From 9a306ca2210b6bdf92693e5dc42818e3ad28f463 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Sat, 5 Mar 2016 01:09:43 -0800 Subject: [PATCH] Update licenses --- licensing/private_license.txt | 6 +++--- licensing/protected_license.txt | 6 +++--- licensing/public_license.txt | 2 +- .../qscripts/examples/ExampleFindCoveredIntervals.scala | 6 +++--- .../queue/qscripts/examples/ExampleHaplotypeCaller.scala | 6 +++--- .../queue/qscripts/examples/ExampleUnifiedGenotyper.scala | 6 +++--- .../examples/ExampleUnifiedGenotyperQueueTest.scala | 6 +++--- .../pipeline/examples/UnmappedExcludedQueueTest.scala | 6 +++--- .../gatk/tools/walkers/cancer/m2/create_M2_pon.scala | 6 +++--- .../gatk/tools/walkers/cancer/m2/run_M2_ICE_NN.scala | 6 +++--- .../gatk/tools/walkers/cancer/m2/run_M2_dream.scala | 6 +++--- public/VectorPairHMM/src/main/c++/Sandbox.java | 2 +- .../src/main/java/org/mycompany/app/MyExampleWalker.java | 2 +- .../org/mycompany/app/MyExampleWalkerIntegrationTest.java | 2 +- .../java/org/mycompany/app/MyExampleWalkerUnitTest.java | 2 +- .../broadinstitute/gatk/engine/CommandLineExecutable.java | 2 +- .../org/broadinstitute/gatk/engine/CommandLineGATK.java | 2 +- .../java/org/broadinstitute/gatk/engine/GATKVCFUtils.java | 2 +- .../broadinstitute/gatk/engine/GenomeAnalysisEngine.java | 2 +- .../java/org/broadinstitute/gatk/engine/ReadMetrics.java | 2 +- .../org/broadinstitute/gatk/engine/ReadProperties.java | 2 +- .../java/org/broadinstitute/gatk/engine/SampleUtils.java | 2 +- .../org/broadinstitute/gatk/engine/WalkerManager.java | 2 +- .../org/broadinstitute/gatk/engine/alignment/Aligner.java | 2 +- .../broadinstitute/gatk/engine/alignment/Alignment.java | 2 +- .../gatk/engine/alignment/bwa/BWAAligner.java | 2 +- .../gatk/engine/alignment/bwa/BWAConfiguration.java | 2 +- .../gatk/engine/alignment/bwa/BWTFiles.java | 2 +- .../engine/alignment/bwa/java/AlignerTestHarness.java | 2 +- .../engine/alignment/bwa/java/AlignmentMatchSequence.java | 2 +- .../gatk/engine/alignment/bwa/java/AlignmentState.java | 2 +- .../gatk/engine/alignment/bwa/java/BWAAlignment.java | 2 +- .../gatk/engine/alignment/bwa/java/BWAJavaAligner.java | 2 +- .../gatk/engine/alignment/bwa/java/LowerBound.java | 2 +- .../gatk/engine/alignment/package-info.java | 2 +- .../gatk/engine/alignment/reference/bwt/AMBWriter.java | 2 +- .../gatk/engine/alignment/reference/bwt/ANNWriter.java | 2 +- .../gatk/engine/alignment/reference/bwt/BWT.java | 2 +- .../gatk/engine/alignment/reference/bwt/BWTReader.java | 2 +- .../reference/bwt/BWTSupplementaryFileGenerator.java | 2 +- .../gatk/engine/alignment/reference/bwt/BWTWriter.java | 2 +- .../gatk/engine/alignment/reference/bwt/Bases.java | 2 +- .../gatk/engine/alignment/reference/bwt/Counts.java | 2 +- .../alignment/reference/bwt/CreateBWTFromReference.java | 2 +- .../engine/alignment/reference/bwt/SequenceBlock.java | 2 +- .../gatk/engine/alignment/reference/bwt/SuffixArray.java | 2 +- .../engine/alignment/reference/bwt/SuffixArrayReader.java | 2 +- .../engine/alignment/reference/bwt/SuffixArrayWriter.java | 2 +- .../reference/packing/BasePackedInputStream.java | 2 +- .../reference/packing/BasePackedOutputStream.java | 2 +- .../reference/packing/CreatePACFromReference.java | 2 +- .../engine/alignment/reference/packing/PackUtils.java | 2 +- .../reference/packing/UnsignedIntPackedInputStream.java | 2 +- .../reference/packing/UnsignedIntPackedOutputStream.java | 2 +- .../gatk/engine/arguments/DbsnpArgumentCollection.java | 2 +- .../gatk/engine/arguments/GATKArgumentCollection.java | 2 +- .../StandardVariantContextInputArgumentCollection.java | 2 +- .../org/broadinstitute/gatk/engine/crypt/CryptUtils.java | 2 +- .../org/broadinstitute/gatk/engine/crypt/GATKKey.java | 2 +- .../gatk/engine/datasources/package-info.java | 2 +- .../gatk/engine/datasources/providers/AllLocusView.java | 2 +- .../engine/datasources/providers/CoveredLocusView.java | 2 +- .../providers/IntervalOverlappingRODsFromStream.java | 2 +- .../providers/IntervalReferenceOrderedView.java | 2 +- .../datasources/providers/InvalidPositionException.java | 2 +- .../engine/datasources/providers/LocusReferenceView.java | 2 +- .../datasources/providers/LocusShardDataProvider.java | 2 +- .../gatk/engine/datasources/providers/LocusView.java | 2 +- .../providers/ManagingReferenceOrderedView.java | 2 +- .../datasources/providers/RODMetaDataContainer.java | 2 +- .../providers/ReadBasedReferenceOrderedView.java | 2 +- .../engine/datasources/providers/ReadReferenceView.java | 2 +- .../datasources/providers/ReadShardDataProvider.java | 2 +- .../gatk/engine/datasources/providers/ReadView.java | 2 +- .../datasources/providers/ReferenceOrderedView.java | 2 +- .../gatk/engine/datasources/providers/ReferenceView.java | 2 +- .../gatk/engine/datasources/providers/RodLocusView.java | 2 +- .../engine/datasources/providers/ShardDataProvider.java | 2 +- .../gatk/engine/datasources/providers/View.java | 2 +- .../gatk/engine/datasources/providers/package-info.java | 2 +- .../datasources/reads/ActiveRegionShardBalancer.java | 2 +- .../gatk/engine/datasources/reads/BAMAccessPlan.java | 2 +- .../gatk/engine/datasources/reads/BAMSchedule.java | 2 +- .../gatk/engine/datasources/reads/BAMScheduler.java | 2 +- .../datasources/reads/BGZFBlockLoadingDispatcher.java | 2 +- .../gatk/engine/datasources/reads/BlockInputStream.java | 2 +- .../gatk/engine/datasources/reads/BlockLoader.java | 2 +- .../gatk/engine/datasources/reads/FileHandleCache.java | 2 +- .../gatk/engine/datasources/reads/FilePointer.java | 2 +- .../gatk/engine/datasources/reads/GATKBAMIndex.java | 2 +- .../gatk/engine/datasources/reads/GATKBAMIndexData.java | 2 +- .../reads/IntervalOverlapFilteringIterator.java | 2 +- .../gatk/engine/datasources/reads/IntervalSharder.java | 2 +- .../gatk/engine/datasources/reads/LocusShard.java | 2 +- .../gatk/engine/datasources/reads/LocusShardBalancer.java | 2 +- .../gatk/engine/datasources/reads/ReadShard.java | 2 +- .../gatk/engine/datasources/reads/ReadShardBalancer.java | 2 +- .../gatk/engine/datasources/reads/SAMDataSource.java | 2 +- .../gatk/engine/datasources/reads/Shard.java | 2 +- .../gatk/engine/datasources/reads/ShardBalancer.java | 2 +- .../gatk/engine/datasources/reads/package-info.java | 2 +- .../engine/datasources/reads/utilities/BAMFileStat.java | 2 +- .../engine/datasources/reads/utilities/BAMTagRenamer.java | 2 +- .../datasources/reads/utilities/FindLargeShards.java | 2 +- .../datasources/reads/utilities/PrintBAMRegion.java | 2 +- .../datasources/reads/utilities/PrintBGZFBounds.java | 2 +- .../datasources/reads/utilities/UnzipSingleBlock.java | 2 +- .../engine/datasources/reads/utilities/package-info.java | 2 +- .../engine/datasources/reference/ReferenceDataSource.java | 2 +- .../gatk/engine/datasources/reference/package-info.java | 2 +- .../gatk/engine/datasources/rmd/DataStreamSegment.java | 2 +- .../gatk/engine/datasources/rmd/EntireStream.java | 2 +- .../gatk/engine/datasources/rmd/MappedStreamSegment.java | 2 +- .../engine/datasources/rmd/ReferenceOrderedDataPool.java | 2 +- .../datasources/rmd/ReferenceOrderedDataSource.java | 2 +- .../gatk/engine/datasources/rmd/ResourcePool.java | 2 +- .../gatk/engine/datasources/rmd/package-info.java | 2 +- .../broadinstitute/gatk/engine/executive/Accumulator.java | 2 +- .../gatk/engine/executive/HierarchicalMicroScheduler.java | 2 +- .../engine/executive/HierarchicalMicroSchedulerMBean.java | 2 +- .../gatk/engine/executive/LinearMicroScheduler.java | 2 +- .../gatk/engine/executive/MicroScheduler.java | 2 +- .../gatk/engine/executive/MicroSchedulerMBean.java | 2 +- .../gatk/engine/executive/OutputMergeTask.java | 2 +- .../broadinstitute/gatk/engine/executive/ReduceTree.java | 2 +- .../gatk/engine/executive/ShardTraverser.java | 2 +- .../broadinstitute/gatk/engine/executive/TreeReducer.java | 2 +- .../broadinstitute/gatk/engine/executive/WindowMaker.java | 2 +- .../gatk/engine/executive/package-info.java | 2 +- .../gatk/engine/filters/BAQReadTransformer.java | 2 +- .../gatk/engine/filters/BadCigarFilter.java | 2 +- .../broadinstitute/gatk/engine/filters/BadMateFilter.java | 2 +- .../gatk/engine/filters/CountingFilteringIterator.java | 2 +- .../gatk/engine/filters/DisableableReadFilter.java | 2 +- .../gatk/engine/filters/DuplicateReadFilter.java | 2 +- .../engine/filters/FailsVendorQualityCheckFilter.java | 2 +- .../broadinstitute/gatk/engine/filters/FilterManager.java | 2 +- .../gatk/engine/filters/LibraryReadFilter.java | 2 +- .../gatk/engine/filters/MalformedReadFilter.java | 2 +- .../gatk/engine/filters/MappingQualityFilter.java | 2 +- .../engine/filters/MappingQualityUnavailableFilter.java | 2 +- .../gatk/engine/filters/MappingQualityZeroFilter.java | 2 +- .../gatk/engine/filters/MateSameStrandFilter.java | 2 +- .../gatk/engine/filters/MaxInsertSizeFilter.java | 2 +- .../gatk/engine/filters/MissingReadGroupFilter.java | 2 +- .../gatk/engine/filters/NDNCigarReadTransformer.java | 2 +- .../engine/filters/NoOriginalQualityScoresFilter.java | 2 +- .../gatk/engine/filters/NotPrimaryAlignmentFilter.java | 2 +- .../gatk/engine/filters/OverclippedReadFilter.java | 2 +- .../gatk/engine/filters/Platform454Filter.java | 2 +- .../gatk/engine/filters/PlatformFilter.java | 2 +- .../gatk/engine/filters/PlatformUnitFilter.java | 2 +- .../gatk/engine/filters/PlatformUnitFilterHelper.java | 2 +- .../broadinstitute/gatk/engine/filters/ReadFilter.java | 2 +- .../gatk/engine/filters/ReadGroupBlackListFilter.java | 2 +- .../gatk/engine/filters/ReadLengthFilter.java | 2 +- .../gatk/engine/filters/ReadNameFilter.java | 2 +- .../gatk/engine/filters/ReadStrandFilter.java | 2 +- .../gatk/engine/filters/ReassignMappingQualityFilter.java | 2 +- .../engine/filters/ReassignOneMappingQualityFilter.java | 2 +- .../broadinstitute/gatk/engine/filters/SampleFilter.java | 2 +- .../gatk/engine/filters/SingleReadGroupFilter.java | 2 +- .../gatk/engine/filters/UnmappedReadFilter.java | 2 +- .../broadinstitute/gatk/engine/filters/package-info.java | 2 +- .../gatk/engine/io/BySampleSAMFileWriter.java | 2 +- .../gatk/engine/io/DirectOutputTracker.java | 2 +- .../broadinstitute/gatk/engine/io/FastqFileWriter.java | 2 +- .../broadinstitute/gatk/engine/io/NWaySAMFileWriter.java | 2 +- .../org/broadinstitute/gatk/engine/io/OutputTracker.java | 2 +- .../gatk/engine/io/ThreadGroupOutputTracker.java | 2 +- .../gatk/engine/io/storage/OutputStreamStorage.java | 2 +- .../gatk/engine/io/storage/SAMFileWriterStorage.java | 2 +- .../broadinstitute/gatk/engine/io/storage/Storage.java | 2 +- .../gatk/engine/io/storage/StorageFactory.java | 2 +- .../engine/io/storage/VariantContextWriterStorage.java | 2 +- .../io/stubs/OutputStreamArgumentTypeDescriptor.java | 2 +- .../gatk/engine/io/stubs/OutputStreamStub.java | 2 +- .../io/stubs/SAMFileWriterArgumentTypeDescriptor.java | 2 +- .../gatk/engine/io/stubs/SAMFileWriterStub.java | 2 +- .../engine/io/stubs/SAMReaderArgumentTypeDescriptor.java | 2 +- .../org/broadinstitute/gatk/engine/io/stubs/Stub.java | 2 +- .../engine/io/stubs/VCFWriterArgumentTypeDescriptor.java | 2 +- .../gatk/engine/io/stubs/VariantContextWriterStub.java | 2 +- .../gatk/engine/iterators/BoundedReadIterator.java | 2 +- .../gatk/engine/iterators/GenomeLocusIterator.java | 2 +- .../gatk/engine/iterators/IterableIterator.java | 2 +- .../iterators/MalformedBAMErrorReformatingIterator.java | 2 +- .../iterators/MisencodedBaseQualityReadTransformer.java | 2 +- .../gatk/engine/iterators/NullSAMIterator.java | 2 +- .../gatk/engine/iterators/PeekingIterator.java | 2 +- .../gatk/engine/iterators/PositionTrackingIterator.java | 2 +- .../gatk/engine/iterators/RNAReadTransformer.java | 2 +- .../gatk/engine/iterators/ReadFormattingIterator.java | 2 +- .../gatk/engine/iterators/ReadTransformer.java | 2 +- .../gatk/engine/iterators/ReadTransformersMode.java | 2 +- .../gatk/engine/iterators/ReadTransformingIterator.java | 2 +- .../gatk/engine/iterators/VerifyingSamIterator.java | 2 +- .../gatk/engine/iterators/package-info.java | 2 +- .../java/org/broadinstitute/gatk/engine/package-info.java | 2 +- .../gatk/engine/phonehome/GATKRunReport.java | 2 +- .../gatk/engine/phonehome/GATKRunReportException.java | 2 +- .../gatk/engine/recalibration/BQSRArgumentSet.java | 2 +- .../gatk/engine/recalibration/BQSRMode.java | 2 +- .../gatk/engine/resourcemanagement/ThreadAllocation.java | 2 +- .../org/broadinstitute/gatk/engine/samples/Affection.java | 2 +- .../org/broadinstitute/gatk/engine/samples/Gender.java | 2 +- .../gatk/engine/samples/MendelianViolation.java | 2 +- .../org/broadinstitute/gatk/engine/samples/PedReader.java | 2 +- .../gatk/engine/samples/PedigreeValidationType.java | 2 +- .../org/broadinstitute/gatk/engine/samples/Sample.java | 2 +- .../org/broadinstitute/gatk/engine/samples/SampleDB.java | 2 +- .../gatk/engine/samples/SampleDBBuilder.java | 2 +- .../java/org/broadinstitute/gatk/engine/samples/Trio.java | 2 +- .../gatk/engine/traversals/ArtificialReadsTraversal.java | 2 +- .../gatk/engine/traversals/TAROrderedReadCache.java | 2 +- .../gatk/engine/traversals/TraversalEngine.java | 2 +- .../gatk/engine/traversals/TraverseActiveRegions.java | 2 +- .../gatk/engine/traversals/TraverseDuplicates.java | 2 +- .../gatk/engine/traversals/TraverseLociNano.java | 2 +- .../gatk/engine/traversals/TraverseReadPairs.java | 2 +- .../gatk/engine/traversals/TraverseReadsNano.java | 2 +- .../gatk/engine/traversals/package-info.java | 2 +- .../engine/walkers/ActiveRegionTraversalParameters.java | 2 +- .../gatk/engine/walkers/ActiveRegionWalker.java | 2 +- .../org/broadinstitute/gatk/engine/walkers/Allows.java | 2 +- .../broadinstitute/gatk/engine/walkers/Attribution.java | 2 +- .../org/broadinstitute/gatk/engine/walkers/BAQMode.java | 2 +- .../java/org/broadinstitute/gatk/engine/walkers/By.java | 2 +- .../broadinstitute/gatk/engine/walkers/DataSource.java | 2 +- .../gatk/engine/walkers/DisabledReadFilters.java | 2 +- .../broadinstitute/gatk/engine/walkers/Downsample.java | 2 +- .../gatk/engine/walkers/DuplicateWalker.java | 2 +- .../broadinstitute/gatk/engine/walkers/FailMethod.java | 2 +- .../broadinstitute/gatk/engine/walkers/LocusWalker.java | 2 +- .../gatk/engine/walkers/NanoSchedulable.java | 2 +- .../broadinstitute/gatk/engine/walkers/PartitionBy.java | 2 +- .../broadinstitute/gatk/engine/walkers/PartitionType.java | 2 +- .../java/org/broadinstitute/gatk/engine/walkers/RMD.java | 2 +- .../broadinstitute/gatk/engine/walkers/ReadFilters.java | 2 +- .../gatk/engine/walkers/ReadPairWalker.java | 2 +- .../broadinstitute/gatk/engine/walkers/ReadWalker.java | 2 +- .../org/broadinstitute/gatk/engine/walkers/RefWalker.java | 2 +- .../org/broadinstitute/gatk/engine/walkers/Reference.java | 2 +- .../gatk/engine/walkers/RemoveProgramRecords.java | 2 +- .../org/broadinstitute/gatk/engine/walkers/Requires.java | 2 +- .../org/broadinstitute/gatk/engine/walkers/RodWalker.java | 2 +- .../broadinstitute/gatk/engine/walkers/TreeReducible.java | 2 +- .../org/broadinstitute/gatk/engine/walkers/Walker.java | 2 +- .../broadinstitute/gatk/engine/walkers/WalkerName.java | 2 +- .../org/broadinstitute/gatk/engine/walkers/Window.java | 2 +- .../gatk/engine/CommandLineGATKUnitTest.java | 2 +- .../gatk/engine/EngineFeaturesIntegrationTest.java | 2 +- .../broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java | 2 +- .../gatk/engine/GenomeAnalysisEngineUnitTest.java | 2 +- .../broadinstitute/gatk/engine/InstantiableWalker.java | 2 +- .../gatk/engine/MaxRuntimeIntegrationTest.java | 2 +- .../broadinstitute/gatk/engine/ReadMetricsUnitTest.java | 2 +- .../broadinstitute/gatk/engine/SampleUtilsUnitTest.java | 2 +- .../broadinstitute/gatk/engine/UninstantiableWalker.java | 2 +- .../broadinstitute/gatk/engine/WalkerManagerUnitTest.java | 2 +- .../gatk/engine/arguments/CramIntegrationTest.java | 2 +- .../gatk/engine/arguments/IntervalIntegrationTest.java | 2 +- .../engine/arguments/InvalidArgumentIntegrationTest.java | 2 +- .../gatk/engine/arguments/LoggingIntegrationTest.java | 2 +- .../gatk/engine/crypt/CryptUtilsUnitTest.java | 2 +- .../gatk/engine/crypt/GATKKeyIntegrationTest.java | 2 +- .../broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java | 2 +- .../datasources/providers/AllLocusViewUnitTest.java | 2 +- .../datasources/providers/CoveredLocusViewUnitTest.java | 2 +- .../providers/IntervalReferenceOrderedViewUnitTest.java | 2 +- .../datasources/providers/LocusReferenceViewUnitTest.java | 2 +- .../engine/datasources/providers/LocusViewTemplate.java | 2 +- .../datasources/providers/ReadReferenceViewUnitTest.java | 2 +- .../providers/ReferenceOrderedViewUnitTest.java | 2 +- .../datasources/providers/ReferenceViewTemplate.java | 2 +- .../datasources/providers/ShardDataProviderUnitTest.java | 2 +- .../reads/ActiveRegionShardBalancerUnitTest.java | 2 +- .../engine/datasources/reads/DownsamplerBenchmark.java | 2 +- .../engine/datasources/reads/FilePointerUnitTest.java | 2 +- .../engine/datasources/reads/GATKBAMIndexUnitTest.java | 2 +- .../engine/datasources/reads/GATKWalkerBenchmark.java | 2 +- .../reads/IntervalOverlapFilteringIteratorUnitTest.java | 2 +- .../gatk/engine/datasources/reads/MockLocusShard.java | 2 +- .../engine/datasources/reads/PicardBaselineBenchmark.java | 2 +- .../engine/datasources/reads/ReadProcessingBenchmark.java | 2 +- .../datasources/reads/ReadShardBalancerUnitTest.java | 2 +- .../engine/datasources/reads/SAMDataSourceUnitTest.java | 2 +- .../engine/datasources/reads/SAMReaderIDUnitTest.java | 2 +- .../datasources/reads/SeekableBufferedStreamUnitTest.java | 2 +- .../datasources/reads/TheoreticalMinimaBenchmark.java | 2 +- .../reference/ReferenceDataSourceIntegrationTest.java | 2 +- .../datasources/rmd/ReferenceOrderedDataPoolUnitTest.java | 2 +- .../rmd/ReferenceOrderedQueryDataPoolUnitTest.java | 2 +- .../engine/downsampling/DownsamplingIntegrationTest.java | 2 +- .../downsampling/DownsamplingReadsIteratorUnitTest.java | 2 +- .../downsampling/FractionalDownsamplerUnitTest.java | 2 +- .../engine/downsampling/LevelingDownsamplerUnitTest.java | 2 +- .../PerSampleDownsamplingReadsIteratorUnitTest.java | 2 +- ...wnsampledArtificialSingleSampleReadStreamAnalyzer.java | 2 +- .../engine/downsampling/ReservoirDownsamplerUnitTest.java | 2 +- .../downsampling/SimplePositionalDownsamplerUnitTest.java | 2 +- .../gatk/engine/executive/ReduceTreeUnitTest.java | 2 +- .../filters/AllowNCigarMalformedReadFilterUnitTest.java | 2 +- .../gatk/engine/filters/BadCigarFilterUnitTest.java | 2 +- .../gatk/engine/filters/BadReadGroupsIntegrationTest.java | 2 +- .../gatk/engine/filters/MalformedReadFilterUnitTest.java | 2 +- .../engine/filters/NDNCigarReadTransformerUnitTest.java | 2 +- .../engine/filters/OverclippedReadFilterUnitTest.java | 2 +- .../gatk/engine/filters/ReadFilterTest.java | 2 +- .../engine/filters/ReadGroupBlackListFilterUnitTest.java | 2 +- .../engine/filters/UnsafeMalformedReadFilterUnitTest.java | 2 +- .../gatk/engine/io/OutputTrackerUnitTest.java | 2 +- .../engine/io/stubs/ArgumentTypeDescriptorUnitTest.java | 2 +- .../engine/iterators/BoundedReadIteratorUnitTest.java | 2 +- .../engine/iterators/GATKSAMIteratorAdapterUnitTest.java | 2 +- .../engine/iterators/MisencodedBaseQualityUnitTest.java | 2 +- .../engine/iterators/ReadFormattingIteratorUnitTest.java | 2 +- .../engine/iterators/VerifyingSamIteratorUnitTest.java | 2 +- .../gatk/engine/phonehome/GATKRunReportUnitTest.java | 2 +- .../gatk/engine/samples/PedReaderUnitTest.java | 2 +- .../gatk/engine/samples/SampleDBUnitTest.java | 2 +- .../gatk/engine/samples/SampleUnitTest.java | 2 +- .../gatk/engine/traversals/DummyActiveRegionWalker.java | 2 +- .../engine/traversals/TAROrderedReadCacheUnitTest.java | 2 +- .../engine/traversals/TraverseActiveRegionsUnitTest.java | 2 +- .../engine/traversals/TraverseDuplicatesUnitTest.java | 2 +- .../gatk/engine/traversals/TraverseReadsUnitTest.java | 2 +- .../gatk/engine/walkers/TestCountLociWalker.java | 2 +- .../gatk/engine/walkers/TestCountReadsWalker.java | 2 +- .../gatk/engine/walkers/TestErrorThrowingWalker.java | 2 +- .../gatk/engine/walkers/TestPrintReadsWalker.java | 2 +- .../gatk/engine/walkers/TestPrintVariantsWalker.java | 2 +- .../broadinstitute/gatk/engine/walkers/WalkerTest.java | 2 +- .../queue/extensions/gatk/ArgumentDefinitionField.java | 2 +- .../gatk/queue/extensions/gatk/ArgumentField.java | 2 +- .../queue/extensions/gatk/GATKExtensionsGenerator.java | 2 +- .../gatk/queue/extensions/gatk/ReadFilterField.java | 2 +- .../qscripts/CNV/ONLY_GENOTYPE_xhmmCNVpipeline.scala | 2 +- .../gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala | 2 +- .../gatk/queue/qscripts/GATKResourcesBundle.scala | 2 +- .../gatk/queue/qscripts/examples/ExampleCountLoci.scala | 2 +- .../gatk/queue/qscripts/examples/ExampleCountReads.scala | 2 +- .../queue/qscripts/examples/ExampleCustomWalker.scala | 2 +- .../gatk/queue/qscripts/examples/ExamplePrintReads.scala | 2 +- .../gatk/queue/qscripts/examples/ExampleReadFilter.scala | 2 +- .../queue/qscripts/examples/ExampleRetryMemoryLimit.scala | 2 +- .../gatk/queue/qscripts/examples/HelloWorld.scala | 2 +- .../broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala | 2 +- .../gatk/queue/qscripts/lib/Vcf2Table.scala | 2 +- .../broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala | 2 +- .../gatk/queue/extensions/cancer/MuTect.scala | 2 +- .../gatk/queue/extensions/gatk/BamGatherFunction.scala | 2 +- .../gatk/queue/extensions/gatk/CatVariantsGatherer.scala | 2 +- .../queue/extensions/gatk/ContigScatterFunction.scala | 2 +- .../extensions/gatk/DistributedScatterFunction.scala | 2 +- .../gatk/queue/extensions/gatk/DoC/package.scala | 2 +- .../gatk/queue/extensions/gatk/GATKIntervals.scala | 2 +- .../gatk/queue/extensions/gatk/GATKScatterFunction.scala | 2 +- .../queue/extensions/gatk/IntervalScatterFunction.scala | 2 +- .../gatk/queue/extensions/gatk/LocusScatterFunction.scala | 2 +- .../gatk/queue/extensions/gatk/ReadScatterFunction.scala | 2 +- .../gatk/queue/extensions/gatk/TaggedFile.scala | 2 +- .../gatk/queue/extensions/gatk/VcfGatherFunction.scala | 2 +- .../extensions/gatk/WriteFlankingIntervalsFunction.scala | 2 +- .../gatk/queue/extensions/gatk/XHMM/package.scala | 2 +- .../queue/extensions/picard/AddOrReplaceReadGroups.scala | 2 +- .../gatk/queue/extensions/picard/CalculateHsMetrics.scala | 2 +- .../queue/extensions/picard/CollectGcBiasMetrics.scala | 2 +- .../queue/extensions/picard/CollectMultipleMetrics.scala | 2 +- .../gatk/queue/extensions/picard/CollectWgsMetrics.scala | 2 +- .../gatk/queue/extensions/picard/FastqToSam.scala | 2 +- .../gatk/queue/extensions/picard/MarkDuplicates.scala | 2 +- .../gatk/queue/extensions/picard/MergeSamFiles.scala | 2 +- .../gatk/queue/extensions/picard/PicardBamFunction.scala | 2 +- .../queue/extensions/picard/PicardMetricsFunction.scala | 2 +- .../gatk/queue/extensions/picard/ReorderSam.scala | 2 +- .../gatk/queue/extensions/picard/RevertSam.scala | 2 +- .../gatk/queue/extensions/picard/SamToFastq.scala | 2 +- .../gatk/queue/extensions/picard/SortSam.scala | 2 +- .../gatk/queue/extensions/picard/ValidateSamFile.scala | 2 +- .../extensions/samtools/SamtoolsCommandLineFunction.scala | 2 +- .../queue/extensions/samtools/SamtoolsIndexFunction.scala | 2 +- .../queue/extensions/samtools/SamtoolsMergeFunction.scala | 2 +- .../gatk/queue/extensions/snpeff/SnpEff.scala | 2 +- .../queue/extensions/gatk/GATKIntervalsUnitTest.scala | 2 +- .../queue/extensions/gatk/QueueFeaturesQueueTest.scala | 2 +- .../pipeline/examples/ExampleCountLociQueueTest.scala | 2 +- .../pipeline/examples/ExampleCountReadsQueueTest.scala | 2 +- .../pipeline/examples/ExamplePrintReadsQueueTest.scala | 2 +- .../pipeline/examples/ExampleReadFilterQueueTest.scala | 2 +- .../examples/ExampleRetryMemoryLimitQueueTest.scala | 2 +- .../queue/pipeline/examples/HelloWorldQueueTest.scala | 2 +- .../java/org/broadinstitute/gatk/queue/QueueVersion.java | 2 +- .../java/org/broadinstitute/gatk/queue/package-info.java | 2 +- .../org/broadinstitute/gatk/queue/QCommandLine.scala | 2 +- .../org/broadinstitute/gatk/queue/QCommandPlugin.scala | 2 +- .../scala/org/broadinstitute/gatk/queue/QException.scala | 2 +- .../scala/org/broadinstitute/gatk/queue/QScript.scala | 2 +- .../org/broadinstitute/gatk/queue/QScriptManager.scala | 2 +- .../scala/org/broadinstitute/gatk/queue/QSettings.scala | 2 +- .../gatk/queue/engine/CommandLineJobManager.scala | 2 +- .../gatk/queue/engine/CommandLineJobRunner.scala | 2 +- .../gatk/queue/engine/CommandLinePluginManager.scala | 2 +- .../broadinstitute/gatk/queue/engine/FunctionEdge.scala | 2 +- .../gatk/queue/engine/InProcessJobManager.scala | 2 +- .../gatk/queue/engine/InProcessRunner.scala | 2 +- .../org/broadinstitute/gatk/queue/engine/JobManager.scala | 2 +- .../org/broadinstitute/gatk/queue/engine/JobRunInfo.scala | 2 +- .../org/broadinstitute/gatk/queue/engine/JobRunner.scala | 2 +- .../broadinstitute/gatk/queue/engine/MappingEdge.scala | 2 +- .../org/broadinstitute/gatk/queue/engine/QEdge.scala | 2 +- .../org/broadinstitute/gatk/queue/engine/QGraph.scala | 2 +- .../broadinstitute/gatk/queue/engine/QGraphSettings.scala | 2 +- .../org/broadinstitute/gatk/queue/engine/QNode.scala | 2 +- .../gatk/queue/engine/QStatusMessenger.scala | 2 +- .../broadinstitute/gatk/queue/engine/RunnerStatus.scala | 2 +- .../gatk/queue/engine/drmaa/DrmaaJobManager.scala | 2 +- .../gatk/queue/engine/drmaa/DrmaaJobRunner.scala | 2 +- .../queue/engine/gridengine/GridEngineJobManager.scala | 2 +- .../queue/engine/gridengine/GridEngineJobRunner.scala | 2 +- .../gatk/queue/engine/lsf/Lsf706JobManager.scala | 2 +- .../gatk/queue/engine/lsf/Lsf706JobRunner.scala | 2 +- .../engine/parallelshell/ParallelShellJobManager.scala | 2 +- .../engine/parallelshell/ParallelShellJobRunner.scala | 2 +- .../parallelshell/ThreadSafeProcessController.scala | 2 +- .../gatk/queue/engine/pbsengine/PbsEngineJobManager.scala | 2 +- .../gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala | 2 +- .../gatk/queue/engine/shell/ShellJobManager.scala | 2 +- .../gatk/queue/engine/shell/ShellJobRunner.scala | 2 +- .../gatk/queue/function/CommandLineFunction.scala | 2 +- .../gatk/queue/function/InProcessFunction.scala | 2 +- .../gatk/queue/function/JavaCommandLineFunction.scala | 2 +- .../gatk/queue/function/ListWriterFunction.scala | 2 +- .../broadinstitute/gatk/queue/function/QFunction.scala | 2 +- .../gatk/queue/function/RetryMemoryLimit.scala | 2 +- .../gatk/queue/function/scattergather/CloneFunction.scala | 2 +- .../function/scattergather/ConcatenateLogsFunction.scala | 2 +- .../queue/function/scattergather/GatherFunction.scala | 2 +- .../queue/function/scattergather/GathererFunction.scala | 2 +- .../queue/function/scattergather/ScatterFunction.scala | 2 +- .../scattergather/ScatterGatherableFunction.scala | 2 +- .../function/scattergather/SimpleTextGatherFunction.scala | 2 +- .../gatk/queue/library/clf/vcf/VCFExtractIntervals.scala | 2 +- .../gatk/queue/library/clf/vcf/VCFExtractSamples.scala | 2 +- .../broadinstitute/gatk/queue/library/ipf/SortByRef.scala | 2 +- .../gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala | 2 +- .../gatk/queue/library/ipf/vcf/VCFExtractSamples.scala | 2 +- .../gatk/queue/library/ipf/vcf/VCFExtractSites.scala | 2 +- .../gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala | 2 +- .../broadinstitute/gatk/queue/util/ClassFieldCache.scala | 2 +- .../broadinstitute/gatk/queue/util/CollectionUtils.scala | 2 +- .../org/broadinstitute/gatk/queue/util/EmailMessage.scala | 2 +- .../broadinstitute/gatk/queue/util/EmailSettings.scala | 2 +- .../org/broadinstitute/gatk/queue/util/Logging.scala | 2 +- .../gatk/queue/util/PrimitiveOptionConversions.scala | 2 +- .../org/broadinstitute/gatk/queue/util/QJobReport.scala | 2 +- .../broadinstitute/gatk/queue/util/QJobsReporter.scala | 2 +- .../org/broadinstitute/gatk/queue/util/QScriptUtils.scala | 2 +- .../broadinstitute/gatk/queue/util/ReflectionUtils.scala | 2 +- .../org/broadinstitute/gatk/queue/util/RemoteFile.scala | 2 +- .../gatk/queue/util/RemoteFileConverter.scala | 2 +- .../scala/org/broadinstitute/gatk/queue/util/Retry.scala | 2 +- .../broadinstitute/gatk/queue/util/RetryException.scala | 2 +- .../queue/util/ScalaCompoundArgumentTypeDescriptor.scala | 2 +- .../org/broadinstitute/gatk/queue/util/ShellUtils.scala | 2 +- .../gatk/queue/util/StringFileConversions.scala | 2 +- .../org/broadinstitute/gatk/queue/util/SystemUtils.scala | 2 +- .../broadinstitute/gatk/queue/util/TextFormatUtils.scala | 2 +- .../gatk/queue/util/VCF_BAM_utilities.scala | 2 +- .../gatk/queue/function/CommandLineFunctionUnitTest.scala | 2 +- .../broadinstitute/gatk/queue/pipeline/QueueTest.scala | 2 +- .../gatk/queue/pipeline/QueueTestEvalSpec.scala | 2 +- .../gatk/queue/pipeline/QueueTestSpec.scala | 2 +- .../gatk/queue/util/ShellUtilsUnitTest.scala | 2 +- .../gatk/queue/util/StringFileConversionsUnitTest.scala | 2 +- .../gatk/queue/util/SystemUtilsUnitTest.scala | 2 +- .../java/org/broadinstitute/gatk/tools/CatVariants.java | 2 +- .../gatk/tools/walkers/annotator/AlleleBalance.java | 2 +- .../tools/walkers/annotator/AlleleBalanceBySample.java | 2 +- .../walkers/annotator/AlleleSpecificAnnotationData.java | 2 +- .../gatk/tools/walkers/annotator/BaseCounts.java | 2 +- .../gatk/tools/walkers/annotator/CompressedDataList.java | 2 +- .../tools/walkers/annotator/FractionInformativeReads.java | 2 +- .../gatk/tools/walkers/annotator/LowMQ.java | 2 +- .../walkers/annotator/MappingQualityZeroBySample.java | 2 +- .../gatk/tools/walkers/annotator/NBaseCount.java | 2 +- .../tools/walkers/annotator/ReducibleAnnotationData.java | 2 +- .../gatk/tools/walkers/annotator/SnpEff.java | 2 +- .../gatk/tools/walkers/annotator/SnpEffUtil.java | 2 +- .../gatk/tools/walkers/annotator/VariantAnnotator.java | 2 +- .../tools/walkers/annotator/VariantAnnotatorEngine.java | 2 +- .../tools/walkers/annotator/VariantOverlapAnnotator.java | 2 +- .../annotator/interfaces/AS_StandardAnnotation.java | 2 +- .../annotator/interfaces/ActiveRegionBasedAnnotation.java | 2 +- .../walkers/annotator/interfaces/AnnotationHelpUtils.java | 2 +- .../annotator/interfaces/AnnotationInterfaceManager.java | 2 +- .../walkers/annotator/interfaces/AnnotationType.java | 2 +- .../walkers/annotator/interfaces/AnnotatorCompatible.java | 2 +- .../annotator/interfaces/ExperimentalAnnotation.java | 2 +- .../walkers/annotator/interfaces/GenotypeAnnotation.java | 2 +- .../walkers/annotator/interfaces/InfoFieldAnnotation.java | 2 +- .../walkers/annotator/interfaces/ReducibleAnnotation.java | 2 +- .../annotator/interfaces/RodRequiringAnnotation.java | 2 +- .../walkers/annotator/interfaces/StandardAnnotation.java | 2 +- .../annotator/interfaces/StandardSomaticAnnotation.java | 2 +- .../annotator/interfaces/StandardUGAnnotation.java | 2 +- .../annotator/interfaces/VariantAnnotatorAnnotation.java | 2 +- .../annotator/interfaces/WorkInProgressAnnotation.java | 2 +- .../gatk/tools/walkers/coverage/CallableLoci.java | 2 +- .../gatk/tools/walkers/coverage/CompareCallableLoci.java | 2 +- .../gatk/tools/walkers/coverage/CoverageUtils.java | 2 +- .../gatk/tools/walkers/coverage/DepthOfCoverage.java | 2 +- .../gatk/tools/walkers/coverage/DepthOfCoverageStats.java | 2 +- .../gatk/tools/walkers/coverage/DoCOutputType.java | 2 +- .../gatk/tools/walkers/coverage/GCContentByInterval.java | 2 +- .../gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java | 2 +- .../tools/walkers/diagnostics/ReadGroupProperties.java | 2 +- .../tools/walkers/diagnostics/ReadLengthDistribution.java | 2 +- .../gatk/tools/walkers/diffengine/DiffObjects.java | 2 +- .../gatk/tools/walkers/examples/GATKDocsExample.java | 2 +- .../gatk/tools/walkers/examples/GATKPaperGenotyper.java | 2 +- .../tools/walkers/fasta/FastaAlternateReferenceMaker.java | 2 +- .../gatk/tools/walkers/fasta/FastaReferenceMaker.java | 2 +- .../gatk/tools/walkers/fasta/FastaSequence.java | 2 +- .../gatk/tools/walkers/fasta/FastaStats.java | 2 +- .../gatk/tools/walkers/filters/ClusteredSnps.java | 2 +- .../gatk/tools/walkers/filters/FiltrationContext.java | 2 +- .../tools/walkers/filters/FiltrationContextWindow.java | 2 +- .../gatk/tools/walkers/filters/VariantFiltration.java | 2 +- .../walkers/haplotypecaller/HCMappingQualityFilter.java | 2 +- .../gatk/tools/walkers/help/WalkerDoclet.java | 2 +- .../tools/walkers/help/WalkerDocumentationHandler.java | 2 +- .../broadinstitute/gatk/tools/walkers/package-info.java | 2 +- .../broadinstitute/gatk/tools/walkers/qc/CheckPileup.java | 2 +- .../broadinstitute/gatk/tools/walkers/qc/CountBases.java | 2 +- .../gatk/tools/walkers/qc/CountIntervals.java | 2 +- .../broadinstitute/gatk/tools/walkers/qc/CountLoci.java | 2 +- .../broadinstitute/gatk/tools/walkers/qc/CountMales.java | 2 +- .../broadinstitute/gatk/tools/walkers/qc/CountRODs.java | 2 +- .../gatk/tools/walkers/qc/CountRODsByRef.java | 2 +- .../gatk/tools/walkers/qc/CountReadEvents.java | 2 +- .../broadinstitute/gatk/tools/walkers/qc/CountReads.java | 2 +- .../gatk/tools/walkers/qc/CountTerminusEvent.java | 2 +- .../gatk/tools/walkers/qc/DocumentationTest.java | 2 +- .../gatk/tools/walkers/qc/ErrorThrowing.java | 2 +- .../broadinstitute/gatk/tools/walkers/qc/FlagStat.java | 2 +- .../org/broadinstitute/gatk/tools/walkers/qc/Pileup.java | 2 +- .../broadinstitute/gatk/tools/walkers/qc/PrintRODs.java | 2 +- .../org/broadinstitute/gatk/tools/walkers/qc/QCRef.java | 2 +- .../gatk/tools/walkers/qc/ReadClippingStats.java | 2 +- .../gatk/tools/walkers/qc/RodSystemValidation.java | 2 +- .../gatk/tools/walkers/readutils/ClipReads.java | 2 +- .../gatk/tools/walkers/readutils/PrintReads.java | 2 +- .../gatk/tools/walkers/readutils/SplitSamFile.java | 2 +- .../gatk/tools/walkers/rnaseq/ASEReadCounter.java | 2 +- .../gatk/tools/walkers/varianteval/VariantEval.java | 2 +- .../walkers/varianteval/VariantEvalReportWriter.java | 2 +- .../tools/walkers/varianteval/evaluators/CompOverlap.java | 2 +- .../walkers/varianteval/evaluators/CountVariants.java | 2 +- .../varianteval/evaluators/IndelLengthHistogram.java | 2 +- .../walkers/varianteval/evaluators/IndelSummary.java | 2 +- .../evaluators/MendelianViolationEvaluator.java | 2 +- .../walkers/varianteval/evaluators/MetricsCollection.java | 2 +- .../varianteval/evaluators/MultiallelicSummary.java | 2 +- .../walkers/varianteval/evaluators/PrintMissingComp.java | 2 +- .../walkers/varianteval/evaluators/StandardEval.java | 2 +- .../varianteval/evaluators/ThetaVariantEvaluator.java | 2 +- .../varianteval/evaluators/TiTvVariantEvaluator.java | 2 +- .../walkers/varianteval/evaluators/ValidationReport.java | 2 +- .../walkers/varianteval/evaluators/VariantEvaluator.java | 2 +- .../walkers/varianteval/evaluators/VariantSummary.java | 2 +- .../walkers/varianteval/stratifications/AlleleCount.java | 2 +- .../varianteval/stratifications/AlleleFrequency.java | 2 +- .../walkers/varianteval/stratifications/CompRod.java | 2 +- .../tools/walkers/varianteval/stratifications/Contig.java | 2 +- .../tools/walkers/varianteval/stratifications/CpG.java | 2 +- .../walkers/varianteval/stratifications/Degeneracy.java | 2 +- .../stratifications/DynamicStratification.java | 2 +- .../walkers/varianteval/stratifications/EvalRod.java | 2 +- .../tools/walkers/varianteval/stratifications/Family.java | 8 ++++---- .../tools/walkers/varianteval/stratifications/Filter.java | 2 +- .../varianteval/stratifications/FunctionalClass.java | 2 +- .../walkers/varianteval/stratifications/IndelSize.java | 2 +- .../stratifications/IntervalStratification.java | 2 +- .../varianteval/stratifications/JexlExpression.java | 2 +- .../walkers/varianteval/stratifications/Novelty.java | 2 +- .../walkers/varianteval/stratifications/OneBPIndel.java | 2 +- .../stratifications/RequiredStratification.java | 2 +- .../tools/walkers/varianteval/stratifications/Sample.java | 2 +- .../stratifications/SnpEffPositionModifier.java | 2 +- .../stratifications/StandardStratification.java | 2 +- .../walkers/varianteval/stratifications/TandemRepeat.java | 2 +- .../varianteval/stratifications/VariantStratifier.java | 2 +- .../walkers/varianteval/stratifications/VariantType.java | 2 +- .../varianteval/stratifications/manager/StratNode.java | 2 +- .../stratifications/manager/StratNodeIterator.java | 2 +- .../stratifications/manager/StratificationManager.java | 2 +- .../varianteval/stratifications/manager/Stratifier.java | 2 +- .../gatk/tools/walkers/varianteval/util/Analysis.java | 2 +- .../walkers/varianteval/util/AnalysisModuleScanner.java | 2 +- .../gatk/tools/walkers/varianteval/util/DataPoint.java | 2 +- .../tools/walkers/varianteval/util/EvaluationContext.java | 2 +- .../gatk/tools/walkers/varianteval/util/Molten.java | 2 +- .../walkers/varianteval/util/SortableJexlVCMatchExp.java | 2 +- .../tools/walkers/varianteval/util/VariantEvalUtils.java | 2 +- .../variantrecalibration/VQSRCalibrationCurve.java | 2 +- .../gatk/tools/walkers/variantutils/CombineVariants.java | 2 +- .../tools/walkers/variantutils/ConcordanceMetrics.java | 2 +- .../tools/walkers/variantutils/GenotypeConcordance.java | 2 +- .../walkers/variantutils/LeftAlignAndTrimVariants.java | 2 +- .../tools/walkers/variantutils/RandomlySplitVariants.java | 2 +- .../gatk/tools/walkers/variantutils/SelectHeaders.java | 2 +- .../gatk/tools/walkers/variantutils/SelectVariants.java | 2 +- .../gatk/tools/walkers/variantutils/ValidateVariants.java | 2 +- .../walkers/variantutils/VariantsToAllelicPrimitives.java | 2 +- .../tools/walkers/variantutils/VariantsToBinaryPed.java | 2 +- .../gatk/tools/walkers/variantutils/VariantsToTable.java | 2 +- .../gatk/tools/walkers/variantutils/VariantsToVCF.java | 2 +- .../gatk/tools/CatVariantsIntegrationTest.java | 2 +- .../gatk/tools/walkers/BAQIntegrationTest.java | 2 +- .../tools/walkers/CNV/SymbolicAllelesIntegrationTest.java | 2 +- .../walkers/annotator/CompressedDataListUnitTest.java | 2 +- .../gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java | 2 +- .../walkers/coverage/CallableLociIntegrationTest.java | 2 +- .../CompareCallableLociWalkerIntegrationTest.java | 2 +- .../coverage/DepthOfCoverageB36IntegrationTest.java | 2 +- .../walkers/coverage/DepthOfCoverageIntegrationTest.java | 2 +- .../walkers/diffengine/DiffObjectsIntegrationTest.java | 2 +- .../tools/walkers/filters/VariantFiltrationUnitTest.java | 2 +- .../gatk/tools/walkers/qc/CheckPileupIntegrationTest.java | 2 +- .../gatk/tools/walkers/qc/CountReadsUnitTest.java | 2 +- .../walkers/qc/DictionaryConsistencyIntegrationTest.java | 2 +- .../gatk/tools/walkers/qc/FlagStatIntegrationTest.java | 2 +- .../tools/walkers/qc/PileupWalkerIntegrationTest.java | 2 +- .../readutils/ClipReadsWalkersIntegrationTest.java | 2 +- .../walkers/readutils/PrintReadsIntegrationTest.java | 2 +- .../tools/walkers/readutils/PrintReadsLargeScaleTest.java | 2 +- .../gatk/tools/walkers/readutils/PrintReadsUnitTest.java | 2 +- .../walkers/readutils/SplitSamFileIntegrationTest.java | 2 +- .../walkers/rnaseq/ASEReadCounterIntegrationTest.java | 2 +- .../walkers/variantutils/SelectVariantsUnitTest.java | 2 +- .../tools/walkers/variantutils/VCFIntegrationTest.java | 2 +- .../src/main/java/htsjdk/samtools/GATKBAMFileSpan.java | 2 +- .../gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java | 2 +- .../src/main/java/htsjdk/samtools/GATKChunk.java | 2 +- .../main/java/htsjdk/samtools/PicardNamespaceUtils.java | 2 +- .../org/broadinstitute/gatk/utils/AutoFormattingTime.java | 2 +- .../java/org/broadinstitute/gatk/utils/BaseUtils.java | 2 +- .../java/org/broadinstitute/gatk/utils/BitSetUtils.java | 2 +- .../org/broadinstitute/gatk/utils/ContigComparator.java | 2 +- .../broadinstitute/gatk/utils/DeprecatedToolChecks.java | 2 +- .../java/org/broadinstitute/gatk/utils/GenomeLoc.java | 2 +- .../org/broadinstitute/gatk/utils/GenomeLocParser.java | 2 +- .../org/broadinstitute/gatk/utils/GenomeLocSortedSet.java | 2 +- .../org/broadinstitute/gatk/utils/HasGenomeLocation.java | 2 +- .../org/broadinstitute/gatk/utils/HeapSizeMonitor.java | 2 +- .../java/org/broadinstitute/gatk/utils/IndelUtils.java | 2 +- .../main/java/org/broadinstitute/gatk/utils/LRUCache.java | 2 +- .../gatk/utils/MRUCachingSAMSequenceDictionary.java | 2 +- .../java/org/broadinstitute/gatk/utils/MannWhitneyU.java | 2 +- .../java/org/broadinstitute/gatk/utils/MathUtils.java | 2 +- .../main/java/org/broadinstitute/gatk/utils/Median.java | 2 +- .../gatk/utils/MultiThreadedErrorTracker.java | 2 +- .../java/org/broadinstitute/gatk/utils/NGSPlatform.java | 2 +- .../java/org/broadinstitute/gatk/utils/PathUtils.java | 2 +- .../java/org/broadinstitute/gatk/utils/QualityUtils.java | 2 +- .../org/broadinstitute/gatk/utils/R/RScriptExecutor.java | 2 +- .../gatk/utils/R/RScriptExecutorException.java | 2 +- .../org/broadinstitute/gatk/utils/R/RScriptLibrary.java | 2 +- .../main/java/org/broadinstitute/gatk/utils/R/RUtils.java | 2 +- .../gatk/utils/SequenceDictionaryUtils.java | 2 +- .../org/broadinstitute/gatk/utils/SequencerFlowClass.java | 2 +- .../java/org/broadinstitute/gatk/utils/SimpleTimer.java | 2 +- .../broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java | 2 +- .../main/java/org/broadinstitute/gatk/utils/Utils.java | 2 +- .../broadinstitute/gatk/utils/ValidationExclusion.java | 2 +- .../gatk/utils/activeregion/ActiveRegion.java | 2 +- .../gatk/utils/activeregion/ActiveRegionReadState.java | 2 +- .../gatk/utils/activeregion/ActivityProfile.java | 2 +- .../gatk/utils/activeregion/ActivityProfileState.java | 2 +- .../gatk/utils/activeregion/BandPassActivityProfile.java | 2 +- .../org/broadinstitute/gatk/utils/analysis/AminoAcid.java | 2 +- .../gatk/utils/analysis/AminoAcidTable.java | 2 +- .../gatk/utils/analysis/AminoAcidUtils.java | 2 +- .../main/java/org/broadinstitute/gatk/utils/baq/BAQ.java | 2 +- .../broadinstitute/gatk/utils/classloader/JVMUtils.java | 2 +- .../gatk/utils/classloader/PluginManager.java | 2 +- .../gatk/utils/classloader/ProtectedPackageSource.java | 2 +- .../gatk/utils/classloader/PublicPackageSource.java | 2 +- .../broadinstitute/gatk/utils/clipping/ClippingOp.java | 2 +- .../gatk/utils/clipping/ClippingRepresentation.java | 2 +- .../broadinstitute/gatk/utils/clipping/ReadClipper.java | 2 +- .../gatk/utils/codecs/beagle/BeagleCodec.java | 2 +- 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.../broadinstitute/gatk/utils/SimpleTimerUnitTest.java | 2 +- .../broadinstitute/gatk/utils/TestNGTestTransformer.java | 2 +- .../java/org/broadinstitute/gatk/utils/UtilsUnitTest.java | 2 +- .../gatk/utils/activeregion/ActiveRegionUnitTest.java | 2 +- .../utils/activeregion/ActivityProfileStateUnitTest.java | 2 +- .../gatk/utils/activeregion/ActivityProfileUnitTest.java | 2 +- .../activeregion/BandPassActivityProfileUnitTest.java | 2 +- .../org/broadinstitute/gatk/utils/baq/BAQUnitTest.java | 2 +- .../gatk/utils/classloader/JVMUtilsUnitTest.java | 2 +- .../gatk/utils/clipping/ReadClipperTestUtils.java | 2 +- .../gatk/utils/clipping/ReadClipperUnitTest.java | 2 +- .../gatk/utils/codecs/beagle/BeagleCodecUnitTest.java | 2 +- .../gatk/utils/codecs/hapmap/HapMapUnitTest.java | 2 +- .../gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java | 2 +- .../utils/codecs/sampileup/SAMPileupCodecUnitTest.java | 2 +- .../gatk/utils/codecs/samread/SAMReadCodecUnitTest.java | 2 +- .../gatk/utils/codecs/table/TableCodecUnitTest.java | 2 +- .../gatk/utils/collections/DefaultHashMapUnitTest.java | 2 +- .../utils/collections/ExpandingArrayListUnitTest.java | 2 +- .../gatk/utils/commandline/ArgumentMatchSiteUnitTest.java | 2 +- .../utils/commandline/ArgumentMatchSourceUnitTest.java | 2 +- .../gatk/utils/commandline/ParsingEngineUnitTest.java | 2 +- .../utils/commandline/RodBindingCollectionUnitTest.java | 2 +- .../gatk/utils/commandline/RodBindingUnitTest.java | 2 +- .../AlleleBiasedDownsamplingUtilsUnitTest.java | 2 +- .../fasta/CachingIndexedFastaSequenceFileUnitTest.java | 2 +- .../gatk/utils/file/FSLockWithSharedUnitTest.java | 2 +- .../gatk/utils/fragments/FragmentUtilsBenchmark.java | 2 +- .../gatk/utils/fragments/FragmentUtilsUnitTest.java | 2 +- .../gatk/utils/haplotype/EventMapUnitTest.java | 2 +- .../gatk/utils/haplotype/HaplotypeUnitTest.java | 2 +- .../gatk/utils/interval/IntervalUtilsUnitTest.java | 2 +- .../org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java | 2 +- .../gatk/utils/jna/clibrary/LibCUnitTest.java | 2 +- .../gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java | 2 +- .../gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java | 2 +- .../gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java | 2 +- .../locusiterator/AlignmentStateMachineUnitTest.java | 2 +- .../gatk/utils/locusiterator/LIBS_position.java | 2 +- .../gatk/utils/locusiterator/LocusIteratorBenchmark.java | 2 +- .../utils/locusiterator/LocusIteratorByStateBaseTest.java | 2 +- .../utils/locusiterator/LocusIteratorByStateUnitTest.java | 2 +- .../locusiterator/PerSampleReadStateManagerUnitTest.java | 2 +- .../gatk/utils/nanoScheduler/InputProducerUnitTest.java | 2 +- .../gatk/utils/nanoScheduler/MapResultUnitTest.java | 2 +- .../gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java | 2 +- .../gatk/utils/nanoScheduler/ReducerUnitTest.java | 2 +- .../gatk/utils/pileup/PileupElementUnitTest.java | 2 +- .../gatk/utils/pileup/ReadBackedPileupUnitTest.java | 2 +- .../utils/progressmeter/ProgressMeterDaemonUnitTest.java | 2 +- .../utils/progressmeter/ProgressMeterDataUnitTest.java | 2 +- .../gatk/utils/recalibration/EventTypeUnitTest.java | 2 +- .../gatk/utils/refdata/RefMetaDataTrackerUnitTest.java | 2 +- .../gatk/utils/refdata/tracks/FeatureManagerUnitTest.java | 2 +- .../utils/refdata/tracks/RMDTrackBuilderUnitTest.java | 2 +- .../refdata/utils/CheckableCloseableTribbleIterator.java | 2 +- .../utils/FeatureToGATKFeatureIteratorUnitTest.java | 2 +- .../utils/refdata/utils/FlashBackIteratorUnitTest.java | 2 +- .../gatk/utils/refdata/utils/TestFeatureReader.java | 2 +- .../gatk/utils/refdata/utils/TestRMDTrackBuilder.java | 2 +- .../gatk/utils/report/GATKReportUnitTest.java | 2 +- .../gatk/utils/report/ReportMarshallerUnitTest.java | 2 +- .../gatk/utils/runtime/ProcessControllerUnitTest.java | 2 +- .../gatk/utils/runtime/RuntimeUtilsUnitTest.java | 2 +- .../gatk/utils/sam/AlignmentUtilsUnitTest.java | 2 +- .../gatk/utils/sam/ArtificialBAMBuilderUnitTest.java | 2 +- .../utils/sam/ArtificialPatternedSAMIteratorUnitTest.java | 2 +- .../gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java | 2 +- .../utils/sam/ArtificialSAMQueryIteratorUnitTest.java | 2 +- .../gatk/utils/sam/ArtificialSAMUtilsUnitTest.java | 2 +- .../sam/ArtificialSingleSampleReadStreamUnitTest.java | 2 +- .../gatk/utils/sam/GATKSAMRecordUnitTest.java | 2 +- .../broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java | 2 +- .../gatk/utils/smithwaterman/SmithWatermanBenchmark.java | 2 +- .../gatk/utils/text/ListFileUtilsUnitTest.java | 2 +- .../gatk/utils/text/TextFormattingUtilsUnitTest.java | 2 +- .../EfficiencyMonitoringThreadFactoryUnitTest.java | 2 +- .../gatk/utils/threading/ThreadPoolMonitorUnitTest.java | 2 +- .../utils/variant/GATKVariantContextUtilsUnitTest.java | 2 +- .../gatk/utils/variant/VariantContextBenchmark.java | 2 +- 1071 files changed, 1094 insertions(+), 1094 deletions(-) diff --git a/licensing/private_license.txt b/licensing/private_license.txt index bbb8dcf9e..5818179e0 100644 --- a/licensing/private_license.txt +++ b/licensing/private_license.txt @@ -4,7 +4,7 @@ BROAD INSTITUTE SOFTWARE LICENSE AGREEMENT FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -20,11 +20,11 @@ The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other th 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. 3. PHONE-HOME FEATURE -LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. 4. OWNERSHIP OF INTELLECTUAL PROPERTY LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -Copyright 2012-2015 Broad Institute, Inc. +Copyright 2012-2016 Broad Institute, Inc. Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. diff --git a/licensing/protected_license.txt b/licensing/protected_license.txt index bbb8dcf9e..f8543c6e1 100644 --- a/licensing/protected_license.txt +++ b/licensing/protected_license.txt @@ -4,7 +4,7 @@ BROAD INSTITUTE SOFTWARE LICENSE AGREEMENT FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -20,11 +20,11 @@ The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other th 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. 3. PHONE-HOME FEATURE -LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. 4. OWNERSHIP OF INTELLECTUAL PROPERTY LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -Copyright 2012-2015 Broad Institute, Inc. +Copyright 2012-2016 Broad Institute, Inc. Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. diff --git a/licensing/public_license.txt b/licensing/public_license.txt index c53c5b34a..cf46512f1 100644 --- a/licensing/public_license.txt +++ b/licensing/public_license.txt @@ -1,4 +1,4 @@ -Copyright 2012-2015 Broad Institute, Inc. +Copyright 2012-2016 Broad Institute, Inc. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation diff --git a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleFindCoveredIntervals.scala b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleFindCoveredIntervals.scala index 00b42a871..70b07f8d7 100644 --- a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleFindCoveredIntervals.scala +++ b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleFindCoveredIntervals.scala @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleHaplotypeCaller.scala b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleHaplotypeCaller.scala index 2f592bcb6..d446ed6ec 100644 --- a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleHaplotypeCaller.scala +++ b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleHaplotypeCaller.scala @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala index 3120995ec..a3c1eaa53 100644 --- a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala +++ b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala b/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala index ffba91845..d33b0ee36 100644 --- a/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala +++ b/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/UnmappedExcludedQueueTest.scala b/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/UnmappedExcludedQueueTest.scala index 3bb34de38..12c227f51 100644 --- a/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/UnmappedExcludedQueueTest.scala +++ b/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/UnmappedExcludedQueueTest.scala @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/create_M2_pon.scala b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/create_M2_pon.scala index 009eebaca..f3ec63163 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/create_M2_pon.scala +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/create_M2_pon.scala @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_ICE_NN.scala b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_ICE_NN.scala index 46d31c461..f4959e296 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_ICE_NN.scala +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_ICE_NN.scala @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_dream.scala b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_dream.scala index 95b5c0043..728c44681 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_dream.scala +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_dream.scala @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/public/VectorPairHMM/src/main/c++/Sandbox.java b/public/VectorPairHMM/src/main/c++/Sandbox.java index 99c91d23b..a1ecb21f9 100644 --- a/public/VectorPairHMM/src/main/c++/Sandbox.java +++ b/public/VectorPairHMM/src/main/c++/Sandbox.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java b/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java index c6188df7d..32e5784c7 100644 --- a/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java +++ b/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java index 9f866bf08..fe1f68b83 100644 --- a/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java +++ b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java index 3c8ca6c81..49d21af1a 100644 --- a/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java +++ b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java index ceb2eda3d..56cfac40b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java index 9f6c16edc..d60c5fcc1 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java index c1daca1e7..c5a137704 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java index ab204ff5d..9f5ccaf93 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadMetrics.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadMetrics.java index f391b45f5..1530137ec 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadMetrics.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadMetrics.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java index 5e4a3559d..e746020ff 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java index 838a4ae24..89b99e740 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java index c0008c32f..c99a4f7f5 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java index eb403c610..fbf541170 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java index 2b2c6b12a..dcf7f309f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java index d9924c70d..8e8b45ef4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java index 54e63e4cc..1ba0757ca 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java index f5a337bfa..6f0fb5b57 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java index 50981a355..fe3f5052c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java index f3ba0e4fe..ffe4df54a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java index 4331b9667..1ab31f3fa 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java index 34be0f885..903f14664 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java index 40dfc030b..3a624e035 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java index 04e165e28..8abf35811 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java index 0daa83e79..845c3a0b5 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java index 90e6b97d1..c8e48b497 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java index 7619d4102..19d9a263c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java index dedb71d48..7a774de70 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java index 956f1e9bb..c2a56b8d4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java index 