[med-svn] [gatk] 02/03: Merge tag 'upstream/3.5+dfsg'
Andreas Tille
tille at debian.org
Thu Nov 26 18:54:35 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository gatk.
commit e7525176587b9941487ee409abb5f95628661b18
Merge: f30b8a2 de4ae38
Author: Andreas Tille <tille at debian.org>
Date: Thu Nov 26 19:52:50 2015 +0100
Merge tag 'upstream/3.5+dfsg'
Upstream version 3.5+dfsg
ant-bridge.sh | 28 +-
licensing/private_license.txt | 2 +-
licensing/protected_license.txt | 2 +-
licensing/public_license.txt | 2 +-
pom.xml | 150 +-
public/VectorPairHMM/pom.xml | 2 +-
public/VectorPairHMM/src/main/c++/Sandbox.java | 10 +-
public/VectorPairHMM/src/main/c++/utils.cc | 26 +-
public/doc/Ant_Help.tex | 9 -
public/doc/GATK_Coding_Standards.pdf | Bin 133046 -> 0 bytes
public/doc/GATK_Coding_Standards.tex | 288 -
public/doc/README | 89 +-
public/external-example/pom.xml | 51 +-
.../java/org/mycompany/app/MyExampleWalker.java | 8 +-
.../app/MyExampleWalkerIntegrationTest.java | 6 +-
.../org/mycompany/app/MyExampleWalkerUnitTest.java | 2 +-
public/gatk-engine/pom.xml | 41 +-
.../gatk/engine/CommandLineExecutable.java | 229 +
.../gatk/engine/CommandLineGATK.java | 370 +
.../broadinstitute/gatk/engine/GATKVCFUtils.java | 422 +
.../gatk/engine/GenomeAnalysisEngine.java | 1325 ++
.../broadinstitute/gatk/engine/ReadMetrics.java | 2 +-
.../broadinstitute/gatk/engine/ReadProperties.java | 197 +
.../broadinstitute/gatk/engine/SampleUtils.java | 258 +
.../broadinstitute/gatk/engine/WalkerManager.java | 451 +
.../gatk/engine/alignment/Aligner.java | 74 +
.../gatk/engine/alignment/Alignment.java | 246 +
.../gatk/engine/alignment/bwa/BWAAligner.java | 63 +
.../engine/alignment/bwa/BWAConfiguration.java | 79 +
.../gatk/engine/alignment/bwa/BWTFiles.java | 259 +
.../alignment/bwa/java/AlignerTestHarness.java | 189 +
.../alignment/bwa/java/AlignmentMatchSequence.java | 175 +
.../engine/alignment/bwa/java/AlignmentState.java | 38 +
.../engine/alignment/bwa/java/BWAAlignment.java | 215 +
.../engine/alignment/bwa/java/BWAJavaAligner.java | 418 +
.../gatk/engine/alignment/bwa/java/LowerBound.java | 113 +
.../gatk/engine/alignment/package-info.java | 26 +
.../engine/alignment/reference/bwt/AMBWriter.java | 93 +
.../engine/alignment/reference/bwt/ANNWriter.java | 120 +
.../gatk/engine/alignment/reference/bwt/BWT.java | 197 +
.../engine/alignment/reference/bwt/BWTReader.java | 114 +
.../bwt/BWTSupplementaryFileGenerator.java | 85 +
.../engine/alignment/reference/bwt/BWTWriter.java | 96 +
.../gatk/engine/alignment/reference/bwt/Bases.java | 133 +
.../engine/alignment/reference/bwt/Counts.java | 176 +
.../reference/bwt/CreateBWTFromReference.java | 200 +
.../alignment/reference/bwt/SequenceBlock.java | 66 +
.../alignment/reference/bwt/SuffixArray.java | 183 +
.../alignment/reference/bwt/SuffixArrayReader.java | 110 +
.../alignment/reference/bwt/SuffixArrayWriter.java | 92 +
.../reference/packing/BasePackedInputStream.java | 120 +
.../reference/packing/BasePackedOutputStream.java | 165 +
.../reference/packing/CreatePACFromReference.java | 64 +
.../alignment/reference/packing/PackUtils.java | 160 +
.../packing/UnsignedIntPackedInputStream.java | 129 +
.../packing/UnsignedIntPackedOutputStream.java | 121 +
.../engine/arguments/DbsnpArgumentCollection.java | 46 +
.../engine/arguments/GATKArgumentCollection.java | 680 +
...ndardVariantContextInputArgumentCollection.java | 48 +
.../gatk/engine/crypt/CryptUtils.java | 391 +
.../broadinstitute/gatk/engine/crypt/GATKKey.java | 350 +
.../gatk/engine/datasources/package-info.java | 26 +
.../engine/datasources/providers/AllLocusView.java | 169 +
.../datasources/providers/CoveredLocusView.java | 63 +
.../IntervalOverlappingRODsFromStream.java | 168 +
.../providers/IntervalReferenceOrderedView.java | 182 +
.../providers/InvalidPositionException.java | 46 +
.../datasources/providers/LocusReferenceView.java | 249 +
.../providers/LocusShardDataProvider.java | 100 +
.../engine/datasources/providers/LocusView.java | 219 +
.../providers/ManagingReferenceOrderedView.java | 116 +
.../providers/RODMetaDataContainer.java | 83 +
.../providers/ReadBasedReferenceOrderedView.java | 60 +
.../datasources/providers/ReadReferenceView.java | 102 +
.../providers/ReadShardDataProvider.java | 82 +
.../engine/datasources/providers/ReadView.java | 88 +
.../providers/ReferenceOrderedView.java | 33 +
.../datasources/providers/ReferenceView.java | 131 +
.../engine/datasources/providers/RodLocusView.java | 196 +
.../datasources/providers/ShardDataProvider.java | 197 +
.../gatk/engine/datasources/providers/View.java | 55 +
.../engine/datasources/providers/package-info.java | 26 +
.../reads/ActiveRegionShardBalancer.java | 85 +
.../engine/datasources/reads/BAMAccessPlan.java | 170 +
.../gatk/engine/datasources/reads/BAMSchedule.java | 531 +
.../engine/datasources/reads/BAMScheduler.java | 321 +
.../reads/BGZFBlockLoadingDispatcher.java | 86 +
.../engine/datasources/reads/BlockInputStream.java | 451 +
.../gatk/engine/datasources/reads/BlockLoader.java | 189 +
.../engine/datasources/reads/FileHandleCache.java | 229 +
.../gatk/engine/datasources/reads/FilePointer.java | 437 +
.../engine/datasources/reads/GATKBAMIndex.java | 469 +
.../engine/datasources/reads/GATKBAMIndexData.java | 121 +
.../reads/IntervalOverlapFilteringIterator.java | 205 +
.../engine/datasources/reads/IntervalSharder.java | 93 +
.../gatk/engine/datasources/reads/LocusShard.java | 61 +
.../datasources/reads/LocusShardBalancer.java | 58 +
.../gatk/engine/datasources/reads/ReadShard.java | 271 +
.../datasources/reads/ReadShardBalancer.java | 231 +
.../engine/datasources/reads/SAMDataSource.java | 1236 ++
.../gatk/engine/datasources/reads/Shard.java | 254 +
.../engine/datasources/reads/ShardBalancer.java | 49 +
.../engine/datasources/reads/package-info.java | 26 +
.../datasources/reads/utilities/BAMFileStat.java | 185 +
.../datasources/reads/utilities/BAMTagRenamer.java | 100 +
.../reads/utilities/FindLargeShards.java | 192 +
.../reads/utilities/PrintBAMRegion.java | 113 +
.../reads/utilities/PrintBGZFBounds.java | 137 +
.../reads/utilities/UnzipSingleBlock.java | 89 +
.../datasources/reads/utilities/package-info.java | 26 +
.../datasources/reference/ReferenceDataSource.java | 166 +
.../engine/datasources/reference/package-info.java | 26 +
.../engine/datasources/rmd/DataStreamSegment.java | 32 +
.../gatk/engine/datasources/rmd/EntireStream.java | 32 +
.../datasources/rmd/MappedStreamSegment.java | 48 +
.../datasources/rmd/ReferenceOrderedDataPool.java | 153 +
.../rmd/ReferenceOrderedDataSource.java | 257 +
.../gatk/engine/datasources/rmd/ResourcePool.java | 188 +
.../gatk/engine/datasources/rmd/package-info.java | 26 +
