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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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