[med-svn] [SCM] picard-tools branch, master, updated. upstream/1.46-39-g4a39ad6

[Charles Plessy]

The following commit has been merged in the master branch:
commit c2d1dc85ad1aed9403b5eab6a2e72ed4b197be96
Author: Charles Plessy <plessy at debian.org>
Date:   Fri Jun 3 20:42:31 2011 +0900

    Documented new commands.

diff --git a/debian/control b/debian/control
index d25624f..e590ba5 100644
--- a/debian/control
+++ b/debian/control
@@ -30,16 +30,17 @@ 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
+ BamToBfq                        IlluminaBasecallsToSam
+ BuildBamIndex                   MarkDuplicates
+ CalculateHsMetrics              MeanQualityByCycle
+ CleanSam                        MergeBamAlignment
+ CollectAlignmentSummaryMetrics  MergeSamFiles
+ CollectGcBiasMetrics            NormalizeFasta
+ CollectInsertSizeMetrics        QualityScoreDistribution
+ CollectRnaSeqMetrics            ReplaceSamHeader
+ CompareSAMs                     RevertSam
+ CreateSequenceDictionary        SamFormatConverter
+ ExtractIlluminaBarcodes         SamToFastq
  EstimateLibraryComplexity       SortSam
  FastqToSam                      ValidateSamFile
  FixMateInformation              ViewSam
- MarkDuplicates
diff --git a/debian/picard-tools.1 b/debian/picard-tools.1
index fd7672e..7d55fe0 100644
--- a/debian/picard-tools.1
+++ b/debian/picard-tools.1
@@ -18,12 +18,15 @@ Picard Tools includes these utilities to manipulate SAM and BAM files:
  CollectGcBiasMetrics
  CollectInsertSizeMetrics
  CollectMultipleMetrics
+ CollectRnaSeqMetrics
  CompareSAMs
  CreateSequenceDictionary
+ ExtractIlluminaBarcodes 
  EstimateLibraryComplexity
  ExtractSequences
  FastqToSam
  FixMateInformation
+ IlluminaBasecallsToSam 
  MarkDuplicates
  MeanQualityByCycle
  MergeBamAlignment

-- 
manipulate SAM and BAM files