.../gatk/engine/executive/Accumulator.java | 211 +
.../executive/HierarchicalMicroScheduler.java | 495 +
.../executive/HierarchicalMicroSchedulerMBean.java | 86 +
.../engine/executive/LinearMicroScheduler.java | 130 +
.../gatk/engine/executive/MicroScheduler.java | 463 +
.../gatk/engine/executive/MicroSchedulerMBean.java | 37 +
.../gatk/engine/executive/OutputMergeTask.java | 102 +
.../gatk/engine/executive/ReduceTree.java | 187 +
.../gatk/engine/executive/ShardTraverser.java | 163 +
.../gatk/engine/executive/TreeReducer.java | 127 +
.../gatk/engine/executive/WindowMaker.java | 218 +
.../gatk/engine/executive/package-info.java | 26 +
.../gatk/engine/filters/BAQReadTransformer.java | 75 +
.../gatk/engine/filters/BadCigarFilter.java | 141 +
.../gatk/engine/filters/BadMateFilter.java | 74 +
.../engine/filters/CountingFilteringIterator.java | 150 +
.../gatk/engine/filters/DisableableReadFilter.java | 35 +
.../gatk/engine/filters/DuplicateReadFilter.java | 91 +
.../filters/FailsVendorQualityCheckFilter.java | 43 +
.../gatk/engine/filters/FilterManager.java | 106 +
.../gatk/engine/filters/LibraryReadFilter.java | 65 +
.../gatk/engine/filters/MalformedReadFilter.java | 277 +
.../gatk/engine/filters/MappingQualityFilter.java | 62 +
.../filters/MappingQualityUnavailableFilter.java | 58 +
.../engine/filters/MappingQualityZeroFilter.java | 56 +
.../gatk/engine/filters/MateSameStrandFilter.java | 65 +
.../gatk/engine/filters/MaxInsertSizeFilter.java | 59 +
.../engine/filters/MissingReadGroupFilter.java | 55 +
.../engine/filters/NDNCigarReadTransformer.java | 123 +
.../filters/NoOriginalQualityScoresFilter.java | 54 +
.../engine/filters/NotPrimaryAlignmentFilter.java | 56 +
.../gatk/engine/filters/OverclippedReadFilter.java | 80 +
.../gatk/engine/filters/Platform454Filter.java | 57 +
.../gatk/engine/filters/PlatformFilter.java | 65 +
.../gatk/engine/filters/PlatformUnitFilter.java | 90 +
.../engine/filters/PlatformUnitFilterHelper.java | 87 +
.../gatk/engine/filters/ReadFilter.java | 60 +
.../engine/filters/ReadGroupBlackListFilter.java | 133 +
.../gatk/engine/filters/ReadLengthFilter.java | 63 +
.../gatk/engine/filters/ReadNameFilter.java | 59 +
.../gatk/engine/filters/ReadStrandFilter.java | 62 +
.../filters/ReassignMappingQualityFilter.java | 88 +
.../filters/ReassignOneMappingQualityFilter.java | 90 +
.../gatk/engine/filters/SampleFilter.java | 61 +
.../gatk/engine/filters/SingleReadGroupFilter.java | 63 +
.../gatk/engine/filters/UnmappedReadFilter.java | 56 +
.../gatk/engine/filters/package-info.java | 26 +
.../gatk/engine/io/BySampleSAMFileWriter.java | 70 +
.../gatk/engine/io/DirectOutputTracker.java | 48 +
.../gatk/engine/io/FastqFileWriter.java | 77 +
.../gatk/engine/io/NWaySAMFileWriter.java | 255 +
.../gatk/engine/io/OutputTracker.java | 193 +
.../gatk/engine/io/ThreadGroupOutputTracker.java | 170 +
.../engine/io/storage/OutputStreamStorage.java | 144 +
.../engine/io/storage/SAMFileWriterStorage.java | 172 +
.../gatk/engine/io/storage/Storage.java | 45 +
.../gatk/engine/io/storage/StorageFactory.java | 92 +
.../io/storage/VariantContextWriterStorage.java | 247 +
.../stubs/OutputStreamArgumentTypeDescriptor.java | 134 +
.../gatk/engine/io/stubs/OutputStreamStub.java | 142 +
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.../gatk/engine/io/stubs/SAMFileWriterStub.java | 373 +
.../io/stubs/SAMReaderArgumentTypeDescriptor.java | 77 +
.../broadinstitute/gatk/engine/io/stubs/Stub.java | 69 +
.../io/stubs/VCFWriterArgumentTypeDescriptor.java | 138 +
.../engine/io/stubs/VariantContextWriterStub.java | 313 +
.../gatk/engine/iterators/BoundedReadIterator.java | 160 +
.../gatk/engine/iterators/GenomeLocusIterator.java | 100 +
.../gatk/engine/iterators/IterableIterator.java | 40 +
.../MalformedBAMErrorReformatingIterator.java | 69 +
.../MisencodedBaseQualityReadTransformer.java | 94 +
.../gatk/engine/iterators/NullSAMIterator.java | 58 +
.../gatk/engine/iterators/PeekingIterator.java | 65 +
.../engine/iterators/PositionTrackingIterator.java | 106 +
.../gatk/engine/iterators/RNAReadTransformer.java | 37 +
.../engine/iterators/ReadFormattingIterator.java | 141 +
.../gatk/engine/iterators/ReadTransformer.java | 205 +
.../engine/iterators/ReadTransformersMode.java | 53 +
.../engine/iterators/ReadTransformingIterator.java | 68 +
.../engine/iterators/VerifyingSamIterator.java | 90 +
.../gatk/engine/iterators/package-info.java | 26 +
.../broadinstitute/gatk/engine/package-info.java | 2 +-
.../gatk/engine/phonehome/GATKRunReport.java | 786 +
.../engine/phonehome/GATKRunReportException.java | 99 +
.../gatk/engine/recalibration/BQSRArgumentSet.java | 100 +
.../gatk/engine/recalibration/BQSRMode.java | 55 +
.../resourcemanagement/ThreadAllocation.java | 116 +
.../gatk/engine/samples/Affection.java | 47 +
.../broadinstitute/gatk/engine/samples/Gender.java | 35 +
.../gatk/engine/samples/MendelianViolation.java | 461 +
.../gatk/engine/samples/PedReader.java | 311 +
.../engine/samples/PedigreeValidationType.java | 42 +
.../broadinstitute/gatk/engine/samples/Sample.java | 261 +
.../gatk/engine/samples/SampleDB.java | 338 +
.../gatk/engine/samples/SampleDBBuilder.java | 161 +
.../broadinstitute/gatk/engine/samples/Trio.java | 70 +
.../traversals/ArtificialReadsTraversal.java | 142 +
.../engine/traversals/TAROrderedReadCache.java | 168 +
.../gatk/engine/traversals/TraversalEngine.java | 124 +
.../engine/traversals/TraverseActiveRegions.java | 719 +
.../gatk/engine/traversals/TraverseDuplicates.java | 205 +
.../gatk/engine/traversals/TraverseLociNano.java | 304 +
.../gatk/engine/traversals/TraverseReadPairs.java | 129 +
.../gatk/engine/traversals/TraverseReadsNano.java | 256 +
.../gatk/engine/traversals/package-info.java | 26 +
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.../gatk/engine/walkers/ActiveRegionWalker.java | 196 +
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.../org/broadinstitute/gatk/engine/walkers/By.java | 53 +
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.../src/main/resources/GATK_public.key | Bin
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.../gatk/engine/CommandLineGATKUnitTest.java | 68 +
.../gatk/engine/EngineFeaturesIntegrationTest.java | 793 +
.../gatk/engine/GATKVCFUtilsUnitTest.java | 159 +
.../gatk/engine/GenomeAnalysisEngineUnitTest.java | 272 +
.../gatk/engine/InstantiableWalker.java | 37 +
.../gatk/engine/MaxRuntimeIntegrationTest.java | 151 +
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.../gatk/engine/arguments/CramIntegrationTest.java | 90 +
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.../gatk/engine/crypt/CryptUtilsUnitTest.java | 200 +
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.../providers/AllLocusViewUnitTest.java | 90 +