551cf1a7e..1879427c1 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java index 636412dbd..2b428c583 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java index d6fa7bd70..7d7dae676 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java index 66ff7e392..b151df17f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java index b9775b274..57ca6f7bc 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java index f4d13024e..0534cf431 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java index f052ee3c7..f68d06bfd 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java index 9bc95e173..cbcfc88df 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java index b98da8cee..e3e88230f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java index f94c351a7..4fed815c7 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java index e14ce625b..6ce0c6a15 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java index 057342c50..e7259f6dc 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java index 4b64c03a6..268d821f3 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java index 5eed18d5e..49cbce6b8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java index b9d94b640..ff9836ad2 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java index 39247f5b4..00655935f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java index 0601034df..9b74d9c57 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java index ff8da29db..66f940c7a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java index d7696d6ca..349a80d91 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java index 3260476eb..88108c6c9 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java index 71a1af2a1..82d56c4de 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java index 865a72b7b..0f6770ae6 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java index 6d961a370..3b92ae427 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java index 1eb58a1d0..4988c2efd 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java index 659a2c7ed..071818f5b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java index b00d1c664..28a2c2c4b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java index ede909e92..0e0e23fa1 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java index bcb148b92..227675eea 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java index 78262b560..583a66868 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java index bb5fcdd92..0b2b6a5eb 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java index 419898581..d119bed7a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java index ae555c3ee..89d3d5e2d 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java index 6687ee658..dcdf565ff 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java index 541787f49..15f861c20 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java index 5c6bf31e4..249ec3ed2 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java index 93a2e0aec..3c4953168 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java index 870d5bafa..e5932bd94 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java index 269cb6f0a..b5786060a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java index 99ad5a577..27c71173a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java index 1611778d9..0020b4de9 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java index db2aabe1c..743a4b71d 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java index cc3fcd185..a905c6de5 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java index 259c77b3c..6956aed6b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java index 71db6022c..8c2a98f2d 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java index 047477905..95bc202b8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java index acb931130..c1494722f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java index 84c55e434..aa9462914 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java index b26297d02..3ea4a8acf 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java index 1765b7b78..e69b63d49 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java index 78b6eab68..4f976dee9 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java index b1d54d2b1..394923b1e 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java index 80d5ba0ce..7c74c0c05 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java index f992cf111..fe4a91361 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java index fd5b73be7..f28dadaf3 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java index d84aa5dd8..b30a97f03 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java index cf4286d35..fe6212544 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java index 399e4bc73..25e35cee0 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java index 5b52c8f29..79de5bc0a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java index c97201b09..dd662f01d 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java index a8f46fabb..d0b7ffa82 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java index fee842db9..41f04ace4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java index 399737b5a..795a8f49d 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java index 69ba13ce9..32bb8368a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java index 5c601ef45..385292d8b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java index 5aaba79c0..7dace7bc5 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java index 95454122e..26f0e4d29 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java index 01299aec1..5ec07390f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java index 399ea3803..d9538cce3 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java index e50a770c8..45bf83f59 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java index 21d1c7c2f..5dc159e27 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java index 77bea8969..4cba4d796 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java index c12933c85..1a34ee3d0 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java index 389f2c6fa..afd4224d5 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java index c4904818d..23f1c08a5 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java index 3ed14bb9f..2196890b0 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java index 1dd8e8fb9..c603b5f61 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java index 213ab28a6..84658a8c2 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java index 402087d7c..bf71ddc71 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java index 8d166e1c8..29580316e 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java index 0f01f76ce..856c931b1 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java index b0fd074a6..ccb3e4cba 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java index 04516da45..22ca49300 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java index 27e0859ff..e40edb760 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java index 06fcfef5e..3365ecd01 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java index 846657ab3..3ecfcf1b4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java index b1ab50b41..d3fa7beca 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java index 5753b0fbb..1c7c70c40 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java index 67a5fabbd..b8dfec49a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java index e2f870d55..f30075877 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java index 400f02881..23d985da7 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java index c3ff6ae16..af3432f8b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java index d4f6cb8a8..e345cb1df 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java index 317322da9..7362287f4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java index de49247a7..650c3441e 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DisableableReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DisableableReadFilter.java index 2898ca1cf..e8f08a00c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DisableableReadFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DisableableReadFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java index bb1d7e82b..2bd69cb7a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java index 1834be5ee..23e47d17a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java index b0dcae564..3517863fd 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java index e56dc27b4..cc05a1c19 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java index eb524eba8..bfb7adebd 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java index 85dda8ece..692113789 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java index f006a3ccf..ce38c1c9b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java index 46f044b69..832249b75 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java index a8a02dafa..780206b5e 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java index 0407d8591..997920c38 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java index 7acc34e7f..642999590 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java index aa449a105..a2ab2d02b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java index 482a54117..81d709e54 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java index 841a139e2..3088e26f7 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java index fe96f9fb9..1e3516aa4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java index 22822dd3a..c97854329 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java index 8c7fcc630..4c742264f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java index c00d52124..18e45b1ae 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java index d92ffe73c..f81b8e51a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java index 1720fdc76..e1ec370cc 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java index 7c57b0d60..7071d9cdf 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java index b0fc108e6..acab773cf 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java index 94548ab3a..3bdfd7fa5 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java index 6cfcdac8a..5f1a0a85b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java index dffd8662e..e68a31bb0 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java index 0a4eeaf8e..44d24de9a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java index df582abb5..01f56edf0 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java index b5f7e4418..69c631b62 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java index e448068cd..c8fc220b4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java index c5ba1d96e..c4fc4ffb3 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java index 15b6f2dff..698ccd56d 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java index d5c6695ab..1c7e998bd 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java index ec9b5ee2b..46b25b0b3 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java index 87a8b6629..e39b937db 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java index 693d70954..87f601923 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java index 70a94a65f..de8e5260e 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java index 7ed538b4d..d5d1b87e9 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java index 108b1f0e7..b1aecb22c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java index e28548413..2f65c5bb7 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java index ac79c367d..45b2d391a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java index 480c9ac3d..b3f76fe2f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java index dd1d691e0..edb88aa48 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java index 5c8274751..67d58e99c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java index 27b59b202..866d4c7a8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java index 3dca0e84c..83c6f7e41 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMReaderArgumentTypeDescriptor.