[med-svn] [picard-tools] branch master updated (bd3256e -> 9679a96)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository picard-tools.

      from  bd3256e   Cleanup d/changelog after unsuccessful merge
       new  18562d8   Imported Upstream version 2.1.1+dfsg
       new  335b0e9   Remove patches applied upstream
       new  42429f8   New upstream version
       new  9679a96   Take over patches from previous version

The 4 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:
 build.sbt                                          |   4 +-
 build.xml                                          | 155 +++++++++++---------
 debian/changelog                                   |   2 +-
 debian/patches/00-for-upstream-fix-testsuite       |  24 ---
 debian/patches/01-for-upstream-fix-classloader     |  47 ------
 debian/patches/10-build.xml                        |  84 ++++-------
 debian/patches/series                              |   2 -
 src/java/picard/Test.java                          |   6 +-
 src/java/picard/analysis/CollectGcBiasMetrics.java |   4 +-
 .../picard/analysis/CollectMultipleMetrics.java    |  44 +++---
 src/java/picard/analysis/CollectRrbsMetrics.java   |   4 +-
 .../picard/analysis/GcBiasMetricsCollector.java    |   6 +-
 src/java/picard/analysis/MeanQualityByCycle.java   |   2 +-
 .../CollectSequencingArtifactMetrics.java          |  16 +-
 .../analysis/directed/TargetMetricsCollector.java  |   4 +-
 src/java/picard/cmdline/CommandLineParser.java     | 147 ++++++++++++-------
 .../CrosscheckReadGroupFingerprints.java           |   2 +-
 src/java/picard/fingerprint/HaplotypeMap.java      |   4 +-
 ...lotypeProbabilitiesFromGenotypeLikelihoods.java |   2 +-
 .../picard/illumina/ClusterDataToSamConverter.java |   6 +-
 .../picard/illumina/ExtractIlluminaBarcodes.java   |  10 +-
 .../picard/illumina/IlluminaBasecallsToFastq.java  |   6 +-
 .../picard/illumina/IlluminaBasecallsToSam.java    |  10 +-
 src/java/picard/illumina/MarkIlluminaAdapters.java |   2 +-
 src/java/picard/illumina/parser/BarcodeParser.java |   2 +-
 .../illumina/parser/FourChannelIntensityData.java  |   8 +-
 .../parser/IlluminaDataProviderFactory.java        |   4 +-
 .../picard/illumina/parser/IlluminaFileUtil.java   |   4 +-
 .../illumina/parser/MultiTileBclFileUtil.java      |   2 +-
 .../picard/illumina/parser/PerTileFileUtil.java    |   2 +-
 src/java/picard/illumina/parser/ReadStructure.java |   4 +-
 src/java/picard/illumina/parser/TileIndex.java     |   2 +-
 .../illumina/parser/fakers/BarcodeFileFaker.java   |   8 +-
 .../illumina/parser/fakers/PosFileFaker.java       |   8 +-
 .../readers/BclQualityEvaluationStrategy.java      |   2 +-
 .../illumina/parser/readers/FilterFileReader.java  |   2 +-
 .../parser/readers/MMapBackedIteratorFactory.java  |   4 +-
 .../quality/CollectHiSeqXPfFailMetrics.java        |   2 +-
 src/java/picard/sam/FastqToSam.java                |   2 +-
 src/java/picard/sam/FilterSamReads.java            |  52 +++++--
 src/java/picard/sam/MergeBamAlignment.java         |   6 +-
 src/java/picard/sam/RevertSam.java                 |   2 +-
 src/java/picard/sam/SamAlignmentMerger.java        |  10 +-
 src/java/picard/sam/SamToFastq.java                |   4 +-
 src/java/picard/sam/SplitSamByLibrary.java         |   2 +-
 .../markduplicates/EstimateLibraryComplexity.java  |   4 +-
 ...ctOpticalDuplicateFinderCommandLineProgram.java |   6 +-
 .../MemoryBasedReadEndsForMarkDuplicatesMap.java   |   2 +-
 src/java/picard/sam/util/PhysicalLocation.java     |   2 +-
 src/java/picard/util/AdapterMarker.java            |   2 +-
 src/java/picard/util/BaitDesigner.java             |   2 +-
 src/java/picard/util/BasicInputParser.java         |   8 +-
 src/java/picard/util/DbSnpBitSetUtil.java          |  71 ++++++---
 src/java/picard/util/IlluminaUtil.java             |  10 +-
 src/java/picard/util/IntervalListTools.java        |   2 +-
 src/java/picard/util/MathUtil.java                 |   2 +-
 .../picard/vcf/CollectVariantCallingMetrics.java   |  13 +-
 src/java/picard/vcf/GenotypeConcordance.java       |   4 +-
 .../picard/vcf/filter/AlleleBalanceFilter.java     |   2 +-
 src/java/picard/vcf/filter/FilterVcf.java          | 131 ++++++++++++-----
 src/java/picard/vcf/processor/VcfFileSegment.java  |   2 +-
 .../vcf/processor/VcfFileSegmentGenerator.java     |   4 +-
 .../CollectAlignmentSummaryMetricsTest.java        |   6 +-
 .../java/picard/cmdline/CommandLineParserTest.java | 162 +++++++++++++++++++++
 .../illumina/CheckIlluminaDirectoryTest.java       |   2 +-
 src/tests/java/picard/sam/FilterSamReadsTest.java  |  77 ++++++++++
 .../java/picard/util/BedToIntervalListTest.java    |   2 +-
 .../java/picard/util/IntervalListToBedTest.java    |   2 +-
 src/tests/java/picard/vcf/SortVcfsTest.java        |   1 -
 .../vcf/UpdateVcfSequenceDictionaryTest.java       |   5 -
 .../picard/vcf/{ => filter}/TestFilterVcf.java     |  41 ++++++
 .../vcf/processor/VcfFileSegmentGeneratorTest.java |   2 +-
 .../picard/sam/FilterSamReads/filterOddStarts.js   |   2 +
 .../filterReadsWithout5primeSoftClip.js            |  10 ++
 .../sam/summary_alignment_stats_test_chimeras.sam  |  22 +--
 75 files changed, 851 insertions(+), 475 deletions(-)
 delete mode 100644 debian/patches/00-for-upstream-fix-testsuite
 delete mode 100644 debian/patches/01-for-upstream-fix-classloader
 create mode 100644 src/tests/java/picard/sam/FilterSamReadsTest.java
 rename src/tests/java/picard/vcf/{ => filter}/TestFilterVcf.java (87%)
 create mode 100644 testdata/picard/sam/FilterSamReads/filterOddStarts.js
 create mode 100644 testdata/picard/sam/FilterSamReads/filterReadsWithout5primeSoftClip.js

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git