.../providers/CoveredLocusViewUnitTest.java | 102 +
.../IntervalReferenceOrderedViewUnitTest.java | 366 +
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.../utils/threading/ThreadEfficiencyMonitor.java | 232 -
.../gatk/utils/threading/ThreadLocalArray.java | 65 -
.../gatk/utils/threading/ThreadPoolMonitor.java | 77 -
.../gatk/utils/threading/package-info.java | 26 -
.../gatk/utils/variant/GATKVCFIndexType.java | 39 -
.../gatk/utils/variant/GATKVCFUtils.java | 316 -
.../utils/variant/GATKVariantContextUtils.java | 1960 --
.../gatk/utils/variant/HomoSapiensConstants.java | 51 -
.../gatk/utils/wiggle/WiggleHeader.java | 56 -
.../gatk/utils/wiggle/WiggleWriter.java | 117 -
.../walkers/variantrecalibration/plot_Tranches.R | 93 -
.../htsjdk/samtools/GATKBAMFileSpanUnitTest.java | 254 -
.../java/htsjdk/samtools/GATKChunkUnitTest.java | 71 -
.../gatk/engine/CommandLineGATKUnitTest.java | 68 -
.../gatk/engine/EngineFeaturesIntegrationTest.java | 736 -
.../gatk/engine/GenomeAnalysisEngineUnitTest.java | 273 -
.../gatk/engine/MaxRuntimeIntegrationTest.java | 151 -
.../gatk/engine/ReadMetricsUnitTest.java | 371 -
.../gatk/engine/WalkerManagerUnitTest.java | 71 -
.../providers/AllLocusViewUnitTest.java | 90 -
.../providers/CoveredLocusViewUnitTest.java | 103 -
.../IntervalReferenceOrderedViewUnitTest.java | 366 -
.../providers/LocusReferenceViewUnitTest.java | 143 -
.../datasources/providers/LocusViewTemplate.java | 405 -
.../providers/ReadReferenceViewUnitTest.java | 160 -
.../providers/ReferenceOrderedViewUnitTest.java | 157 -
.../providers/ReferenceViewTemplate.java | 122 -
.../providers/ShardDataProviderUnitTest.java | 152 -
.../reads/ActiveRegionShardBalancerUnitTest.java | 102 -
.../datasources/reads/DownsamplerBenchmark.java | 94 -
.../datasources/reads/FilePointerUnitTest.java | 129 -
.../datasources/reads/GATKBAMIndexUnitTest.java | 108 -
.../datasources/reads/GATKWalkerBenchmark.java | 141 -
.../IntervalOverlapFilteringIteratorUnitTest.java | 150 -
.../engine/datasources/reads/MockLocusShard.java | 51 -
.../datasources/reads/PicardBaselineBenchmark.java | 101 -
.../datasources/reads/ReadProcessingBenchmark.java | 83 -
.../reads/ReadShardBalancerUnitTest.java | 195 -
.../datasources/reads/SAMDataSourceUnitTest.java | 253 -
.../datasources/reads/SAMReaderIDUnitTest.java | 49 -
.../reads/SeekableBufferedStreamUnitTest.java | 101 -
.../reads/TheoreticalMinimaBenchmark.java | 114 -
.../ReferenceDataSourceIntegrationTest.java | 75 -
.../rmd/ReferenceOrderedDataPoolUnitTest.java | 208 -
.../rmd/ReferenceOrderedQueryDataPoolUnitTest.java | 89 -
.../AlleleBiasedDownsamplingUtilsUnitTest.java | 219 -
.../downsampling/DownsamplingIntegrationTest.java | 44 -
.../DownsamplingReadsIteratorUnitTest.java | 139 -
.../FractionalDownsamplerUnitTest.java | 158 -
.../downsampling/LevelingDownsamplerUnitTest.java | 163 -
...PerSampleDownsamplingReadsIteratorUnitTest.java | 299 -
...edArtificialSingleSampleReadStreamAnalyzer.java | 127 -
.../downsampling/ReservoirDownsamplerUnitTest.java | 131 -
.../SimplePositionalDownsamplerUnitTest.java | 331 -
.../gatk/engine/executive/ReduceTreeUnitTest.java | 254 -
.../AllowNCigarMalformedReadFilterUnitTest.java | 77 -
.../engine/filters/BadCigarFilterUnitTest.java | 91 -
.../filters/BadReadGroupsIntegrationTest.java | 52 -
.../filters/MalformedReadFilterUnitTest.java | 246 -
.../filters/NDNCigarReadTransformerUnitTest.java | 70 -
.../gatk/engine/filters/ReadFilterTest.java | 370 -
.../filters/ReadGroupBlackListFilterUnitTest.java | 247 -
.../filters/UnsafeMalformedReadFilterUnitTest.java | 50 -
.../gatk/engine/io/OutputTrackerUnitTest.java | 84 -
.../iterators/BoundedReadIteratorUnitTest.java | 145 -
.../iterators/GATKSAMIteratorAdapterUnitTest.java | 176 -
.../iterators/ReadFormattingIteratorUnitTest.java | 50 -
.../iterators/VerifyingSamIteratorUnitTest.java | 128 -
.../engine/phonehome/GATKRunReportUnitTest.java | 310 -
.../engine/refdata/RefMetaDataTrackerUnitTest.java | 290 -
.../refdata/tracks/FeatureManagerUnitTest.java | 163 -
.../refdata/tracks/RMDTrackBuilderUnitTest.java | 190 -
.../utils/CheckableCloseableTribbleIterator.java | 90 -
.../FeatureToGATKFeatureIteratorUnitTest.java | 61 -
.../refdata/utils/FlashBackIteratorUnitTest.java | 364 -
.../engine/refdata/utils/TestFeatureReader.java | 53 -
.../engine/refdata/utils/TestRMDTrackBuilder.java | 71 -
.../gatk/engine/report/GATKReportUnitTest.java | 285 -
.../gatk/engine/samples/PedReaderUnitTest.java | 354 -
.../gatk/engine/samples/SampleDBUnitTest.java | 251 -
.../gatk/engine/samples/SampleUnitTest.java | 89 -
.../engine/traversals/DummyActiveRegionWalker.java | 116 -
.../traversals/TAROrderedReadCacheUnitTest.java | 111 -
.../traversals/TraverseActiveRegionsUnitTest.java | 679 -
.../traversals/TraverseDuplicatesUnitTest.java | 162 -
.../engine/traversals/TraverseReadsUnitTest.java | 166 -
.../gatk/engine/walkers/WalkerTest.java | 455 -
.../gatk/tools/CatVariantsIntegrationTest.java | 197 +-
.../gatk/tools/walkers/BAQIntegrationTest.java | 6 +-
.../CNV/SymbolicAllelesIntegrationTest.java | 6 +-
.../annotator/CompressedDataListUnitTest.java | 118 +
.../walkers/annotator/SnpEffUtilUnitTest.java | 2 +-
.../coverage/CallableLociIntegrationTest.java | 2 +-
.../CompareCallableLociWalkerIntegrationTest.java | 2 +-
.../DepthOfCoverageB36IntegrationTest.java | 2 +-
.../coverage/DepthOfCoverageIntegrationTest.java | 35 +-
.../diffengine/DiffObjectsIntegrationTest.java | 76 +
.../walkers/filters/VariantFiltrationUnitTest.java | 107 +
.../walkers/qc/CheckPileupIntegrationTest.java | 2 +-
.../gatk/tools/walkers/qc/CountReadsUnitTest.java | 2 +-
.../qc/DictionaryConsistencyIntegrationTest.java | 2 +-
.../tools/walkers/qc/FlagStatIntegrationTest.java | 2 +-
.../walkers/qc/PileupWalkerIntegrationTest.java | 2 +-
.../readutils/ClipReadsWalkersIntegrationTest.java | 28 +-
.../readutils/PrintReadsIntegrationTest.java | 34 +-
.../readutils/PrintReadsLargeScaleTest.java | 2 +-
.../walkers/readutils/PrintReadsUnitTest.java | 6 +-
.../ReadAdaptorTrimmerIntegrationTest.java | 60 -
.../readutils/SplitSamFileIntegrationTest.java | 60 +
.../rnaseq/ASEReadCounterIntegrationTest.java | 112 +
.../variantutils/FilterLiftedVariantsUnitTest.java | 54 -
.../variantutils/SelectVariantsUnitTest.java | 30 +-
.../walkers/variantutils/VCFIntegrationTest.java | 395 +
.../gatk/utils/AutoFormattingTimeUnitTest.java | 118 -
.../org/broadinstitute/gatk/utils/BaseTest.java | 568 -
.../gatk/utils/BaseUtilsUnitTest.java | 179 -
.../gatk/utils/BitSetUtilsUnitTest.java | 85 -
.../gatk/utils/ExampleToCopyUnitTest.java | 241 -
.../gatk/utils/GATKTextReporter.java | 41 -
