides classes
 to manipulate SAM and BAM files.
 .
 This package contains the javadoc of the picard java library.

picard-tools: Command line tools to manipulate SAM and BAM files

 SAM (Sequence Alignment/Map) format is a generic format for storing
 large nucleotide sequence alignments. Picard Tools includes these
 utilities to manipulate SAM and BAM files:
  AddCommentsToBam FifoBuffer
  AddOrReplaceReadGroups FilterSamReads
  BaitDesigner FilterVcf
  BamIndexStats FixMateInformation
  BamToBfq GatherBamFiles
  BedToIntervalList GatherVcfs
  BuildBamIndex GenotypeConcordance
  CalculateHsMetrics IlluminaBasecallsToFastq
  CalculateReadGroupChecksum IlluminaBasecallsToSam
  CheckIlluminaDirectory LiftOverIntervalList
  CheckTerminatorBlock LiftoverVcf
  CleanSam MakeSitesOnlyVcf
  CollectAlignmentSummaryMetrics MarkDuplicates
  CollectBaseDistributionByCycle MarkDuplicatesWithMateCigar
  CollectGcBiasMetrics MarkIlluminaAdapters
  CollectHiSeqXPfFailMetrics MeanQualityByCycle
  CollectIlluminaBasecallingMetrics MergeBamAlignment
  CollectIlluminaLaneMetrics MergeSamFiles
  CollectInsertSizeMetrics MergeVcfs
  CollectJumpingLibraryMetrics NormalizeFasta
  CollectMultipleMetrics PositionBasedDownsampleSam
  CollectOxoGMetrics QualityScoreDistribution
  CollectQualityYieldMetrics RenameSampleInVcf
  CollectRawWgsMetrics ReorderSam
  CollectRnaSeqMetrics ReplaceSamHeader
  CollectRrbsMetrics RevertOriginalBaseQualitiesAndAddMateCigar
  CollectSequencingArtifactMetrics RevertSam
  CollectTargetedPcrMetrics SamFormatConverter
  CollectVariantCallingMetrics SamToFastq
  CollectWgsMetrics ScatterIntervalsByNs
  CompareMetrics SortSam
  CompareSAMs SortVcf
  ConvertSequencingArtifactToOxoG SplitSamByLibrary
  CreateSequenceDictionary SplitVcfs
  DownsampleSam UpdateVcfSequenceDictionary
  EstimateLibraryComplexity ValidateSamFile
  ExtractIlluminaBarcodes VcfFormatConverter
  ExtractSequences VcfToIntervalList
  FastqToSam ViewSam