[med-svn] [SCM] picard-tools branch, master, updated. debian/1.90-3-7-g53b7a12
Olivier Sallou
olivier.sallou at debian.org
Thu Jul 25 12:38:35 UTC 2013
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
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