Source: picard-tools
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Shaun Jackman <sjackman@debian.org>,
 Charles Plessy <plessy@debian.org>
Build-Depends: ant, openjdk-6-jdk|java-compiler, testng,
 debhelper (>= 7.0.50~)
Standards-Version: 3.9.1
Homepage: http://picard.sourceforge.net/
Vcs-Git: git://git.debian.org/git/debian-med/picard-tools.git
Vcs-Browser: http://git.debian.org/?p=debian-med/picard-tools.git

Package: libsam-java
Section: java
Architecture: all
Depends: ${misc:Depends}
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.

Package: picard-tools
Architecture: all
Depends: openjdk-6-jre|java-runtime, ${misc:Depends},
 libsam-java (>= ${source:Version})
Suggests: python, r-base-core
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:
 BamToBfq                        MeanQualityByCycle
 BuildBamIndex                   MergeBamAlignment
 CalculateHsMetrics              MergeSamFiles
 CleanSam                        NormalizeFasta
 CollectAlignmentSummaryMetrics  QualityScoreDistribution
 CollectGcBiasMetrics            ReplaceSamHeader
 CollectInsertSizeMetrics        RevertSam
 CompareSAMs                     SamFormatConverter
 CreateSequenceDictionary        SamToFastq
 EstimateLibraryComplexity       SortSam
 FastqToSam                      ValidateSamFile
 FixMateInformation              ViewSam
 MarkDuplicates