.../gatk/utils/GenomeLocParserBenchmark.java | 81 -
.../gatk/utils/GenomeLocParserUnitTest.java | 509 -
.../gatk/utils/GenomeLocSortedSetUnitTest.java | 405 -
.../gatk/utils/GenomeLocUnitTest.java | 386 -
.../java/org/broadinstitute/gatk/utils/MD5DB.java | 312 -
.../org/broadinstitute/gatk/utils/MD5Mismatch.java | 67 -
.../MRUCachingSAMSequencingDictionaryUnitTest.java | 97 -
.../org/broadinstitute/gatk/utils/MWUnitTest.java | 131 -
.../gatk/utils/MathUtilsUnitTest.java | 913 -
.../broadinstitute/gatk/utils/MedianUnitTest.java | 115 -
.../gatk/utils/NGSPlatformUnitTest.java | 167 -
.../gatk/utils/PathUtilsUnitTest.java | 65 -
.../gatk/utils/QualityUtilsUnitTest.java | 189 -
.../gatk/utils/R/RScriptExecutorUnitTest.java | 110 -
.../gatk/utils/R/RScriptLibraryUnitTest.java | 47 -
.../gatk/utils/R/RUtilsUnitTest.java | 65 -
.../gatk/utils/SampleUtilsUnitTest.java | 52 -
.../utils/SequenceDictionaryUtilsUnitTest.java | 241 -
.../gatk/utils/SimpleTimerUnitTest.java | 179 -
.../gatk/utils/TestNGTestTransformer.java | 62 -
.../broadinstitute/gatk/utils/UtilsUnitTest.java | 363 -
.../utils/activeregion/ActiveRegionUnitTest.java | 395 -
.../activeregion/ActivityProfileStateUnitTest.java | 92 -
.../activeregion/ActivityProfileUnitTest.java | 491 -
.../BandPassActivityProfileUnitTest.java | 339 -
.../broadinstitute/gatk/utils/baq/BAQUnitTest.java | 257 -
.../gatk/utils/classloader/JVMUtilsUnitTest.java | 75 -
.../gatk/utils/clipping/ReadClipperTestUtils.java | 144 -
.../gatk/utils/clipping/ReadClipperUnitTest.java | 421 -
.../gatk/utils/codecs/hapmap/HapMapUnitTest.java | 164 -
.../utils/collections/DefaultHashMapUnitTest.java | 159 -
.../collections/ExpandingArrayListUnitTest.java | 177 -
.../commandline/ArgumentMatchSiteUnitTest.java | 80 -
.../commandline/ArgumentMatchSourceUnitTest.java | 99 -
.../ArgumentTypeDescriptorUnitTest.java | 233 -
.../InvalidArgumentIntegrationTest.java | 66 -
.../utils/commandline/LoggingIntegrationTest.java | 117 -
.../utils/commandline/ParsingEngineUnitTest.java | 1140 --
.../commandline/RodBindingCollectionUnitTest.java | 133 -
.../gatk/utils/commandline/RodBindingUnitTest.java | 82 -
.../gatk/utils/crypt/CryptUtilsUnitTest.java | 199 -
.../gatk/utils/crypt/GATKKeyIntegrationTest.java | 157 -
.../gatk/utils/crypt/GATKKeyUnitTest.java | 129 -
.../CachingIndexedFastaSequenceFileUnitTest.java | 264 -
.../gatk/utils/file/FSLockWithSharedUnitTest.java | 60 -
.../utils/fragments/FragmentUtilsBenchmark.java | 81 -
.../utils/fragments/FragmentUtilsUnitTest.java | 390 -
.../gatk/utils/haplotype/EventMapUnitTest.java | 203 -
.../gatk/utils/haplotype/HaplotypeUnitTest.java | 249 -
.../utils/interval/IntervalIntegrationTest.java | 304 -
.../gatk/utils/interval/IntervalUtilsUnitTest.java | 1110 -
.../gatk/utils/io/IOUtilsUnitTest.java | 326 -
.../gatk/utils/jna/clibrary/LibCUnitTest.java | 70 -
.../utils/jna/drmaa/v1_0/JnaSessionQueueTest.java | 165 -
.../utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java | 257 -
.../gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java | 162 -
.../AlignmentStateMachineUnitTest.java | 110 -
.../gatk/utils/locusiterator/LIBS_position.java | 155 -
.../locusiterator/LocusIteratorBenchmark.java | 142 -
.../LocusIteratorByStateBaseTest.java | 252 -
.../LocusIteratorByStateUnitTest.java | 753 -
.../PerSampleReadStateManagerUnitTest.java | 188 -
.../utils/nanoScheduler/InputProducerUnitTest.java | 94 -
.../utils/nanoScheduler/MapResultUnitTest.java | 65 -
.../utils/nanoScheduler/NanoSchedulerUnitTest.java | 343 -
.../gatk/utils/nanoScheduler/ReducerUnitTest.java | 236 -
.../gatk/utils/pileup/PileupElementUnitTest.java | 189 -
.../utils/pileup/ReadBackedPileupUnitTest.java | 328 -
.../progressmeter/ProgressMeterDaemonUnitTest.java | 121 -
.../progressmeter/ProgressMeterDataUnitTest.java | 86 -
.../utils/recalibration/EventTypeUnitTest.java | 61 -
.../utils/report/ReportMarshallerUnitTest.java | 64 -
.../utils/runtime/ProcessControllerUnitTest.java | 518 -
.../gatk/utils/runtime/RuntimeUtilsUnitTest.java | 42 -
.../gatk/utils/sam/AlignmentUtilsUnitTest.java | 1044 -
.../utils/sam/ArtificialBAMBuilderUnitTest.java | 121 -
.../ArtificialPatternedSAMIteratorUnitTest.java | 122 -
.../utils/sam/ArtificialSAMFileWriterUnitTest.java | 120 -
.../sam/ArtificialSAMQueryIteratorUnitTest.java | 138 -
.../gatk/utils/sam/ArtificialSAMUtilsUnitTest.java | 108 -
.../ArtificialSingleSampleReadStreamUnitTest.java | 186 -
.../gatk/utils/sam/GATKSAMRecordUnitTest.java | 78 -
.../utils/sam/MisencodedBaseQualityUnitTest.java | 96 -
.../gatk/utils/sam/ReadUtilsUnitTest.java | 340 -
.../smithwaterman/SmithWatermanBenchmark.java | 87 -
.../gatk/utils/text/ListFileUtilsUnitTest.java | 159 -
.../utils/text/TextFormattingUtilsUnitTest.java | 89 -
.../EfficiencyMonitoringThreadFactoryUnitTest.java | 189 -
.../utils/threading/ThreadPoolMonitorUnitTest.java | 64 -
.../gatk/utils/variant/GATKVCFUtilsUnitTest.java | 138 -
.../variant/GATKVariantContextUtilsUnitTest.java | 1612 --
.../gatk/utils/variant/VCFIntegrationTest.java | 377 -
.../utils/variant/VariantContextBenchmark.java | 377 -
public/gatk-utils/pom.xml | 46 +-
.../src/main/assembly/example-resources.xml | 0
.../gatk/utils/help/log4j.properties | 7 -
.../main/java/htsjdk/samtools/GATKBAMFileSpan.java | 308 +
.../src/main/java/htsjdk/samtools/GATKBin.java | 146 +
.../src/main/java/htsjdk/samtools/GATKChunk.java | 116 +
.../java/htsjdk/samtools/PicardNamespaceUtils.java | 40 +
.../gatk/utils/AutoFormattingTime.java | 185 +
.../org/broadinstitute/gatk/utils/BaseUtils.java | 671 +
.../org/broadinstitute/gatk/utils/BitSetUtils.java | 134 +
.../gatk/utils/ContigComparator.java | 80 +
.../gatk/utils/DeprecatedToolChecks.java | 107 +
.../org/broadinstitute/gatk/utils/GenomeLoc.java | 3 +-
.../broadinstitute/gatk/utils/GenomeLocParser.java | 622 +
.../gatk/utils/GenomeLocSortedSet.java | 476 +
.../gatk/utils/HasGenomeLocation.java | 2 +-
.../broadinstitute/gatk/utils/HeapSizeMonitor.java | 107 +
.../org/broadinstitute/gatk/utils/IndelUtils.java | 262 +
.../org/broadinstitute/gatk/utils/LRUCache.java | 45 +
.../utils/MRUCachingSAMSequenceDictionary.java | 186 +
.../broadinstitute/gatk/utils/MannWhitneyU.java | 507 +
.../org/broadinstitute/gatk/utils/MathUtils.java | 1689 ++
.../java/org/broadinstitute/gatk/utils/Median.java | 94 +
.../gatk/utils/MultiThreadedErrorTracker.java | 105 +
.../org/broadinstitute/gatk/utils/NGSPlatform.java | 146 +
.../org/broadinstitute/gatk/utils/PathUtils.java | 195 +
.../broadinstitute/gatk/utils/QualityUtils.java | 397 +
.../gatk/utils/R/RScriptExecutor.java | 191 +
.../gatk/utils/R/RScriptExecutorException.java | 34 +
.../gatk/utils/R/RScriptLibrary.java | 66 +
