[med-svn] [picard-tools] branch master updated (9676116 -> b73c16a)
Andreas Tille
tille at debian.org
Sun Dec 11 07:58:19 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository picard-tools.
from 9676116 Ensure tighter dependencies with htsjdk
new d654328 New upstream version 2.8.0+dfsg
new a9ac554 Merge tag 'upstream/2.8.0+dfsg'
new 8221026 New upstream version
new d0f5728 debhelper 10
new 10e9b4f d/watch: version=4
new b73c16a Ensure that major version of htsjdk is 2.8
The 6 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 +-
debian/changelog | 9 +
debian/compat | 2 +-
debian/control | 6 +-
debian/watch | 2 +-
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 +-
80 files changed, 8554 insertions(+), 920 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%)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git
More information about the debian-med-commit
mailing list