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commit 66f771ce01b349db0771b3bd8d188d17392bbcfe Merge: a20d45a 5b5cca4 Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
