[med-svn] [picard-tools] branch upstream updated (0c4debd -> 115543b)

[Andreas Tille]

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

      from  0c4debd   Imported Upstream version 2.1.0+dfsg
       new  115543b   Imported Upstream version 2.1.1+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:
 build.sbt                                          |   4 +-
 build.xml                                          | 155 +++++++++++---------
 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 +--
 70 files changed, 821 insertions(+), 346 deletions(-)
 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

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