.../org/broadinstitute/gatk/utils/R/RUtils.java | 91 +
.../gatk/utils/SequenceDictionaryUtils.java | 540 +
.../gatk/utils/SequencerFlowClass.java | 38 +
.../org/broadinstitute/gatk/utils/SimpleTimer.java | 2 +-
.../gatk/utils/UnvalidatingGenomeLoc.java | 50 +
.../java/org/broadinstitute/gatk/utils/Utils.java | 1174 ++
.../gatk/utils/ValidationExclusion.java | 71 +
.../gatk/utils/activeregion/ActiveRegion.java | 500 +
.../utils/activeregion/ActiveRegionReadState.java | 40 +
.../gatk/utils/activeregion/ActivityProfile.java | 520 +
.../utils/activeregion/ActivityProfileState.java | 112 +
.../activeregion/BandPassActivityProfile.java | 194 +
.../gatk/utils/analysis/AminoAcid.java | 114 +
.../gatk/utils/analysis/AminoAcidTable.java | 94 +
.../gatk/utils/analysis/AminoAcidUtils.java | 77 +
.../org/broadinstitute/gatk/utils/baq/BAQ.java | 713 +
.../gatk/utils/classloader/JVMUtils.java | 309 +
.../gatk/utils/classloader/PluginManager.java | 356 +
.../utils/classloader/ProtectedPackageSource.java | 28 +
.../utils/classloader/PublicPackageSource.java | 28 +
.../gatk/utils/clipping/ClippingOp.java | 617 +
.../utils/clipping/ClippingRepresentation.java | 63 +
.../gatk/utils/clipping/ReadClipper.java | 568 +
.../gatk/utils/codecs/beagle/BeagleCodec.java | 287 +
.../gatk/utils/codecs/beagle/BeagleFeature.java | 118 +
.../gatk/utils/codecs/hapmap/RawHapMapCodec.java | 135 +
.../gatk/utils/codecs/hapmap/RawHapMapFeature.java | 204 +
.../gatk/utils/codecs/refseq/RefSeqCodec.java | 181 +
.../gatk/utils/codecs/refseq/RefSeqFeature.java | 331 +
.../gatk/utils/codecs/refseq/Transcript.java | 78 +
.../utils/codecs/sampileup/SAMPileupCodec.java | 365 +
.../utils/codecs/sampileup/SAMPileupFeature.java | 284 +
.../gatk/utils/codecs/samread/SAMReadCodec.java | 134 +
.../gatk/utils/codecs/samread/SAMReadFeature.java | 207 +
.../gatk/utils/codecs/table/BedTableCodec.java | 58 +
.../gatk/utils/codecs/table/TableCodec.java | 136 +
.../gatk/utils/codecs/table/TableFeature.java | 104 +
.../gatk/utils/collections/DefaultHashMap.java | 56 +
.../gatk/utils/collections/ExpandingArrayList.java | 69 +
.../gatk/utils/collections/IndexedSet.java | 342 +
.../collections/LoggingNestedIntegerArray.java | 120 +
.../gatk/utils/collections/NestedIntegerArray.java | 221 +
.../gatk/utils/collections/Pair.java | 93 +
.../gatk/utils/collections/Permutation.java | 103 +
.../gatk/utils/collections/PrimitivePair.java | 200 +
.../gatk/utils/collections/RODMergingIterator.java | 160 +
.../gatk/utils/commandline/Advanced.java | 41 +
.../gatk/utils/commandline/Argument.java | 125 +
.../gatk/utils/commandline/ArgumentCollection.java | 45 +
.../gatk/utils/commandline/ArgumentDefinition.java | 297 +
.../utils/commandline/ArgumentDefinitionGroup.java | 99 +
.../utils/commandline/ArgumentDefinitions.java | 195 +
.../gatk/utils/commandline/ArgumentException.java | 38 +
.../gatk/utils/commandline/ArgumentIOType.java | 52 +
.../gatk/utils/commandline/ArgumentMatch.java | 292 +
.../utils/commandline/ArgumentMatchFileValue.java | 52 +
.../gatk/utils/commandline/ArgumentMatchSite.java | 77 +
.../utils/commandline/ArgumentMatchSource.java | 97 +
.../utils/commandline/ArgumentMatchSourceType.java | 33 +
.../commandline/ArgumentMatchStringValue.java | 49 +
.../gatk/utils/commandline/ArgumentMatchValue.java | 43 +
.../gatk/utils/commandline/ArgumentMatches.java | 209 +
.../gatk/utils/commandline/ArgumentSource.java | 243 +
.../utils/commandline/ArgumentTypeDescriptor.java | 1038 +
.../gatk/utils/commandline/ClassType.java | 40 +
.../gatk/utils/commandline/CommandLineProgram.java | 460 +
.../gatk/utils/commandline/CommandLineUtils.java | 192 +
.../commandline/EnumerationArgumentDefault.java | 65 +
.../gatk/utils/commandline/Gather.java | 41 +
.../gatk/utils/commandline/Gatherer.java | 47 +
.../gatk/utils/commandline/Hidden.java | 41 +
.../gatk/utils/commandline/Input.java | 83 +
.../commandline/IntervalArgumentCollection.java | 88 +
.../gatk/utils/commandline/IntervalBinding.java | 101 +
.../commandline/MissingArgumentValueException.java | 50 +
.../gatk/utils/commandline/Multiplex.java | 44 +
.../gatk/utils/commandline/Multiplexer.java | 52 +
.../gatk/utils/commandline/Output.java | 90 +
.../gatk/utils/commandline/ParsedArgs.java | 38 +
.../gatk/utils/commandline/ParsedListArgs.java | 55 +
.../gatk/utils/commandline/ParsingEngine.java | 829 +
.../commandline/ParsingEngineArgumentFiles.java | 55 +
.../commandline/ParsingEngineArgumentProvider.java | 37 +
.../gatk/utils/commandline/ParsingMethod.java | 127 +
.../gatk/utils/commandline/RodBinding.java | 197 +
.../utils/commandline/RodBindingCollection.java | 89 +
.../gatk/utils/commandline/Tags.java | 112 +
.../gatk/utils/commandline/package-info.java | 26 +
.../gatk/utils/contexts/AlignmentContext.java | 154 +
.../gatk/utils/contexts/AlignmentContextUtils.java | 150 +
.../gatk/utils/contexts/ReferenceContext.java | 217 +
.../gatk/utils/diffengine/BAMDiffableReader.java | 119 +
.../gatk/utils/diffengine/DiffElement.java | 125 +
.../gatk/utils/diffengine/DiffEngine.java | 437 +
.../gatk/utils/diffengine/DiffNode.java | 249 +
.../gatk/utils/diffengine/DiffValue.java | 90 +
.../gatk/utils/diffengine/DiffableReader.java | 66 +
.../gatk/utils/diffengine/Difference.java | 137 +
.../utils/diffengine/GATKReportDiffableReader.java | 104 +
.../gatk/utils/diffengine/VCFDiffableReader.java | 145 +
.../AlleleBiasedDownsamplingUtils.java | 369 +
.../gatk/utils/downsampling/DownsampleType.java | 39 +
.../gatk/utils/downsampling/Downsampler.java | 161 +
.../utils/downsampling/DownsamplingMethod.java | 121 +
.../downsampling/DownsamplingReadsIterator.java | 116 +
.../gatk/utils/downsampling/DownsamplingUtils.java | 107 +
.../utils/downsampling/FractionalDownsampler.java | 129 +
.../downsampling/FractionalDownsamplerFactory.java | 46 +
.../utils/downsampling/LevelingDownsampler.java | 242 +
.../utils/downsampling/PassThroughDownsampler.java | 111 +
.../PerSampleDownsamplingReadsIterator.java | 207 +
.../gatk/utils/downsampling/ReadsDownsampler.java | 56 +
.../downsampling/ReadsDownsamplerFactory.java | 38 +
.../utils/downsampling/ReservoirDownsampler.java | 219 +
.../downsampling/ReservoirDownsamplerFactory.java | 46 +
.../downsampling/SimplePositionalDownsampler.java | 171 +
.../SimplePositionalDownsamplerFactory.java | 46 +
.../gatk/utils/duplicates/DupUtils.java | 142 +
.../gatk/utils/duplicates/DuplicateComp.java | 66 +
.../DynamicClassResolutionException.java | 54 +
.../gatk/utils/exceptions/GATKException.java | 2 +-
.../utils/exceptions/ReviewedGATKException.java | 2 +-
.../gatk/utils/exceptions/UserException.java | 490 +
.../gatk/utils/fasta/ArtificialFastaUtils.java | 154 +
