[med-svn] [picard-tools] branch upstream updated (de94da5 -> d654328)
Andreas Tille
tille at debian.org
Sun Dec 11 07:58:21 UTC 2016
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tille pushed a change to branch upstream
in repository picard-tools.
from de94da5 Imported Upstream version 2.7.1+dfsg
new d654328 New upstream version 2.8.0+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:
.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} | 22 +-
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 +
...{chrM.interval_list => two-small.interval_list} | 3 +-
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} | 80 +-
...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 +
...uth-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf} | 178 ++--
.../picard/vcf/{CEUTrio-snps.vcf => empty.vcf} | 0
testdata/picard/vcf/empty.vcf.idx | Bin 0 -> 26399 bytes
...IST.selected.vcf => normalize_alleles_call.vcf} | 56 +-
...ST.selected.vcf => normalize_alleles_truth.vcf} | 56 +-
76 files changed, 8540 insertions(+), 915 deletions(-)
create mode 100644 .github/ISSUE_TEMPLATE.md
create mode 100644 .github/PULL_REQUEST_TEMPLATE.md
create mode 100644 src/main/java/picard/sam/markduplicates/ElcDuplicatesFinder.java
create mode 100644 src/main/java/picard/sam/markduplicates/ElcDuplicatesFinderResolver.java
create mode 100644 src/main/java/picard/sam/markduplicates/ElcHashBasedDuplicatesFinder.java
create mode 100644 src/main/java/picard/sam/markduplicates/ElcIdenticalBasesDuplicatesFinder.java
create mode 100644 src/main/java/picard/vcf/MendelianViolations/FindMendelianViolations.java
create mode 100644 src/main/java/picard/vcf/MendelianViolations/MendelianViolationDetector.java
create mode 100644 src/main/java/picard/vcf/MendelianViolations/MendelianViolationMetrics.java
copy src/main/java/picard/{cmdline/programgroups/Fingerprinting.java => vcf/MendelianViolations/MendelianViolationsByFamily.java} (71%)
create mode 100644 src/test/java/picard/analysis/CollectWgsMetricsTestUtils.java
create mode 100644 src/test/java/picard/sam/markduplicates/ElcHashBasedDuplicatesFinderTest.java
create mode 100644 src/test/java/picard/sam/markduplicates/ElcIdenticalBasesDuplicatesFinderTest.java
create mode 100644 src/test/java/picard/vcf/ByIntervalListVariantContextIteratorTest.java
create mode 100644 src/test/java/picard/vcf/MendelianViolations/FindMendelianViolationsTest.java
create mode 100644 testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam
copy testdata/picard/analysis/directed/CollectHsMetrics/{chrM.interval_list => two-small.interval_list} (79%)
create mode 100644 testdata/picard/quality/chrM.reference.dict
create mode 100644 testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam
create mode 100644 testdata/picard/sam/EstimateLibraryComplexity/big_dupes_with_sos.sam
create mode 100644 testdata/picard/sam/MergeBamAlignment/aligned.both.strands.sam
copy testdata/picard/vcf/{CEUTrio-indels-dissimilar-contigs.vcf => CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff.vcf} (56%)
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff.vcf
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff.vcf
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff.vcf
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows.vcf
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.vcf
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.vcf
create mode 100644 testdata/picard/vcf/CEUTrio_plus_FAKE.vcf
create mode 100644 testdata/picard/vcf/CEUTrio_plus_FAKE.vcf.idx
create mode 100644 testdata/picard/vcf/NA12878.ped
copy testdata/picard/vcf/{NIST.selected.vcf => NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf} (54%)
copy testdata/picard/vcf/{CEUTrio-snps.vcf => empty.vcf} (100%)
create mode 100644 testdata/picard/vcf/empty.vcf.idx
copy testdata/picard/vcf/{NIST.selected.vcf => normalize_alleles_call.vcf} (86%)
copy testdata/picard/vcf/{NIST.selected.vcf => normalize_alleles_truth.vcf} (86%)
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