[med-svn] [picard-tools] 03/07: Merge tag 'upstream/1.141+dfsg.1'
Andreas Tille
tille at debian.org
Thu Nov 26 10:47:45 UTC 2015
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tille pushed a commit to branch master
in repository picard-tools.
commit 1f297d03b3cca1c4241209cae835adc047ba34aa
Merge: 25df4d9 c2bd278
Author: Andreas Tille <tille at debian.org>
Date: Thu Nov 26 11:13:10 2015 +0100
Merge tag 'upstream/1.141+dfsg.1'
Upstream version 1.141+dfsg.1
Dockerfile | 6 +-
README.md | 26 +-
build.sbt | 4 +-
build.xml | 3 +-
.../analysis/CollectAlignmentSummaryMetrics.java | 2 +-
src/java/picard/analysis/CollectGcBiasMetrics.java | 114 ++-----
.../picard/analysis/CollectInsertSizeMetrics.java | 4 +-
.../picard/analysis/CollectMultipleMetrics.java | 111 +++++--
src/java/picard/analysis/CollectOxoGMetrics.java | 6 +
.../analysis/CollectQualityYieldMetrics.java | 16 +-
src/java/picard/analysis/CollectRnaSeqMetrics.java | 2 +-
src/java/picard/analysis/CollectWgsMetrics.java | 29 +-
.../analysis/CollectWgsMetricsFromQuerySorted.java | 298 +++++++++++++++++
.../CollectWgsMetricsFromSampledSites.java | 62 ++++
.../{directed => }/GcBiasMetricsCollector.java | 97 ++++--
src/java/picard/analysis/GcBiasSummaryMetrics.java | 2 +-
src/java/picard/analysis/GcBiasUtils.java | 122 +++++++
.../analysis/directed/TargetMetricsCollector.java | 34 +-
src/java/picard/cmdline/ClassFinder.java | 20 +-
src/java/picard/cmdline/CommandLineProgram.java | 3 +
.../illumina/IlluminaBasecallsConverter.java | 24 +-
.../picard/illumina/IlluminaBasecallsToFastq.java | 6 +-
.../picard/illumina/IlluminaBasecallsToSam.java | 6 +-
src/java/picard/pedigree/PedFile.java | 10 +-
src/java/picard/sam/AbstractAlignmentMerger.java | 67 +++-
src/java/picard/sam/DownsampleSam.java | 71 ++++-
src/java/picard/sam/DuplicationMetrics.java | 2 +-
src/java/picard/sam/HitsForInsert.java | 38 +--
src/java/picard/sam/MergeBamAlignment.java | 10 +-
src/java/picard/sam/RevertSam.java | 9 +-
src/java/picard/sam/SamAlignmentMerger.java | 36 ++-
.../markduplicates/EstimateLibraryComplexity.java | 170 +++++++++-
.../picard/sam/markduplicates/MarkDuplicates.java | 162 ++++++++--
.../DiskBasedReadEndsForMarkDuplicatesMap.java | 10 +-
.../util/ReadEndsForMarkDuplicates.java | 29 +-
.../util/ReadEndsForMarkDuplicatesCodec.java | 4 +-
.../ReadEndsForMarkDuplicatesWithBarcodes.java | 41 +++
...ReadEndsForMarkDuplicatesWithBarcodesCodec.java | 75 +++++
src/java/picard/util/MathUtil.java | 9 +
.../util/QuerySortedReadPairIteratorUtil.java | 65 ++++
src/java/picard/vcf/GenotypeConcordance.java | 2 +-
.../vcf/GenotypeConcordanceContingencyMetrics.java | 12 +-
src/java/picard/vcf/GenotypeConcordanceCounts.java | 28 +-
src/java/picard/vcf/LiftoverVcf.java | 49 ++-
src/java/picard/vcf/SortVcf.java | 3 +-
src/java/picard/vcf/filter/FilterVcf.java | 19 +-
src/scripts/picard/analysis/insertSizeHistogram.R | 113 ++++---
src/scripts/picard/docker_helper.sh | 2 +-
.../picard/analysis/CollectGcBiasMetricsTest.java | 351 ++++++++++++++-------
.../analysis/CollectInsertSizeMetricsTest.java | 18 ++
.../analysis/CollectMultipleMetricsTest.java | 21 +-
.../picard/analysis/CollectRnaSeqMetricsTest.java | 5 +
.../CollectWgsMetricsFromQuerySortedTest.java | 52 +++
.../CollectWgsMetricsFromSampledSitesTest.java | 98 ++++++
.../directed/CollectTargetedMetricsTest.java | 158 ++++++++++
.../java/picard/cmdline/PicardCommandLineTest.java | 18 ++
.../illumina/CheckIlluminaDirectoryTest.java | 1 +
.../illumina/IlluminaBasecallsToFastqTest.java | 15 +-
.../IlluminaBasecallsToSamAdapterClippingTest.java | 1 +
.../illumina/IlluminaBasecallsToSamTest.java | 2 +
.../illumina/IlluminaLaneMetricsCollectorTest.java | 3 +-
.../illumina/parser/IlluminaDataProviderTest.java | 10 +-
.../java/picard/sam/AddCommentsToBamTest.java | 6 +
src/tests/java/picard/sam/GatherBamFilesTest.java | 2 +
.../java/picard/sam/MergeBamAlignmentTest.java | 72 +++--
src/tests/java/picard/sam/RevertSamTest.java | 2 +
.../java/picard/sam/SamFileConverterTest.java | 1 +
.../sam/markduplicates/MarkDuplicatesTest.java | 102 ++++++
src/tests/java/picard/util/FifoBufferTest.java | 2 +-
.../util/QuerySortedReadPairIteratorUtilTest.java | 93 ++++++
src/tests/java/picard/vcf/LiftoverVcfTest.java | 95 ++++++
src/tests/java/picard/vcf/TestFilterVcf.java | 48 ++-
.../multiple_orientation.sam.insert_size_metrics | 312 ++++++++++++++++++
testdata/picard/metrics/chrMNO.reference.fasta | 65 ++++
testdata/picard/quality/chrM.empty.interval_list | 4 +
testdata/picard/quality/chrM.reference.fasta.fai | 1 +
testdata/picard/quality/chrM.single.interval_list | 3 +
.../picard/sam/CollectGcBiasMetrics/MNOheader.dict | 4 +
.../sam/MergeBamAlignment/contam.aligned.sam | 25 ++
.../sam/MergeBamAlignment/contam.expected.sam | 16 +
.../sam/MergeBamAlignment/contam.unmapped.sam | 12 +
testdata/picard/sam/contiguous.interval_list | 11 +
testdata/picard/sam/forMetrics.sam | 23 ++
testdata/picard/sam/namesorted.test.sam | 33 ++
testdata/picard/sam/onePos.interval_list | 10 +
testdata/picard/vcf/dummy.reference.dict | 2 +
testdata/picard/vcf/dummy.reference.fasta | 10 +
.../vcf/filter/testFilteringNoSeqDictionary.vcf | 65 ++++
testdata/picard/vcf/test.over.chain | 3 +
testdata/picard/vcf/testLiftover.vcf | 4 +
90 files changed, 3234 insertions(+), 578 deletions(-)
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