.../fasta/CachingIndexedFastaSequenceFile.java | 370 +
.../gatk/utils/fasta/package-info.java | 26 +
.../gatk/utils/file/FSLockWithShared.java | 293 +
.../gatk/utils/fragments/FragmentCollection.java | 67 +
.../gatk/utils/fragments/FragmentUtils.java | 377 +
.../gatk/utils/genotyper/AlleleList.java | 41 +
.../utils/genotyper/AlleleListPermutation.java | 35 +
.../gatk/utils/genotyper/AlleleListUtils.java | 334 +
.../gatk/utils/genotyper/DiploidGenotype.java | 125 +
.../gatk/utils/genotyper/IndexedAlleleList.java | 95 +
.../gatk/utils/genotyper/IndexedSampleList.java | 96 +
.../gatk/utils/genotyper/MostLikelyAllele.java | 134 +
.../genotyper/PerReadAlleleLikelihoodMap.java | 417 +
.../gatk/utils/genotyper/ReadLikelihoods.java | 1586 ++
.../gatk/utils/genotyper/SampleList.java | 42 +
.../gatk/utils/genotyper/SampleListUtils.java | 224 +
.../gatk/utils/haplotype/EventMap.java | 423 +
.../gatk/utils/haplotype/Haplotype.java | 343 +
.../utils/haplotype/HaplotypeBaseComparator.java | 42 +
.../utils/haplotype/HaplotypeScoreComparator.java | 39 +
.../haplotype/HaplotypeSizeAndBaseComparator.java | 47 +
.../gatk/utils/help/ApplicationDetails.java | 95 +
.../gatk/utils/help/DocletUtils.java | 80 +
.../gatk/utils/help/DocumentedGATKFeature.java | 50 +
.../utils/help/DocumentedGATKFeatureHandler.java | 99 +
.../utils/help/DocumentedGATKFeatureObject.java | 61 +
.../gatk/utils/help/ForumAPIUtils.java | 173 +
.../gatk/utils/help/ForumDiscussion.java | 84 +
.../gatk/utils/help/GATKDocUtils.java | 75 +
.../gatk/utils/help/GATKDocWorkUnit.java | 127 +
.../broadinstitute/gatk/utils/help/GATKDoclet.java | 580 +
.../gatk/utils/help/GSONArgument.java | 83 +
.../gatk/utils/help/GSONWorkUnit.java | 86 +
.../utils/help/GenericDocumentationHandler.java | 722 +
.../gatk/utils/help/HelpConstants.java | 82 +
.../gatk/utils/help/HelpFormatter.java | 336 +
.../utils/help/ResourceBundleExtractorDoclet.java | 281 +
.../gatk/utils/instrumentation/Sizeof.java | 146 +
.../gatk/utils/interval/IntervalMergingRule.java | 35 +
.../gatk/utils/interval/IntervalSetRule.java | 36 +
.../gatk/utils/interval/IntervalUtils.java | 895 +
.../gatk/utils/io/FileExtension.java | 37 +
.../utils/io/HardThresholdingOutputStream.java | 56 +
.../org/broadinstitute/gatk/utils/io/IOUtils.java | 575 +
.../gatk/utils/io/ReferenceBacked.java | 33 +
.../org/broadinstitute/gatk/utils/io/Resource.java | 142 +
.../gatk/utils/iterators/GATKSAMIterator.java | 56 +
.../utils/iterators/GATKSAMIteratorAdapter.java | 136 +
.../gatk/utils/iterators/PushbackIterator.java | 82 +
.../gatk/utils/jna/clibrary/JNAUtils.java | 59 +
.../gatk/utils/jna/clibrary/LibC.java | 200 +
.../gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java | 101 +
.../gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java | 316 +
.../gatk/utils/jna/drmaa/v1_0/JnaSession.java | 461 +
.../utils/jna/drmaa/v1_0/JnaSessionFactory.java | 40 +
.../gatk/utils/jna/drmaa/v1_0/LibDrmaa.java | 723 +
.../gatk/utils/jna/lsf/v7_0_6/LibBat.java | 20014 +++++++++++++++++++
.../gatk/utils/jna/lsf/v7_0_6/LibLsf.java | 1780 ++
.../utils/locusiterator/AlignmentStateMachine.java | 372 +
.../utils/locusiterator/LIBSDownsamplingInfo.java | 51 +
.../gatk/utils/locusiterator/LIBSPerformance.java | 191 +
.../gatk/utils/locusiterator/LocusIterator.java | 62 +
.../utils/locusiterator/LocusIteratorByState.java | 457 +
.../locusiterator/PerSampleReadStateManager.java | 261 +
.../gatk/utils/locusiterator/ReadStateManager.java | 289 +
.../utils/locusiterator/SamplePartitioner.java | 172 +
.../gatk/utils/nanoScheduler/EOFMarkedValue.java | 105 +
.../gatk/utils/nanoScheduler/InputProducer.java | 217 +
.../gatk/utils/nanoScheduler/MapResult.java | 75 +
.../gatk/utils/nanoScheduler/MapResultsQueue.java | 116 +
.../gatk/utils/nanoScheduler/NSMapFunction.java | 44 +
.../utils/nanoScheduler/NSProgressFunction.java | 37 +
.../gatk/utils/nanoScheduler/NSReduceFunction.java | 43 +
.../gatk/utils/nanoScheduler/NanoScheduler.java | 494 +
.../gatk/utils/nanoScheduler/Reducer.java | 169 +
.../broadinstitute/gatk/utils/package-info.java | 2 +-
.../gatk/utils/pairhmm/BatchPairHMM.java | 41 +
.../gatk/utils/pairhmm/Log10PairHMM.java | 220 +
.../gatk/utils/pairhmm/N2MemoryPairHMM.java | 98 +
.../broadinstitute/gatk/utils/pairhmm/PairHMM.java | 390 +
.../gatk/utils/pairhmm/PairHMMModel.java | 435 +
.../gatk/utils/pairhmm/PairHMMReadyHaplotypes.java | 182 +
.../utils/pileup/MergingPileupElementIterator.java | 76 +
.../gatk/utils/pileup/PileupElement.java | 539 +
.../gatk/utils/pileup/PileupElementFilter.java | 36 +
.../gatk/utils/pileup/PileupElementTracker.java | 154 +
.../gatk/utils/pileup/ReadBackedPileup.java | 295 +
.../gatk/utils/pileup/ReadBackedPileupImpl.java | 1040 +
.../org/broadinstitute/gatk/utils/pileup2/Notes | 0
.../gatk/utils/progressmeter/ProgressMeter.java | 465 +
.../utils/progressmeter/ProgressMeterDaemon.java | 111 +
.../utils/progressmeter/ProgressMeterData.java | 79 +
.../gatk/utils/recalibration/EventType.java | 72 +
.../gatk/utils/refdata/RODRecordListImpl.java | 129 +
.../gatk/utils/refdata/RefMetaDataTracker.java | 497 +
.../refdata/ReferenceDependentFeatureCodec.java | 42 +
.../gatk/utils/refdata/ReferenceOrderedDatum.java | 66 +
.../gatk/utils/refdata/SeekableRODIterator.java | 412 +
.../gatk/utils/refdata/VariantContextAdaptors.java | 265 +
.../gatk/utils/refdata/package-info.java | 26 +
.../gatk/utils/refdata/tracks/FeatureManager.java | 280 +
.../utils/refdata/tracks/IndexDictionaryUtils.java | 114 +
.../gatk/utils/refdata/tracks/RMDTrack.java | 147 +
.../gatk/utils/refdata/tracks/RMDTrackBuilder.java | 469 +
.../utils/FeatureToGATKFeatureIterator.java | 74 +
.../utils/refdata/utils/FlashBackIterator.java | 221 +
.../gatk/utils/refdata/utils/GATKFeature.java | 114 +
.../utils/LocationAwareSeekableRODIterator.java | 49 +
.../gatk/utils/refdata/utils/RMDTriplet.java | 92 +
.../gatk/utils/refdata/utils/RODRecordList.java | 45 +
.../gatk/utils/report/GATKReport.java | 376 +
.../gatk/utils/report/GATKReportColumn.java | 147 +
.../gatk/utils/report/GATKReportColumnFormat.java | 63 +
.../gatk/utils/report/GATKReportDataType.java | 236 +
.../gatk/utils/report/GATKReportGatherer.java | 62 +
.../gatk/utils/report/GATKReportTable.java | 779 +
.../gatk/utils/report/GATKReportVersion.java | 100 +
.../gatk/utils/runtime/CapturedStreamOutput.java | 134 +
.../gatk/utils/runtime/InputStreamSettings.java | 116 +
.../gatk/utils/runtime/OutputStreamSettings.java | 127 +
.../gatk/utils/runtime/ProcessController.java | 387 +
.../gatk/utils/runtime/ProcessOutput.java | 57 +
.../gatk/utils/runtime/ProcessSettings.java | 140 +
.../gatk/utils/runtime/RuntimeUtils.java | 77 +
