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Source: picard-tools
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>,
Olivier Sallou <osallou@debian.org>,
Vincent Danjean <vdanjean@debian.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: default-jdk (>= 2:1.8),
debhelper (>= 10),
javahelper,
gradle-debian-helper,
maven-repo-helper,
libguava-java (>= 15.0),
# htsjdk and picard-tools are relased nearly together
libhtsjdk-java (>= 2.8~),
libhtsjdk-java (<< 2.9~),
# required for tests:
testng (>= 6.9.10),
r-base-core,
# required for links and dependencies in documentation:
default-jdk-doc,
libhtsjdk-java-doc,
libguava-java-doc
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/picard-tools.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/picard-tools.git
Homepage: http://broadinstitute.github.io/picard/
Package: picard-tools
Architecture: all
Depends: default-jre | java6-runtime,
${misc:Depends},
libpicard-java (= ${binary:Version})
Description: 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
Package: libpicard-java
Architecture: all
Section: java
Depends: ${misc:Depends},
# Getting versionned depends from Build-Depends
# This avoid mismatch, but each library must be extracted in debian/rules
${bd:libguava-java},
${bd:libhtsjdk-java}
# avoid ${java:Depends} that contains openjdk-8-jdk-headless
# due to tools.jar in classpath
Recommends: ${java:Recommends},
r-base-core
Suggests: picard-tools
Breaks: picard-tools (<< 1.114)
Replaces: picard-tools (<< 1.114)
Description: 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.
Package: libpicard-java-doc
Architecture: all
Section: doc
Depends: ${misc:Depends},
${java:Depends}
Recommends: ${java:Recommends}
Description: 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.
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