picard-tools_2.8.1+dfsg-2_all.deb


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Description

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

Property Value
Distribution Ubuntu 17.10 (Artful Aardvark)
Repository Ubuntu Universe i386
Package name picard-tools
Package version 2.8.1+dfsg
Package release 2
Package architecture all
Package type deb
Installed size 333 B
Download size 302.11 KB
Official Mirror archive.ubuntu.com
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

Alternatives

Package Version Architecture Repository
picard-tools_2.8.1+dfsg-2_all.deb 2.8.1+dfsg all Ubuntu Universe
picard-tools - - -

Requires

Name Value
default-jre -
java6-runtime -
libpicard-java = 2.8.1+dfsg-2

Download

Type URL
Binary Package picard-tools_2.8.1+dfsg-2_all.deb
Source Package picard-tools

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install picard-tools deb package:
    # sudo apt-get install picard-tools

Files

Path
/usr/bin/PicardCommandLine
/usr/bin/picard-tools
/usr/share/doc/picard-tools/changelog.Debian.gz
/usr/share/doc/picard-tools/copyright
/usr/share/doc/picard-tools/mini.vcf.gz
/usr/share/doc/picard-tools/mini.vcf.idx
/usr/share/doc/picard-tools/test.fasta
/usr/share/doc/picard-tools/test.sam
/usr/share/doc/picard-tools/unmapped.sam
/usr/share/man/man1/PicardCommandLine.1.gz
/usr/share/man/man1/picard-tools.1.gz

Changelog

2017-03-31 - Nadiya Sitdykova <rovenskasa@gmailc.om>
picard-tools (2.8.1+dfsg-2) unstable; urgency=medium
* Team upload.
* Add simple autopkgtest test-suite
Closes: #848334
* Add README.test
2017-01-10 - Andreas Tille <tille@debian.org>
picard-tools (2.8.1+dfsg-1) unstable; urgency=medium
[ Vincent Danjean ]
* Ensure versioned B-D and Depends are in sync
[ Andreas Tille ]
* New upstream version
2016-12-20 - Andreas Tille <tille@debian.org>
picard-tools (2.8.0+dfsg-2) unstable; urgency=medium
* Fix versioned Depends
Closes: #848831
2016-12-18 - Andreas Tille <tille@debian.org>
picard-tools (2.8.0+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
* debhelper 10
* d/watch: version=4
* Ensure that major version of htsjdk is 2.8
[ Vincent Danjean ]
* Really force C locale for tests
* Fix parameter type for one test
* cleanup generated test files 
2016-11-27 - Vincent Danjean <vdanjean@debian.org>
picard-tools (2.7.1+dfsg-2) unstable; urgency=medium
* Rebuild with htsjdk 2.7
* Ensure for build and runtime that major versions of picard-tools
and htsjdk are the same.
2016-10-27 - Andreas Tille <tille@debian.org>
picard-tools (2.7.1+dfsg-1) unstable; urgency=medium
* New upstream version
2016-09-10 - Sascha Steinbiss <satta@debian.org>
picard-tools (2.6.0+dfsg-1) unstable; urgency=medium
* Team upload.
[ Andreas Tille ]
* New upstream version
* Bump versioned dependency of libhtsjdk-java
* d/copyright: remove *.bak files which are removed in clean target anyway
[ Vincent Danjean ]
* Avoid warnings when running PicardCommandLine
[ Sascha Steinbiss ]
* Patch build.gradle to remove shadowJar.
* Fix test case with mismatching data provider and test method.
* Drop unneeded jh_installlibs override.
* Remove duplicated build-deps.
2016-07-07 - Vincent Danjean <vdanjean@debian.org>
picard-tools (2.5.0-gradle+dfsg-1) unstable; urgency=medium
* New upstream release
* Switch to gradle build system
2016-04-05 - Andreas Tille <tille@debian.org>
picard-tools (2.1.1+dfsg-1) unstable; urgency=medium
* New upstream version
* Adapt debian/watch to use xz compression
* Remove Shaun Jackman and add myself as Uploader
* cme fix dpkg-control
[ Steffen Moeller and Jon Ison ]
* Added EDAM annotation to debian/upstream/edam
2015-09-08 - Vincent Danjean <vdanjean@debian.org>
picard-tools (1.138+dfsg.1-1) unstable; urgency=medium
* New release from new upstream location (github). Closes: #798051
* Full reorganization of the packaging

See Also

Package Description
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