[med-svn] [picard-tools] branch master updated (a20d45a -> 3c64108)

[Andreas Tille]

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tille pushed a change to branch master
in repository picard-tools.

      from  a20d45a   Bug was just closed - leave they way better approach from Vincent for future updates
       new  5b5cca4   New upstream version 2.8.1+dfsg
       new  66f771c   Merge tag 'upstream/2.8.1+dfsg'
       new  8f68f5f   New upstream version
       new  3c64108   Upload to unstable

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repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
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Summary of changes:
 debian/changelog                                   |  10 +-
 .../java/picard/analysis/CollectGcBiasMetrics.java |  15 +-
 .../picard/analysis/CollectMultipleMetrics.java    |   1 +
 .../java/picard/analysis/CollectWgsMetrics.java    |  11 +-
 .../java/picard/analysis/GcBiasDetailMetrics.java  |   2 +
 .../picard/analysis/GcBiasMetricsCollector.java    | 174 ++++++----
 .../java/picard/analysis/GcBiasSummaryMetrics.java |   3 +
 .../java/picard/fingerprint/CheckFingerprint.java  |   2 +-
 .../picard/illumina/ClusterDataToSamConverter.java |  11 +-
 .../CollectIlluminaBasecallingMetrics.java         |   5 +
 .../illumina/CollectIlluminaLaneMetrics.java       |  39 ++-
 .../java/picard/sam/AbstractAlignmentMerger.java   |  31 +-
 .../java/picard/sam/CreateSequenceDictionary.java  | 180 +++++++++--
 src/main/java/picard/util/IlluminaUtil.java        |   2 +-
 src/main/java/picard/vcf/GatherVcfs.java           |  36 ++-
 src/main/resources/picard/analysis/gcBias.R        |   3 +-
 .../picard/analysis/CollectGcBiasMetricsTest.java  | 100 +++++-
 .../analysis/CollectMultipleMetricsTest.java       |   3 +-
 .../CollectIlluminaBasecallingMetricsTest.java     |  18 +-
 .../illumina/IlluminaLaneMetricsCollectorTest.java |  53 +--
 .../picard/sam/AbstractAlignmentMergerTest.java    |  65 ++++
 .../picard/sam/CreateSequenceDictionaryTest.java   |  68 +++-
 .../sams/nonBarcodedWithMolecularIndex4M4M.sam     | 360 ++++++++++-----------
 ...nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam | 360 ++++++++++-----------
 .../nonBarcodedWithTagPerMolecularIndex4M4M.sam    | 360 ++++++++++-----------
 .../illumina/25T8B25T/sams_with_4M4M/AACAATGG.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/AACGCATT.sam  |  28 +-
 .../illumina/25T8B25T/sams_with_4M4M/ACAGGTAT.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/ACAGTTGA.sam  |   8 +-
 .../illumina/25T8B25T/sams_with_4M4M/ACTAAGAC.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/ACTGTATC.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/AGCATGGA.sam  |  12 +-
 .../illumina/25T8B25T/sams_with_4M4M/AGGTAAGG.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/AGGTCGCA.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/ATTATCAA.sam  |  20 +-
 .../illumina/25T8B25T/sams_with_4M4M/ATTCCTCT.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/CAACTCTC.sam  |  20 +-
 .../illumina/25T8B25T/sams_with_4M4M/CAATAGTC.sam  |  28 +-
 .../illumina/25T8B25T/sams_with_4M4M/CAGCGGTA.sam  |  20 +-
 .../illumina/25T8B25T/sams_with_4M4M/CCAACATT.sam  |  28 +-
 .../illumina/25T8B25T/sams_with_4M4M/CCAGCACC.sam  |  12 +-
 .../illumina/25T8B25T/sams_with_4M4M/CGCCTTCC.sam  |   8 +-
