[med-svn] [picard-tools] branch upstream updated (4957015 -> c2bd278)
Andreas Tille
tille at debian.org
Thu Nov 26 10:47:46 UTC 2015
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tille pushed a change to branch upstream
in repository picard-tools.
from 4957015 Imported Upstream version 1.138+dfsg.1
new c2bd278 Imported Upstream version 1.141+dfsg.1
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:
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 +
.../sam/{merger.dict => contiguous.interval_list} | 4 +-
testdata/picard/sam/forMetrics.sam | 23 ++
testdata/picard/sam/namesorted.test.sam | 33 ++
.../sam/{merger.dict => onePos.interval_list} | 3 +-
testdata/picard/vcf/dummy.reference.dict | 2 +
testdata/picard/vcf/dummy.reference.fasta | 10 +
...tering.vcf => testFilteringNoSeqDictionary.vcf} | 85 -----
testdata/picard/vcf/test.over.chain | 3 +
testdata/picard/vcf/testLiftover.vcf | 4 +
90 files changed, 3153 insertions(+), 665 deletions(-)
create mode 100644 src/java/picard/analysis/CollectWgsMetricsFromQuerySorted.java
create mode 100644 src/java/picard/analysis/CollectWgsMetricsFromSampledSites.java
rename src/java/picard/analysis/{directed => }/GcBiasMetricsCollector.java (79%)
create mode 100644 src/java/picard/analysis/GcBiasUtils.java
create mode 100644 src/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesWithBarcodes.java
create mode 100644 src/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesWithBarcodesCodec.java
create mode 100644 src/java/picard/util/QuerySortedReadPairIteratorUtil.java
create mode 100644 src/tests/java/picard/analysis/CollectWgsMetricsFromQuerySortedTest.java
create mode 100755 src/tests/java/picard/analysis/CollectWgsMetricsFromSampledSitesTest.java
create mode 100644 src/tests/java/picard/analysis/directed/CollectTargetedMetricsTest.java
create mode 100644 src/tests/java/picard/cmdline/PicardCommandLineTest.java
create mode 100644 src/tests/java/picard/util/QuerySortedReadPairIteratorUtilTest.java
create mode 100644 src/tests/java/picard/vcf/LiftoverVcfTest.java
create mode 100644 testdata/picard/analysis/directed/CollectInsertSizeMetrics/multiple_orientation.sam.insert_size_metrics
create mode 100644 testdata/picard/metrics/chrMNO.reference.fasta
create mode 100644 testdata/picard/quality/chrM.empty.interval_list
create mode 100644 testdata/picard/quality/chrM.reference.fasta.fai
create mode 100644 testdata/picard/quality/chrM.single.interval_list
create mode 100644 testdata/picard/sam/CollectGcBiasMetrics/MNOheader.dict
create mode 100644 testdata/picard/sam/MergeBamAlignment/contam.aligned.sam
create mode 100644 testdata/picard/sam/MergeBamAlignment/contam.expected.sam
create mode 100644 testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam
copy testdata/picard/sam/{merger.dict => contiguous.interval_list} (93%)
create mode 100644 testdata/picard/sam/forMetrics.sam
create mode 100644 testdata/picard/sam/namesorted.test.sam
copy testdata/picard/sam/{merger.dict => onePos.interval_list} (95%)
create mode 100644 testdata/picard/vcf/dummy.reference.dict
create mode 100644 testdata/picard/vcf/dummy.reference.fasta
copy testdata/picard/vcf/filter/{testFiltering.vcf => testFilteringNoSeqDictionary.vcf} (84%)
create mode 100644 testdata/picard/vcf/test.over.chain
create mode 100644 testdata/picard/vcf/testLiftover.vcf
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