[med-svn] [picard-tools] 02/04: Merge tag 'upstream/2.8.1+dfsg'

[Andreas Tille]

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

commit 66f771ce01b349db0771b3bd8d188d17392bbcfe
Merge: a20d45a 5b5cca4
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jan 10 11:18:39 2017 +0100

    Merge tag 'upstream/2.8.1+dfsg'
    
    Upstream version 2.8.1+dfsg

 .../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 0 -> 429 bytes
 .../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(-)

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