.../gatk/utils/runtime/StreamLocation.java | 33 +
.../gatk/utils/runtime/StreamOutput.java | 69 +
.../gatk/utils/sam/AlignmentStartComparator.java | 50 +
.../sam/AlignmentStartWithNoTiesComparator.java | 73 +
.../gatk/utils/sam/AlignmentUtils.java | 1339 ++
.../gatk/utils/sam/ArtificialBAMBuilder.java | 242 +
.../utils/sam/ArtificialGATKSAMFileWriter.java | 129 +
.../utils/sam/ArtificialMultiSampleReadStream.java | 87 +
.../utils/sam/ArtificialPatternedSAMIterator.java | 172 +
.../gatk/utils/sam/ArtificialSAMFileReader.java | 155 +
.../gatk/utils/sam/ArtificialSAMIterator.java | 212 +
.../gatk/utils/sam/ArtificialSAMQueryIterator.java | 259 +
.../gatk/utils/sam/ArtificialSAMUtils.java | 484 +
.../sam/ArtificialSingleSampleReadStream.java | 213 +
.../ArtificialSingleSampleReadStreamAnalyzer.java | 282 +
.../broadinstitute/gatk/utils/sam/CigarUtils.java | 273 +
.../gatk/utils/sam/GATKSAMFileWriter.java | 56 +
.../gatk/utils/sam/GATKSAMReadGroupRecord.java | 116 +
.../gatk/utils/sam/GATKSAMRecord.java | 623 +
.../gatk/utils/sam/GATKSAMRecordIterator.java | 64 +
.../ReadUnclippedStartWithNoTiesComparator.java | 73 +
.../broadinstitute/gatk/utils/sam/ReadUtils.java | 957 +
.../gatk/utils/sam/SAMReaderBuilder.java | 102 +
.../broadinstitute/gatk/utils/sam/SAMReaderID.java | 134 +
.../gatk/utils/sam/SimplifyingSAMFileWriter.java | 86 +
.../gatk/utils/sam/package-info.java | 26 +
.../GlobalEdgeGreedySWPairwiseAlignment.java | 208 +
.../gatk/utils/smithwaterman/Parameters.java | 62 +
.../utils/smithwaterman/SWPairwiseAlignment.java | 599 +
.../smithwaterman/SWPairwiseAlignmentMain.java | 221 +
.../gatk/utils/smithwaterman/SWParameterSet.java | 51 +
.../gatk/utils/smithwaterman/SmithWaterman.java | 57 +
.../gatk/utils/text/ListFileUtils.java | 344 +
.../gatk/utils/text/TextFormattingUtils.java | 182 +
.../broadinstitute/gatk/utils/text/XReadLines.java | 208 +
.../EfficiencyMonitoringThreadFactory.java | 160 +
.../gatk/utils/threading/NamedThreadFactory.java | 51 +
.../utils/threading/ThreadEfficiencyMonitor.java | 232 +
.../gatk/utils/threading/ThreadLocalArray.java | 65 +
.../gatk/utils/threading/ThreadPoolMonitor.java | 77 +
.../gatk/utils/threading/package-info.java | 26 +
.../utils/variant/ChromosomeCountConstants.java | 44 +
.../gatk/utils/variant/GATKVCFConstants.java | 175 +
.../gatk/utils/variant/GATKVCFHeaderLines.java | 200 +
.../gatk/utils/variant/GATKVCFIndexType.java | 39 +
.../utils/variant/GATKVariantContextUtils.java | 2124 ++
.../gatk/utils/variant/HomoSapiensConstants.java | 51 +
.../gatk/utils/variant/VCIterable.java | 92 +
.../gatk/utils/wiggle/WiggleHeader.java | 56 +
.../gatk/utils/wiggle/WiggleWriter.java | 117 +
.../htsjdk/samtools/GATKBAMFileSpanUnitTest.java | 254 +
.../java/htsjdk/samtools/GATKChunkUnitTest.java | 71 +
.../gatk/utils/AutoFormattingTimeUnitTest.java | 118 +
.../org/broadinstitute/gatk/utils/BaseTest.java | 564 +
.../gatk/utils/BaseUtilsUnitTest.java | 177 +
.../gatk/utils/BitSetUtilsUnitTest.java | 84 +
.../gatk/utils/ExampleToCopyUnitTest.java | 239 +
.../gatk/utils/GATKTextReporter.java | 41 +
.../gatk/utils/GenomeLocParserBenchmark.java | 81 +
.../gatk/utils/GenomeLocParserUnitTest.java | 509 +
.../gatk/utils/GenomeLocSortedSetUnitTest.java | 405 +
.../gatk/utils/GenomeLocUnitTest.java | 386 +
.../java/org/broadinstitute/gatk/utils/MD5DB.java | 312 +
.../org/broadinstitute/gatk/utils/MD5Mismatch.java | 67 +
.../MRUCachingSAMSequencingDictionaryUnitTest.java | 97 +
.../org/broadinstitute/gatk/utils/MWUnitTest.java | 131 +
.../gatk/utils/MathUtilsUnitTest.java | 913 +
.../broadinstitute/gatk/utils/MedianUnitTest.java | 115 +
.../gatk/utils/NGSPlatformUnitTest.java | 167 +
.../gatk/utils/PathUtilsUnitTest.java | 65 +
.../gatk/utils/QualityUtilsUnitTest.java | 189 +
.../gatk/utils/R/RScriptExecutorUnitTest.java | 110 +
.../gatk/utils/R/RScriptLibraryUnitTest.java | 47 +
.../gatk/utils/R/RUtilsUnitTest.java | 65 +
.../utils/SequenceDictionaryUtilsUnitTest.java | 239 +
.../gatk/utils/SimpleTimerUnitTest.java | 179 +
.../gatk/utils/TestNGTestTransformer.java | 62 +
.../broadinstitute/gatk/utils/UtilsUnitTest.java | 362 +
.../utils/activeregion/ActiveRegionUnitTest.java | 395 +
.../activeregion/ActivityProfileStateUnitTest.java | 92 +
.../activeregion/ActivityProfileUnitTest.java | 491 +
.../BandPassActivityProfileUnitTest.java | 339 +
.../broadinstitute/gatk/utils/baq/BAQUnitTest.java | 257 +
.../gatk/utils/classloader/JVMUtilsUnitTest.java | 75 +
.../gatk/utils/clipping/ReadClipperTestUtils.java | 162 +
.../gatk/utils/clipping/ReadClipperUnitTest.java | 421 +
.../utils/codecs/beagle/BeagleCodecUnitTest.java | 42 +
.../gatk/utils/codecs/hapmap/HapMapUnitTest.java | 174 +
.../utils/codecs/refseq/RefSeqCodecUnitTest.java | 42 +
.../codecs/sampileup/SAMPileupCodecUnitTest.java | 42 +
.../utils/codecs/samread/SAMReadCodecUnitTest.java | 42 +
.../utils/codecs/table/TableCodecUnitTest.java | 42 +
.../utils/collections/DefaultHashMapUnitTest.java | 159 +
.../collections/ExpandingArrayListUnitTest.java | 177 +
.../commandline/ArgumentMatchSiteUnitTest.java | 80 +
.../commandline/ArgumentMatchSourceUnitTest.java | 99 +
.../utils/commandline/ParsingEngineUnitTest.java | 1140 ++
.../commandline/RodBindingCollectionUnitTest.java | 133 +
.../gatk/utils/commandline/RodBindingUnitTest.java | 82 +
.../AlleleBiasedDownsamplingUtilsUnitTest.java | 219 +
.../CachingIndexedFastaSequenceFileUnitTest.java | 264 +
.../gatk/utils/file/FSLockWithSharedUnitTest.java | 60 +
.../utils/fragments/FragmentUtilsBenchmark.java | 81 +
.../utils/fragments/FragmentUtilsUnitTest.java | 390 +
.../gatk/utils/haplotype/EventMapUnitTest.java | 203 +
.../gatk/utils/haplotype/HaplotypeUnitTest.java | 249 +
.../gatk/utils/interval/IntervalUtilsUnitTest.java | 1114 ++
.../gatk/utils/io/IOUtilsUnitTest.java | 326 +
.../gatk/utils/jna/clibrary/LibCUnitTest.java | 70 +
.../utils/jna/drmaa/v1_0/JnaSessionQueueTest.java | 165 +
.../utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java | 257 +
.../gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java | 162 +
.../AlignmentStateMachineUnitTest.java | 116 +
.../gatk/utils/locusiterator/LIBS_position.java | 155 +
.../locusiterator/LocusIteratorBenchmark.java | 142 +
.../LocusIteratorByStateBaseTest.java | 232 +
.../LocusIteratorByStateUnitTest.java | 743 +
.../PerSampleReadStateManagerUnitTest.java | 188 +
.../utils/nanoScheduler/InputProducerUnitTest.java | 94 +
.../utils/nanoScheduler/MapResultUnitTest.java | 65 +
.../utils/nanoScheduler/NanoSchedulerUnitTest.java | 343 +
.../gatk/utils/nanoScheduler/ReducerUnitTest.java | 236 +
.../gatk/utils/pileup/PileupElementUnitTest.java | 189 +
.../utils/pileup/ReadBackedPileupUnitTest.java | 328 +