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMReaderArgumentTypeDescriptor.java index 8b9b6217f..24427b00a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMReaderArgumentTypeDescriptor.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMReaderArgumentTypeDescriptor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java index a8b8c3fea..57e4ea98f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java index 4219930f3..166ddaeb8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java index a35c978e7..6cd63497a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java index 7ab11e3e5..e634c4a3e 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java index 3a21d5a32..d9b6dcda8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java index 7ef375b93..3cb384e0b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java index d04ddaa4e..10b92404a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java index f7c408004..f64619bce 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java index 743847e59..21e077d78 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java index 8db59fbe2..af6ce2c29 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java index dfeb73921..53d6acea3 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java index 2b92758e0..cfa9cacba 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java index 223c2faec..b4474652b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java index 575aebfe5..32be95eeb 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java index fc7e77364..09bc074af 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java index e3d676b47..11394af8a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java index 6c0004c71..e8dc6cec5 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java index e450d451c..6abf3d488 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/package-info.java index 51722e707..1babac7f1 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java index d81c27088..0186823a5 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java index 46158825b..6b53c2bf4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java index 491451103..26fb4bbfb 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java index 13e97f810..2104ad23c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java index 867647625..3bdef1477 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java index 2dac6e111..87aa118a2 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java index fd721edbc..3e239f341 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java index 0e37cb4bb..d97306b96 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java index 0bbc3c8a9..85858bb0a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java index 1a373e114..40f1a35a9 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java index 41cc0b229..87c00ced2 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java index c0502da06..97b19dd96 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java index 2b5427f76..650a394a7 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java index 3bbf7bfb6..32c5c80b3 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java index 91ba863ea..edce309b8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java index 858a557fd..634c5378a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java index 3671ded82..8be9c931a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java index 9eb732cc3..33b2d9dff 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java index 41738a09f..5962ea4a1 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java index 0c2676b5a..3150852d4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java index 4387436fe..6228e7187 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java index ccc81599a..855725c87 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java index b203e39c3..f9c6f51f5 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java index f017cfb27..4ad25373e 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java index 3e92ff73b..bb3145d6f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java index ef2251e50..a5e1bfc9a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java index 613b6b2e4..1a97f5a38 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java index 8a500c180..75d75ba56 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java index 903f5bd13..0e7fbca56 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java index e6deb7635..64e8cd16b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DisabledReadFilters.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DisabledReadFilters.java index 5708e2664..2d569ec51 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DisabledReadFilters.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DisabledReadFilters.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java index 19929988c..654f1aa2d 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java index 46691e44a..d3235144a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java index a2d12dc46..898cf5fc8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java index 66f34b3a0..90ff64f33 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java index 329aaaca3..de45808ea 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java index 5078d4ea7..c38f88c94 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java index eb6b6040b..a6d3edf2e 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java index 8a221cb35..6b8aa70a2 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java index 3438232bc..7b5453eb8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java index 9b8e3be01..a1e1d2753 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java index 81731315a..06999f225 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java index 0535acaff..b1db76e6c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java index c3cee866f..6ca5e302b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java index 8f6f5e3c1..af7df6363 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java index 9dec898aa..c0361cd3f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java index ef94e7e2d..8adb123cc 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java index a0411484a..805e20de9 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java index 9d08422eb..987c8d34f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java index 2c8dca90b..ff71fa36b 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java index f613607c6..1aca36b6c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java index a5ddd0654..19b350d8a 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java index 9f5d88114..973d6cd44 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java index 439c7e5ab..f08ea506e 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java index 79fdb9253..9af6cc20a 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java index 7258e4d86..7de3b8ece 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java index 9ae72597b..836ef9b66 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java index 6a1c3407d..a5a77ca73 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java index 972816ca6..ea2acd747 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java index 32fcee33d..5f8eefcad 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java index 5173dcb89..a2f79db4c 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java index 31565a69c..475015939 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java index 6de2f969e..e39f8aa5b 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java index 985c3444a..85da8c9da 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java index abb5fb61d..3f11597ea 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java index 51d4c2434..78e2d1295 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java index 2d2ce2bd3..fcf3afa6a 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java index 2d1579501..fdd7addaa 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java index 02751f664..cf242801d 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java index 2c45ebc8c..77b28e1f3 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java index 27936b5fe..ccb610113 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java index 4115b97b1..57e45ba1f 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java index fc7857d84..f2dff4ea6 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java index 342c9ca14..582169830 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java index ec26ba2b4..3ca67276a 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java index 68ecabc10..c113b3392 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java index 3ada2445f..72dc60229 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java index afa700116..952ab7cde 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java index 553ca998f..b45db15b0 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java index 7c016c3fa..fd59eb2d3 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java index 13f356959..f6be513bf 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java index 1a42dd067..44256efb6 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java index 817fcc112..de5a34309 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java index d006fcaba..073f74b98 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java index 90c75598e..a05a852d2 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java index a8973e16b..d176249d5 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java index 20a99f754..a1f9bae1d 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java index 16f43f98e..606c3aa72 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java index b8bf0eadb..0e01d930c 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java