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picard-tools package

picard-tools 3.1.1+dfsg-1 source package in Ubuntu

Changelog

picard-tools (3.1.1+dfsg-1) unstable; urgency=medium

  * New upstream version 3.1.1+dfsg
  * Refreshing patches
  * Enabling the test with BarclayParser again
  * Patching out more code portions using google-nio

 -- Pierre Gruet <email address hidden>  Sat, 16 Dec 2023 22:38:31 +0100

Upload details

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

See full publishing history Publishing

Series Pocket Published Component Section
Oracular release universe science
Noble release universe science

Builds

Noble: [FULLYBUILT] amd64

Downloads

File Size SHA-256 Checksum
picard-tools_3.1.1+dfsg-1.dsc 2.7 KiB d30484cc18e8f60c7215827bfd50971b93f46b6763405eacaadfd35a1264a04f
picard-tools_3.1.1+dfsg.orig.tar.xz 19.5 MiB 3360065cec9d152ed3445b93f228b716c0be3018406ebf8e742e5da907151209
picard-tools_3.1.1+dfsg-1.debian.tar.xz 22.2 KiB e76aca503be04dda1795b023aad8f491319e3b41553311517fc1e2ef3b3a143e

Available diffs

No changes file available.

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
                                    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