[med-svn] [SCM] picard-tools branch, master, updated. debian/1.90-3-7-g53b7a12

[Olivier Sallou]

The following commit has been merged in the master branch:
commit 0afae2088ecfda16cf5c7b573c4b0994aaf4731d
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Thu Jul 25 14:21:01 2013 +0200

    update with new commands

diff --git a/debian/bin/picard-tools b/debian/bin/picard-tools
index 867a469..1392b40 100755
--- a/debian/bin/picard-tools
+++ b/debian/bin/picard-tools
@@ -20,21 +20,31 @@ case $command in
 	BamToBfq)                       main=net.sf.picard.fastq.BamToBfq;;
 	BuildBamIndex)                  main=net.sf.picard.sam.BuildBamIndex;;
 	CalculateHsMetrics)             main=net.sf.picard.analysis.directed.CalculateHsMetrics;;
+	CheckIlluminaDirectory)         main=net.sf.picard.illumina.CheckIlluminaDirectory;;
 	CleanSam)                       main=net.sf.picard.sam.CleanSam;;
 	CollectAlignmentSummaryMetrics) main=net.sf.picard.analysis.CollectAlignmentSummaryMetrics;;
 	CollectGcBiasMetrics)           main=net.sf.picard.analysis.CollectGcBiasMetrics;;
 	CollectInsertSizeMetrics)       main=net.sf.picard.analysis.CollectInsertSizeMetrics;;
 	CollectMultipleMetrics)         main=net.sf.picard.analysis.CollectMultipleMetrics;;
+	CollectRnaSeqMetrics)           main=net.sf.picard.analysis.CollectRnaSeqMetrics;;
+	CollectTargetedPcrMetrics)      main=net.sf.picard.analysis.CollectTargetedPcrMetrics;;
 	CompareSAMs)                    main=net.sf.picard.sam.CompareSAMs;;
 	CreateSequenceDictionary)       main=net.sf.picard.sam.CreateSequenceDictionary;;
+	DownsampleSam)                  main=net.sf.picard.sam.DownsampleSam;;
 	EstimateLibraryComplexity)      main=net.sf.picard.sam.EstimateLibraryComplexity;;
+	ExtractIlluminaBarcodes)        main=net.sf.picard.illumina.ExtractIlluminaBarcodes;;
 	ExtractSequences)               main=net.sf.picard.reference.ExtractSequences;;
 	FastqToSam)                     main=net.sf.picard.sam.FastqToSam;;
+	FilterSamReads)                 main=net.sf.picard.sam.FilterSamReads;;
 	FixMateInformation)             main=net.sf.picard.sam.FixMateInformation;;
+	IlluminaBasecallsToFastq)       main=net.sf.picard.illumina.IlluminaBasecallsToFastq;;
+	IlluminaBasecallsToSam)         main=net.sf.picard.illumina.IlluminaBasecallsToSam;;
+	IntervalListTools)              main=net.sf.picard.util.IntervalList;;
 	MarkDuplicates)                 main=net.sf.picard.sam.MarkDuplicates;;
 	MeanQualityByCycle)             main=net.sf.picard.analysis.MeanQualityByCycle;;
 	MergeBamAlignment)              main=net.sf.picard.sam.MergeBamAlignment;;
 	MergeSamFiles)                  main=net.sf.picard.sam.MergeSamFiles;;
+	MergeVcfs)                      main=net.sf.picard.vcf.MergeVcfs;;
 	NormalizeFasta)                 main=net.sf.picard.reference.NormalizeFasta;;
 	QualityScoreDistribution)       main=net.sf.picard.analysis.QualityScoreDistribution;;
 	ReorderSam)                     main=net.sf.picard.sam.ReorderSam;;
@@ -43,7 +53,9 @@ case $command in
 	SamFormatConverter)             main=net.sf.picard.sam.SamFormatConverter;;
 	SamToFastq)                     main=net.sf.picard.sam.SamToFastq;;
 	SortSam)                        main=net.sf.picard.sam.SortSam;;
+	SplitVcfs)                      main=net.sf.picard.vcf.SplitVcfs;;
 	ValidateSamFile)                main=net.sf.picard.sam.ValidateSamFile;;
+	VcfFormatConverter)             main=net.sf.picard.vcf.VcfFormatConverter;;
 	ViewSam)                        main=net.sf.picard.sam.ViewSam;;
 
 	--help)
@@ -62,4 +74,4 @@ EOF
 esac
 
 p=/usr/share/java
-exec java $JAVA_OPTIONS -XX:MaxPermSize=256m -cp $p/jbzip2.jar:$p/picard.jar:$p/sam.jar:$p/cofoja.jar:$p/commons-jexl2.jar $main "$@"
+exec java ${JAVA_OPTIONS-} -XX:MaxPermSize=256m -cp $p/jbzip2.jar:$p/picard.jar:$p/sam.jar:$p/cofoja.jar:$p/commons-jexl2.jar $main "$@"
diff --git a/debian/picard-tools.1 b/debian/picard-tools.1
index 7d55fe0..35f7995 100644
--- a/debian/picard-tools.1
+++ b/debian/picard-tools.1
@@ -1,4 +1,4 @@
-.TH picard-tools "1" "July 2010" "picard-tools 1.27" "User Commands"
+.TH picard-tools "1" "July 2013" "picard-tools 1.95" "User Commands"
 .SH NAME
 picard-tools \- manipulate SAM and BAM files
 .SH SYNOPSIS
@@ -9,8 +9,8 @@ large nucleotide sequence alignments.
 
 Picard Tools includes these utilities to manipulate SAM and BAM files:
  AddOrReplaceReadGroups
- BamIndexStats
  BamToBfq
+ BamIndexStats
  BuildBamIndex
  CalculateHsMetrics
  CleanSam
@@ -18,20 +18,27 @@ Picard Tools includes these utilities to manipulate SAM and BAM files:
  CollectGcBiasMetrics
  CollectInsertSizeMetrics
  CollectMultipleMetrics
+ CollectTargetedPcrMetrics
  CollectRnaSeqMetrics
  CompareSAMs
  CreateSequenceDictionary
- ExtractIlluminaBarcodes 
+ DownsampleSam
+ ExtractIlluminaBarcodes
  EstimateLibraryComplexity
- ExtractSequences
  FastqToSam
+ FilterSamReads
  FixMateInformation
- IlluminaBasecallsToSam 
+ IlluminaBasecallsToFastq
+ IlluminaBasecallsToSam
+ CheckIlluminaDirectory
+ IntervalListTools
  MarkDuplicates
  MeanQualityByCycle
  MergeBamAlignment
  MergeSamFiles
+ MergeVcfs
  NormalizeFasta
+ ExtractSequences
  QualityScoreDistribution
  ReorderSam
  ReplaceSamHeader
@@ -39,6 +46,8 @@ Picard Tools includes these utilities to manipulate SAM and BAM files:
  SamFormatConverter
  SamToFastq
  SortSam
+ VcfFormatConverter
+ SplitVcfs
  ValidateSamFile
  ViewSam
 .SH "REPORTING BUGS"

-- 
manipulate SAM and BAM files