[med-svn] [picard-tools] 02/02: Merge tag 'upstream/2.7.1+dfsg'

[Andreas Tille]

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

commit 8d3783cfcb2a81c89970ebc2cfe1c424cd214d39
Merge: 4ca28fd de94da5
Author: Andreas Tille <tille at debian.org>
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(-)

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