This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository picard-tools.
commit 8d3783cfcb2a81c89970ebc2cfe1c424cd214d39 Merge: 4ca28fd de94da5 Author: Andreas Tille <[email protected]> Date: Thu Oct 27 17:09:15 2016 +0200 Merge tag 'upstream/2.7.1+dfsg' Upstream version 2.7.1+dfsg Conflicts: README.md src/main/java/picard/sam/FastqToSam.java README.md | 4 + .../analysis/AlignmentSummaryMetricsCollector.java | 12 +- src/main/java/picard/analysis/ChimeraUtil.java | 5 +- .../picard/analysis/CollectMultipleMetrics.java | 22 +- .../java/picard/analysis/CollectOxoGMetrics.java | 7 +- .../analysis/CollectQualityYieldMetrics.java | 4 +- .../java/picard/analysis/CollectRawWgsMetrics.java | 55 ++- .../java/picard/analysis/CollectWgsMetrics.java | 430 ++++++++++++++++----- .../CollectWgsMetricsFromSampledSites.java | 52 ++- .../CollectWgsMetricsWithNonZeroCoverage.java | 98 ++++- .../picard/analysis/GcBiasMetricsCollector.java | 4 +- .../java/picard/analysis/GcBiasSummaryMetrics.java | 2 +- .../{replicates => }/MergeableMetricBase.java | 22 +- .../picard/analysis/TheoreticalSensitivity.java | 4 +- .../CollectSequencingArtifactMetrics.java | 91 +++-- .../analysis/artifacts/ErrorSummaryMetrics.java | 36 ++ .../artifacts/SequencingArtifactMetrics.java | 5 +- .../analysis/directed/CalculateHsMetrics.java | 4 +- .../picard/analysis/directed/CollectHsMetrics.java | 4 +- .../analysis/directed/CollectTargetedMetrics.java | 4 +- .../directed/InsertSizeMetricsCollector.java | 2 +- .../analysis/directed/TargetMetricsCollector.java | 18 +- .../CollectIndependentReplicateMetrics.java | 4 +- .../replicates/IndependentReplicateMetric.java | 2 + .../java/picard/cmdline/PicardCommandLine.java | 2 +- .../programgroups/Fingerprinting.java} | 38 +- .../java/picard/fingerprint/CheckFingerprint.java | 137 +++++-- .../CrosscheckReadGroupFingerprints.java | 4 +- .../picard/fingerprint/FingerprintChecker.java | 73 +++- .../picard/fingerprint/FingerprintResults.java | 18 +- .../picard/illumina/parser/readers/BclReader.java | 2 +- .../java/picard/sam/AbstractAlignmentMerger.java | 30 +- src/main/java/picard/sam/DuplicationMetrics.java | 56 +-- src/main/java/picard/sam/FastqToSam.java | 26 +- src/main/java/picard/sam/MergeBamAlignment.java | 4 +- src/main/java/picard/sam/RevertSam.java | 14 +- src/main/java/picard/sam/SetNmAndUqTags.java | 79 +--- .../{SetNmAndUqTags.java => SetNmMdAndUqTags.java} | 21 +- .../markduplicates/EstimateLibraryComplexity.java | 2 +- .../picard/sam/markduplicates/MarkDuplicates.java | 10 +- .../SimpleMarkDuplicatesWithMateCigar.java | 19 +- .../UmiAwareDuplicateSetIterator.java | 124 ++++++ .../UmiAwareMarkDuplicatesWithMateCigar.java | 89 +++++ .../java/picard/sam/markduplicates/UmiGraph.java | 218 +++++++++++ .../AbstractMarkDuplicatesCommandLineProgram.java | 2 +- ...ctOpticalDuplicateFinderCommandLineProgram.java | 4 +- src/main/java/picard/util/DbSnpBitSetUtil.java | 29 +- .../picard/vcf/CollectVariantCallingMetrics.java | 3 +- src/main/java/picard/vcf/filter/FilterVcf.java | 2 +- src/main/resources/picard/analysis/wgsHistogram.R | 4 +- .../analysis/CollectInsertSizeMetricsTest.java | 52 +-- .../picard/analysis/CollectWgsMetricsTest.java | 8 +- .../CollectWgsMetricsWithNonZeroCoverageTest.java | 127 ++++++ .../{replicates => }/MergeableMetricBaseTest.java | 27 +- .../analysis/TheoreticalSensitivityTest.java | 15 +- src/test/java/picard/analysis/WgsMetricsTest.java | 108 ++++++ .../CollectSequencingArtifactMetricsTest.java | 1 + .../directed/CollectTargetedMetricsTest.java | 4 +- .../picard/fingerprint/FingerprintCheckerTest.java | 43 ++- .../java/picard/sam/DuplicationMetricsTest.java | 91 +++++ .../java/picard/sam/MergeBamAlignmentTest.java | 100 +++-- src/test/java/picard/sam/RevertSamTest.java | 2 +- ...ndUqTagsTest.java => SetNmMdAndUqTagsTest.java} | 6 +- ...ractMarkDuplicatesCommandLineProgramTester.java | 2 +- .../UmiAwareMarkDuplicatesWithMateCigarTest.java | 166 ++++++++ .../UmiAwareMarkDuplicatesWithMateCigarTester.java | 167 ++++++++ .../java/picard/sam/testers/SamFileTester.java | 4 +- src/test/java/picard/vcf/VcfTestUtils.java | 40 ++ .../no_bq_cutoff.error_summary_metrics | 15 + .../no_mq_cutoff.error_summary_metrics | 15 + .../unmapped_mate.error_summary_metrics | 15 + .../with_context.error_summary_metrics | 15 + .../with_dbsnp.error_summary_metrics | 15 + .../with_intervals.error_summary_metrics | 15 + ...apiens_assembly19.haplotype_database.subset.txt | 92 +++++ testdata/picard/fingerprint/NA12891.fp.vcf | 101 +++++ testdata/picard/fingerprint/NA12891.vcf | 101 +++++ testdata/picard/fingerprint/NA12892.fp.vcf | 101 +++++ testdata/picard/fingerprint/NA12892.vcf | 101 +++++ .../sam/MergeBamAlignment/cliptest.aligned.sam | 20 +- .../sam/MergeBamAlignment/cliptest.unmapped.sam | 8 +- .../sam/MergeBamAlignment/contam.expected.sam | 8 +- .../sam/MergeBamAlignment/removetags.aligned.sam | 10 + .../picard/sam/MergeBamAlignment/removetags.dict | 2 + .../picard/sam/MergeBamAlignment/removetags.fasta | 21 + .../sam/MergeBamAlignment/removetags.fasta.fai | 1 + .../sam/MergeBamAlignment/removetags.unmapped.sam | 10 + 87 files changed, 2979 insertions(+), 551 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
