[med-svn] [picard-tools] branch upstream updated (d654328 -> 5b5cca4)

[Andreas Tille]

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

      from  d654328   New upstream version 2.8.0+dfsg
       new  5b5cca4   New upstream version 2.8.1+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .../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 +
 77 files changed, 1645 insertions(+), 1080 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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