.../progressmeter/ProgressMeterDaemonUnitTest.java | 121 +
.../progressmeter/ProgressMeterDataUnitTest.java | 86 +
.../utils/recalibration/EventTypeUnitTest.java | 61 +
.../utils/refdata/RefMetaDataTrackerUnitTest.java | 290 +
.../refdata/tracks/FeatureManagerUnitTest.java | 163 +
.../refdata/tracks/RMDTrackBuilderUnitTest.java | 190 +
.../utils/CheckableCloseableTribbleIterator.java | 90 +
.../FeatureToGATKFeatureIteratorUnitTest.java | 61 +
.../refdata/utils/FlashBackIteratorUnitTest.java | 369 +
.../utils/refdata/utils/TestFeatureReader.java | 53 +
.../utils/refdata/utils/TestRMDTrackBuilder.java | 70 +
.../gatk/utils/report/GATKReportUnitTest.java | 289 +
.../utils/report/ReportMarshallerUnitTest.java | 64 +
.../utils/runtime/ProcessControllerUnitTest.java | 518 +
.../gatk/utils/runtime/RuntimeUtilsUnitTest.java | 42 +
.../gatk/utils/sam/AlignmentUtilsUnitTest.java | 1045 +
.../utils/sam/ArtificialBAMBuilderUnitTest.java | 121 +
.../ArtificialPatternedSAMIteratorUnitTest.java | 122 +
.../utils/sam/ArtificialSAMFileWriterUnitTest.java | 120 +
.../sam/ArtificialSAMQueryIteratorUnitTest.java | 138 +
.../gatk/utils/sam/ArtificialSAMUtilsUnitTest.java | 108 +
.../ArtificialSingleSampleReadStreamUnitTest.java | 186 +
.../gatk/utils/sam/GATKSAMRecordUnitTest.java | 78 +
.../gatk/utils/sam/ReadUtilsUnitTest.java | 339 +
.../smithwaterman/SmithWatermanBenchmark.java | 87 +
.../gatk/utils/text/ListFileUtilsUnitTest.java | 154 +
.../utils/text/TextFormattingUtilsUnitTest.java | 89 +
.../EfficiencyMonitoringThreadFactoryUnitTest.java | 189 +
.../utils/threading/ThreadPoolMonitorUnitTest.java | 64 +
.../variant/GATKVariantContextUtilsUnitTest.java | 1665 ++
.../utils/variant/VariantContextBenchmark.java | 377 +
.../gatk-utils/src/test/resources/exampleBAM.bam | Bin 0 -> 3609 bytes
.../src/test/resources/exampleBAM.bam.bai | Bin 0 -> 232 bytes
.../src/test/resources/exampleBAM.simple.bai | Bin 0 -> 232 bytes
.../src/test/resources/exampleBAM.simple.bam | Bin 0 -> 3602 bytes
.../test/resources/exampleBAM_with_unmapped.bai | Bin 0 -> 232 bytes
.../test/resources/exampleBAM_with_unmapped.bam | Bin 0 -> 3575 bytes
.../test/resources/exampleCRAM-nobai-nocrai.cram | Bin 0 -> 13353 bytes
.../test/resources/exampleCRAM-nobai-withcrai.cram | Bin 0 -> 13353 bytes
.../resources/exampleCRAM-nobai-withcrai.cram.crai | Bin 0 -> 47 bytes
.../gatk-utils/src/test/resources/exampleCRAM.cram | Bin 0 -> 5281 bytes
.../src/test/resources/exampleCRAM.cram.bai | Bin 0 -> 136 bytes
.../src/test/resources/exampleCRAM.cram.crai | Bin 0 -> 44 bytes
.../src/test/resources/exampleDBSNP.vcf | 0
.../src/test/resources/exampleDBSNP.vcf.idx | Bin
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.../src/test/resources/exampleFASTA-windows.fasta | 0
.../src/test/resources/exampleFASTA.dict | 0
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.../src/test/resources/exampleFASTA.fasta.amb | 0
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.../src/test/resources/exampleFASTA.fasta.bwt | Bin
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.../src/test/resources/exampleFASTA.fasta.pac | Bin
.../src/test/resources/exampleFASTA.fasta.rbwt | Bin
.../src/test/resources/exampleFASTA.fasta.rpac | Bin
.../src/test/resources/exampleFASTA.fasta.rsa | Bin
.../src/test/resources/exampleFASTA.fasta.sa | Bin
.../src/test/resources/exampleGATKReport.eval | 0
.../src/test/resources/exampleGATKReportv1.tbl | 0
.../src/test/resources/exampleGATKReportv2.tbl | 0
.../src/test/resources/exampleGRP.grp | 0
.../src/test/resources/exampleINTERVAL.intervals | 0
.../gatk-utils/src/test/resources/exampleNORG.bam | Bin 0 -> 3612 bytes
.../src/test/resources/exampleNORG.bam.bai | Bin 0 -> 232 bytes
.../test/resources/forAlleleFractionSimulation.vcf | 0
.../resources/forAlleleFractionSimulation.vcf.idx | Bin
.../src/test/resources/forLongInsert.vcf | 0
.../src/test/resources/forLongInsert.vcf.idx | Bin
.../src/test/resources/forSimulation.vcf | 0
.../src/test/resources/forSimulation.vcf.idx | Bin
.../src/test/resources/testProperties.properties | 0
.../src/test/resources/testfile.sam | 0
public/gsalib/pom.xml | 10 +-
public/gsalib/src/R/DESCRIPTION | 15 +-
public/gsalib/src/R/NAMESPACE | 3 +-
public/gsalib/src/R/R/gsa.error.R | 12 -
public/gsalib/src/R/R/gsa.getargs.R | 116 -
public/gsalib/src/R/R/gsa.message.R | 3 -
public/gsalib/src/R/R/gsa.plot.venn.R | 50 -
public/gsalib/src/R/R/gsa.read.eval.R | 83 -
public/gsalib/src/R/R/gsa.read.gatkreport.R | 2 +-
public/gsalib/src/R/R/gsa.read.squidmetrics.R | 28 -
public/gsalib/src/R/R/gsa.read.vcf.R | 23 -
.../gsalib/src/R/R/gsa.reshape.concordance.table.R | 20 +
public/gsalib/src/R/R/gsa.variantqc.utils.R | 246 -
public/gsalib/src/R/R/gsa.warn.R | 3 -
public/gsalib/src/R/Read-and-delete-me | 9 -
.../src/R/inst/extdata/test_gatkreport.table | 20 +
.../src/R/inst/extdata/test_genconcord.table | 30 +
public/gsalib/src/R/man/gsa.error.Rd | 49 -
public/gsalib/src/R/man/gsa.getargs.Rd | 57 -
public/gsalib/src/R/man/gsa.message.Rd | 44 -
public/gsalib/src/R/man/gsa.plot.venn.Rd | 75 -
public/gsalib/src/R/man/gsa.read.eval.Rd | 111 -
public/gsalib/src/R/man/gsa.read.gatkreport.Rd | 37 +-
public/gsalib/src/R/man/gsa.read.gatkreportv0.Rd | 26 +
public/gsalib/src/R/man/gsa.read.gatkreportv1.Rd | 26 +
public/gsalib/src/R/man/gsa.read.squidmetrics.Rd | 48 -
public/gsalib/src/R/man/gsa.read.vcf.Rd | 53 -
.../src/R/man/gsa.reshape.concordance.table.Rd | 48 +
public/gsalib/src/R/man/gsa.warn.Rd | 46 -
public/gsalib/src/R/man/gsalib-internal.Rd | 7 +
public/gsalib/src/R/man/gsalib-package.Rd | 70 +-
public/gsalib/src/R/man/test_gatkreport.table.Rd | 13 +
public/gsalib/src/R/man/test_genconcord.table.Rd | 13 +
public/package-tests/pom.xml | 12 +-
public/perl/liftOverVCF.pl | 83 -
public/perl/sortByRef.pl | 127 -
public/pom.xml | 2 +-
.../cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar | Bin 378205 -> 0 bytes
.../cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom | 9 -
.../cofoja/1.2-20140817/cofoja-1.2-20140817.jar | Bin 0 -> 216297 bytes
.../cofoja/1.2-20140817/cofoja-1.2-20140817.pom | 89 +
.../picard/picard/1.120.1579/picard-1.120.1579.jar | Bin 1380569 -> 0 bytes
.../picard/picard/1.120.1579/picard-1.120.1579.pom | 34 -
.../htsjdk/1.120.1620/htsjdk-1.120.1620.jar | Bin 2185840 -> 0 bytes
.../htsjdk/1.120.1620/htsjdk-1.120.1620.pom | 27 -
public/src/main/assembly/binary-dist.xml | 22 +
.../main/scripts/shell/check_utils_engine_tools.sh | 25 +
settings/helpTemplates/generic.index.template.html | 2 +-
settings/helpTemplates/generic.template.html | 13 +-
1916 files changed, 167568 insertions(+), 164559 deletions(-)
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