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in repository picard-tools.
from 4ca28fd remove more duplicated build-deps
adds 1d84a5c New upstream version 2.6.0+dfsg
adds 0ce17ad New upstream version 2.6.0+dfsg
new de94da5 Imported Upstream version 2.7.1+dfsg
new 8d3783c Merge tag 'upstream/2.7.1+dfsg'
The 2 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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