[med-svn] [picard-tools] branch upstream updated (0ce17ad -> de94da5)
Andreas Tille
tille at debian.org
Thu Oct 27 16:11:04 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository picard-tools.
from 0ce17ad New upstream version 2.6.0+dfsg
new de94da5 Imported Upstream version 2.7.1+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:
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} | 14 +-
.../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 +
...piens_assembly19.haplotype_database.subset.txt} | 11 +-
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 +
.../{cliptest.dict => removetags.dict} | 0
.../{cliptest.fasta => removetags.fasta} | 0
.../sam/MergeBamAlignment/removetags.fasta.fai | 1 +
.../sam/MergeBamAlignment/removetags.unmapped.sam | 10 +
87 files changed, 2870 insertions(+), 532 deletions(-)
rename src/main/java/picard/analysis/{replicates => }/MergeableMetricBase.java (90%)
create mode 100644 src/main/java/picard/analysis/artifacts/ErrorSummaryMetrics.java
copy src/main/java/picard/{filter/CountingDuplicateFilter.java => cmdline/programgroups/Fingerprinting.java} (75%)
copy src/main/java/picard/sam/{SetNmAndUqTags.java => SetNmMdAndUqTags.java} (85%)
rename src/{test => main}/java/picard/sam/markduplicates/SimpleMarkDuplicatesWithMateCigar.java (95%)
create mode 100644 src/main/java/picard/sam/markduplicates/UmiAwareDuplicateSetIterator.java
create mode 100644 src/main/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigar.java
create mode 100644 src/main/java/picard/sam/markduplicates/UmiGraph.java
create mode 100644 src/test/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverageTest.java
rename src/test/java/picard/analysis/{replicates => }/MergeableMetricBaseTest.java (81%)
create mode 100644 src/test/java/picard/analysis/WgsMetricsTest.java
create mode 100644 src/test/java/picard/sam/DuplicationMetricsTest.java
rename src/test/java/picard/sam/{SetNmAndUqTagsTest.java => SetNmMdAndUqTagsTest.java} (92%)
create mode 100644 src/test/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigarTest.java
create mode 100644 src/test/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigarTester.java
create mode 100644 src/test/java/picard/vcf/VcfTestUtils.java
create mode 100644 testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/ExpectedMetricsOutput/no_bq_cutoff.error_summary_metrics
create mode 100644 testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/ExpectedMetricsOutput/no_mq_cutoff.error_summary_metrics
create mode 100644 testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/ExpectedMetricsOutput/unmapped_mate.error_summary_metrics
create mode 100644 testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/ExpectedMetricsOutput/with_context.error_summary_metrics
create mode 100644 testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/ExpectedMetricsOutput/with_dbsnp.error_summary_metrics
create mode 100644 testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/ExpectedMetricsOutput/with_intervals.error_summary_metrics
copy testdata/picard/{util/scatterable.interval_list => fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt} (98%)
create mode 100755 testdata/picard/fingerprint/NA12891.fp.vcf
create mode 100755 testdata/picard/fingerprint/NA12891.vcf
create mode 100755 testdata/picard/fingerprint/NA12892.fp.vcf
create mode 100755 testdata/picard/fingerprint/NA12892.vcf
create mode 100644 testdata/picard/sam/MergeBamAlignment/removetags.aligned.sam
copy testdata/picard/sam/MergeBamAlignment/{cliptest.dict => removetags.dict} (100%)
copy testdata/picard/sam/MergeBamAlignment/{cliptest.fasta => removetags.fasta} (100%)
create mode 100644 testdata/picard/sam/MergeBamAlignment/removetags.fasta.fai
create mode 100644 testdata/picard/sam/MergeBamAlignment/removetags.unmapped.sam
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