 .../illumina/25T8B25T/sams_with_4M4M/CGCTATGT.sam  |  20 +-
 .../illumina/25T8B25T/sams_with_4M4M/CTAACTCG.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/CTATGCGT.sam  |  28 +-
 .../illumina/25T8B25T/sams_with_4M4M/CTGCGGAT.sam  |  12 +-
 .../illumina/25T8B25T/sams_with_4M4M/CTGTAATC.sam  |  24 +-
 .../illumina/25T8B25T/sams_with_4M4M/GAAGGAAG.sam  |  12 +-
 .../illumina/25T8B25T/sams_with_4M4M/GACCAGGA.sam  |  28 +-
 .../illumina/25T8B25T/sams_with_4M4M/GACCGTTG.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/GACCTAAC.sam  |   4 +-
 .../illumina/25T8B25T/sams_with_4M4M/GATATCCA.sam  |  12 +-
 .../illumina/25T8B25T/sams_with_4M4M/GCCGTCGA.sam  |  20 +-
 .../illumina/25T8B25T/sams_with_4M4M/GCCTAGCC.sam  |  20 +-
 .../illumina/25T8B25T/sams_with_4M4M/GTAACATC.sam  |   8 +-
 .../illumina/25T8B25T/sams_with_4M4M/GTCCACAG.sam  |   8 +-
 .../picard/illumina/25T8B25T/sams_with_4M4M/N.sam  |  64 ++--
 .../illumina/25T8B25T/sams_with_4M4M/TAAGCACA.sam  |   8 +-
 .../illumina/25T8B25T/sams_with_4M4M/TATCCAGG.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/TATCTGCC.sam  |  28 +-
 .../illumina/25T8B25T/sams_with_4M4M/TCGCTAGA.sam  |  20 +-
 .../illumina/25T8B25T/sams_with_4M4M/TCTGCAAG.sam  |   4 +-
 .../illumina/25T8B25T/sams_with_4M4M/TGCAAGTA.sam  |   8 +-
 .../illumina/25T8B25T/sams_with_4M4M/TGCTGCTG.sam  |  16 +-
 .../illumina/25T8B25T/sams_with_4M4M/TGTAACTC.sam  |   4 +-
 .../illumina/25T8B25T/sams_with_4M4M/TGTAATCA.sam  |  12 +-
 .../illumina/25T8B25T/sams_with_4M4M/TTGTCTAT.sam  |  16 +-
 .../25T8B25T/barcodes_dir}/s_1_1101_barcode.txt.gz | Bin
 .../130318_SL-HBB_0226_BFCC1WYMACXX/RunInfo.xml    |  13 +
 .../RunInfo.xml                                    |  13 +
 .../130401_SL-HAC_0022_BH07PBADXX/RunInfo.xml      |  13 +
 .../tileRuns/A67HY/RunInfo.xml                     |   9 +
 .../tileRuns/A7LE0/RunInfo.xml                     |  11 +
 .../tileRuns/C2MFAACXX/RunInfo.xml                 |   9 +
 .../tileRuns/H7BATADXX/RunInfo.xml                 |  10 +
 .../tileRuns/H7H7RADXX/RunInfo.xml                 |  11 +
 testdata/picard/metrics/chrM_NO_SEQ.sam            |   5 +
 testdata/picard/reference/csd_dict.dict            |   9 +
 78 files changed, 1652 insertions(+), 1083 deletions(-)
 create mode 100644 src/test/java/picard/sam/AbstractAlignmentMergerTest.java
 copy testdata/picard/illumina/{25T8B25T/Data/Intensities/BaseCalls => CollectIlluminaBasecallingMetrics/25T8B25T/barcodes_dir}/s_1_1101_barcode.txt.gz (100%)
 create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/130318_SL-HBB_0226_BFCC1WYMACXX/RunInfo.xml
 create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/130321_SL-MAK_0035_FC000000000-A306B/RunInfo.xml
 create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/130401_SL-HAC_0022_BH07PBADXX/RunInfo.xml
 create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/A67HY/RunInfo.xml
 create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/A7LE0/RunInfo.xml
 create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/C2MFAACXX/RunInfo.xml
 create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/H7BATADXX/RunInfo.xml
 create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/H7H7RADXX/RunInfo.xml
 create mode 100644 testdata/picard/metrics/chrM_NO_SEQ.sam
 create mode 100644 testdata/picard/reference/csd_dict.dict

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