[med-svn] [picard-tools] 02/06: Merge tag 'upstream/2.8.0+dfsg'

[Andreas Tille]

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

commit a9ac554864496496c4447f34e0bc3baa3cb1a9c2
Merge: 9676116 d654328
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 11 08:52:31 2016 +0100

    Merge tag 'upstream/2.8.0+dfsg'
    
    Upstream version 2.8.0+dfsg

 .github/ISSUE_TEMPLATE.md                          |   52 +
 .github/PULL_REQUEST_TEMPLATE.md                   |   25 +
 build.gradle                                       |    8 +-
 gradle/wrapper/gradle-wrapper.properties           |    4 +-
 .../java/picard/analysis/CollectRawWgsMetrics.java |   19 +-
 .../java/picard/analysis/CollectWgsMetrics.java    |  239 +++--
 .../CollectWgsMetricsFromSampledSites.java         |   19 +-
 .../CollectWgsMetricsWithNonZeroCoverage.java      |   57 +-
 .../java/picard/analysis/MergeableMetricBase.java  |   34 +-
 .../CollectSequencingArtifactMetrics.java          |   18 +-
 .../analysis/directed/TargetMetricsCollector.java  |  267 +++--
 .../picard/illumina/ExtractIlluminaBarcodes.java   |    2 +
 .../picard/illumina/IlluminaBasecallsToSam.java    |    2 +-
 .../java/picard/sam/AbstractAlignmentMerger.java   |   35 +-
 src/main/java/picard/sam/RevertSam.java            |   34 +-
 src/main/java/picard/sam/ValidateSamFile.java      |    2 +-
 .../sam/markduplicates/ElcDuplicatesFinder.java    |   79 ++
 .../ElcDuplicatesFinderResolver.java               |   80 ++
 .../ElcHashBasedDuplicatesFinder.java              |  216 ++++
 .../ElcIdenticalBasesDuplicatesFinder.java         |  116 +++
 .../markduplicates/EstimateLibraryComplexity.java  |  139 +--
 .../MarkDuplicatesWithMateCigar.java               |   12 +-
 .../UmiAwareMarkDuplicatesWithMateCigar.java       |   21 +-
 src/main/java/picard/util/ClippingUtility.java     |    2 +-
 src/main/java/picard/util/DbSnpBitSetUtil.java     |   14 +-
 .../vcf/ByIntervalListVariantContextIterator.java  |   40 +-
 src/main/java/picard/vcf/GenotypeConcordance.java  |  440 ++++++--
 .../java/picard/vcf/GenotypeConcordanceStates.java |   26 +-
 .../FindMendelianViolations.java                   |  303 ++++++
 .../MendelianViolationDetector.java                |  358 +++++++
 .../MendelianViolationMetrics.java                 |   86 ++
 .../MendelianViolationsByFamily.java               |   41 +
 src/main/java/picard/vcf/RenameSampleInVcf.java    |   18 +-
 .../vcf/processor/VariantIteratorProducer.java     |   45 +-
 .../picard/analysis/CollectGcBiasMetricsTest.java  |   24 +
 .../analysis/CollectMultipleMetricsTest.java       |    2 +-
 .../CollectWgsMetricsFromSampledSitesTest.java     |   22 +-
 .../picard/analysis/CollectWgsMetricsTest.java     |  124 ++-
 .../analysis/CollectWgsMetricsTestUtils.java       |  104 ++
 .../CollectWgsMetricsWithNonZeroCoverageTest.java  |   88 +-
 .../picard/analysis/MergeableMetricBaseTest.java   |   17 +
 src/test/java/picard/analysis/WgsMetricsTest.java  |    4 +-
 .../analysis/directed/CollectHsMetricsTest.java    |   60 +-
 .../directed/CollectTargetedMetricsTest.java       |    6 +-
 .../java/picard/sam/MergeBamAlignmentTest.java     |   43 +
 .../ElcHashBasedDuplicatesFinderTest.java          |  182 ++++
 .../ElcIdenticalBasesDuplicatesFinderTest.java     |  208 ++++
 .../EstimateLibraryComplexityTest.java             |  112 +-
 .../ByIntervalListVariantContextIteratorTest.java  |  141 +++
 .../java/picard/vcf/GenotypeConcordanceTest.java   |  144 ++-
 .../FindMendelianViolationsTest.java               |  162 +++
 .../directed/CollectHsMetrics/lowbaseq.sam         |   19 +-
 .../CollectHsMetrics/single-short-read.sam         |    4 +
 .../CollectHsMetrics/two-small.interval_list       |    4 +
 testdata/picard/quality/chrM.empty.interval_list   |    2 +-
 testdata/picard/quality/chrM.reference.dict        |    2 +
 testdata/picard/quality/chrM.single.interval_list  |    2 +-
 .../sam/EstimateLibraryComplexity/big_dupes.sam    | 1092 +++++++++++++++++++
 .../big_dupes_with_sos.sam                         | 1096 ++++++++++++++++++++
 .../sam/MergeBamAlignment/aligned.both.strands.sam |   17 +
 ...-indels_vs_CEUTrio-indels_GtConcordanceDiff.vcf |  168 +++
 ...nps_CEUTrio-snps_del_line_GtConcordanceDiff.vcf |  356 +++++++
 ...s_CEUTrio-snps_first_line_GtConcordanceDiff.vcf |  356 +++++++
 ...ps_CEUTrio-snps_last_line_GtConcordanceDiff.vcf |  357 +++++++
 ...Trio-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf |  356 +++++++
 ...s_vs_CEUTrio-snps_GtConcordanceDiff_AllRows.vcf |  356 +++++++
 ...nps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.vcf |  356 +++++++
 ...nps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.vcf |  356 +++++++
 testdata/picard/vcf/CEUTrio_plus_FAKE.vcf          |   76 ++
 testdata/picard/vcf/CEUTrio_plus_FAKE.vcf.idx      |  Bin 0 -> 1864 bytes
 testdata/picard/vcf/NA12878.ped                    |    2 +
 ...ruth-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf |  207 ++++
 testdata/picard/vcf/empty.vcf                      |  406 ++++++++
 testdata/picard/vcf/empty.vcf.idx                  |  Bin 0 -> 26399 bytes
 testdata/picard/vcf/normalize_alleles_call.vcf     |  147 +++
 testdata/picard/vcf/normalize_alleles_truth.vcf    |  147 +++
 76 files changed, 9499 insertions(+), 681 deletions(-)

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