The following commit has been merged in the master branch:
commit 3a1681dc47839538cb988eb664a5c330dc48468b
Author: Shaun Jackman <[email protected]>
Date: Tue Mar 22 10:59:07 2011 -0700
* New upstream release. Closes: #619201.
* Add five commands to bin/picard-tools and picard-tools.1.
diff --git a/debian/bin/picard-tools b/debian/bin/picard-tools
index 0840841..f529f7d 100755
--- a/debian/bin/picard-tools
+++ b/debian/bin/picard-tools
@@ -15,6 +15,8 @@ else
fi
case $command in
+ AddOrReplaceReadGroups)
main=net.sf.picard.sam.AddOrReplaceReadGroups;;
+ BamIndexStats) main=net.sf.picard.sam.BamIndexStats;;
BamToBfq) main=net.sf.picard.fastq.BamToBfq;;
BuildBamIndex) main=net.sf.picard.util.BuildBamIndex;;
CalculateHsMetrics)
main=net.sf.picard.analysis.directed.CalculateHsMetrics;;
@@ -22,9 +24,11 @@ case $command in
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;;
CompareSAMs) main=net.sf.picard.sam.CompareSAMs;;
CreateSequenceDictionary)
main=net.sf.picard.sam.CreateSequenceDictionary;;
EstimateLibraryComplexity)
main=net.sf.picard.sam.EstimateLibraryComplexity;;
+ ExtractSequences)
main=net.sf.picard.reference.ExtractSequences;;
FastqToSam) main=net.sf.picard.sam.FastqToSam;;
FixMateInformation)
main=net.sf.picard.sam.FixMateInformation;;
MarkDuplicates) main=net.sf.picard.sam.MarkDuplicates;;
@@ -33,6 +37,7 @@ case $command in
MergeSamFiles) main=net.sf.picard.sam.MergeSamFiles;;
NormalizeFasta)
main=net.sf.picard.reference.NormalizeFasta;;
QualityScoreDistribution)
main=net.sf.picard.analysis.QualityScoreDistribution;;
+ ReorderSam) main=net.sf.picard.sam.ReorderSam;;
ReplaceSamHeader)
main=net.sf.picard.sam.ReplaceSamHeader;;
RevertSam) main=net.sf.picard.sam.RevertSam;;
SamFormatConverter)
main=net.sf.picard.sam.SamFormatConverter;;
diff --git a/debian/changelog b/debian/changelog
index c088c32..44b7f97 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+picard-tools (1.41-1) unstable; urgency=low
+
+ * New upstream release. Closes: #619201.
+ * Add five commands to bin/picard-tools and picard-tools.1.
+
+ -- Shaun Jackman <[email protected]> Tue, 22 Mar 2011 10:52:23 -0700
+
picard-tools (1.27-1) unstable; urgency=low
* New upstream release.
diff --git a/debian/picard-tools.1 b/debian/picard-tools.1
index a48bbfb..fd7672e 100644
--- a/debian/picard-tools.1
+++ b/debian/picard-tools.1
@@ -8,6 +8,8 @@ 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:
+ AddOrReplaceReadGroups
+ BamIndexStats
BamToBfq
BuildBamIndex
CalculateHsMetrics
@@ -15,9 +17,11 @@ Picard Tools includes these utilities to manipulate SAM and
BAM files:
CollectAlignmentSummaryMetrics
CollectGcBiasMetrics
CollectInsertSizeMetrics
+ CollectMultipleMetrics
CompareSAMs
CreateSequenceDictionary
EstimateLibraryComplexity
+ ExtractSequences
FastqToSam
FixMateInformation
MarkDuplicates
@@ -26,6 +30,7 @@ Picard Tools includes these utilities to manipulate SAM and
BAM files:
MergeSamFiles
NormalizeFasta
QualityScoreDistribution
+ ReorderSam
ReplaceSamHeader
RevertSam
SamFormatConverter
--
manipulate SAM and BAM files
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