Source: picard-tools Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Olivier Sallou , Vincent Danjean , Andreas Tille , Steffen Moeller , Pierre Gruet Section: science Priority: optional Build-Depends: default-jdk, debhelper-compat (= 13), javahelper, gradle-debian-helper, maven-repo-helper, libguava-java, libcommons-collections4-java, libcommons-io-java, libcommons-lang-java, libcommons-lang3-java, libcommons-math3-java, libbarclay-java, libgkl-java (>= 0.8.6+dfsg-2), libgkl-jni [amd64], libgatk-native-bindings-java, # htsjdk and picard-tools are relased nearly together libhtsjdk-java (>= 3.0.2+dfsg), libjoptsimple-java, # required for tests: testng, r-base-core, # required for links and dependencies in documentation: default-jdk-doc, libhtsjdk-java-doc, libjs-jquery Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/picard-tools Vcs-Git: https://salsa.debian.org/med-team/picard-tools.git Homepage: https://broadinstitute.github.io/picard/ Rules-Requires-Root: no 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 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}, libbarclay-java, libgkl-java, libcommons-lang3-java, libcommons-math3-java, libgatk-native-bindings-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 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 Multi-Arch: foreign Section: doc Depends: ${misc:Depends}, ${java:Depends}, libjs-jquery 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.