[med-svn] [picard-tools] branch master updated (33ced40 -> 6df0a22)
Andreas Tille
tille at debian.org
Thu Nov 26 10:47:44 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository picard-tools.
from 33ced40 Ready for upload
new 25df4d9 New upstream version, add get-orig-source target
new c2bd278 Imported Upstream version 1.141+dfsg.1
new 1f297d0 Merge tag 'upstream/1.141+dfsg.1'
new d292e17 Remove Shaun Jackman and add myself as Uploader
new 1488a9f Removed outdated information from README.source
new 0750677 Try to provide maven input file
new 6df0a22 Try to implement Emmanuel Bourg's hints
The 7 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 +-
debian/README.source | 28 +-
debian/changelog | 8 +
debian/control | 7 +-
debian/pom-picard.xml | 68 ++++
debian/rules | 7 +
.../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 +
95 files changed, 3255 insertions(+), 681 deletions(-)
create mode 100644 debian/pom-picard.xml
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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