index 201d9c41d..c704c8ce1 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java index 039ca4d5e..01ec4238f 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java index 36cbb58bf..a7f3edd4b 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java index 15bc5b731..1ab027d06 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java index 0f6f9e384..99cd61cbe 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java index 8dac72faa..7537f88de 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java index 4fbb02a92..8bcc2717a 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java index af7e5716c..fe0f8c86f 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java index e3f2fee1a..1015a2010 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java index 219307802..736f10547 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java index d23fb1b7c..b4c13e36f 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java index 87e2ac868..d18d6b66b 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java index 47a1179b2..a7c04fe74 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java index 44432cfac..f8065028b 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java index c0e48a974..f172024bc 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java index 109c64c72..85025bfcf 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java index 9f21233aa..ef0423269 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java index aec599099..ae4c4d0a4 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java index 6a35f0b3e..83c081405 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java index 2e28ef0da..7ce853fa9 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java index 9c3e3904d..eb4b7cd0c 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java index 8f11220ac..6dbf60e28 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java index 38b1cb7c2..22ca03808 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java index 1e00065a4..042fab650 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java index ecffcfc55..e764b40b0 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java index 3c5d84cf0..51a7f44d9 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java index 9f2589d70..98cb23219 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java index d743d0021..0ad2a4c06 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java index a931bcb18..bdc2ab143 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java index 4e3c20590..83f89a796 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java index bcfb60c38..7a151bbec 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java index b059f8d50..4816c78bf 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java index d6d1ed216..83240edb7 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java index 4e63d5dbe..17460e356 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java index e17ff3e73..765a4d19a 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java index 88421abc0..6277646e6 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java index c69774b7b..d0b8c7170 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java index 10f6801f3..cf5196c14 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java index 099d9e20c..45bc8da46 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java index 8bf453300..1b8dd1eee 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java index 7362c4d3c..80b2b0a27 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java index d5308a375..72888d94e 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java index e3c852eae..c394e8220 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java index 89d630d9f..1d91f3048 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java index e19f6c8dd..b56618ce2 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java index 849d994ae..a1db9cb87 100644 --- a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java +++ b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java index d4e0aea36..99ba25e46 100644 --- a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java +++ b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/GATKExtensionsGenerator.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/GATKExtensionsGenerator.java index 90adfc206..e67f4c2cc 100644 --- a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/GATKExtensionsGenerator.java +++ b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/GATKExtensionsGenerator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ReadFilterField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ReadFilterField.java index 581aef077..e8d77b19b 100644 --- a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ReadFilterField.java +++ b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ReadFilterField.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/ONLY_GENOTYPE_xhmmCNVpipeline.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/ONLY_GENOTYPE_xhmmCNVpipeline.scala index c2ff1c4b6..02237288a 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/ONLY_GENOTYPE_xhmmCNVpipeline.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/ONLY_GENOTYPE_xhmmCNVpipeline.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala index fd7698f09..eba31757e 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/GATKResourcesBundle.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/GATKResourcesBundle.scala index ef6baffbb..9f3a355fd 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/GATKResourcesBundle.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/GATKResourcesBundle.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala index 0900b369f..7c37ea77f 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala index 65da43863..22bd3d832 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCustomWalker.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCustomWalker.scala index 9826494f7..a7f65b08f 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCustomWalker.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCustomWalker.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala index 8d300f988..a629da59f 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala index 20798a38e..3460654bf 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala index 34a25562e..a4fc74553 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala index 7564da943..13a50ec3f 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala index 2cf5b765c..c53b767fe 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala index aaa071d28..513ab93d3 100755 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala index 85bb70f0c..c5dd9b047 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala index d8ade79a5..9e79fca00 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/BamGatherFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/BamGatherFunction.scala index e502bb701..8d4cfe062 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/BamGatherFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/BamGatherFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/CatVariantsGatherer.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/CatVariantsGatherer.scala index e111e1984..233379204 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/CatVariantsGatherer.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/CatVariantsGatherer.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ContigScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ContigScatterFunction.scala index d7d79bc27..f40b04897 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ContigScatterFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ContigScatterFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DistributedScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DistributedScatterFunction.scala index 49d51ef69..3b9a20089 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DistributedScatterFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DistributedScatterFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala index 4df0ac7cb..b806f05f2 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala index 72e73956e..1c2994872 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKScatterFunction.scala index afe465563..55aee8faf 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKScatterFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKScatterFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/IntervalScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/IntervalScatterFunction.scala index 8fd76224d..313bd2b84 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/IntervalScatterFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/IntervalScatterFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/LocusScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/LocusScatterFunction.scala index 7983f56e2..8dfbc3c55 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/LocusScatterFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/LocusScatterFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ReadScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ReadScatterFunction.scala index 4a7deeac1..02ce460d4 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ReadScatterFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ReadScatterFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/TaggedFile.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/TaggedFile.scala index 967a00d5a..56ca39387 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/TaggedFile.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/TaggedFile.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/VcfGatherFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/VcfGatherFunction.scala index 6ba815b8e..eeee0ec9d 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/VcfGatherFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/VcfGatherFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala index 0f89fe38e..bd5a63901 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/XHMM/package.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/XHMM/package.scala index 153cf4b95..bbc3671a5 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/XHMM/package.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/XHMM/package.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/AddOrReplaceReadGroups.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/AddOrReplaceReadGroups.scala index e02863f20..22373173e 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/AddOrReplaceReadGroups.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/AddOrReplaceReadGroups.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala index fb6e4d538..aa7658687 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectGcBiasMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectGcBiasMetrics.scala index f36d14afd..f3f5f6fa3 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectGcBiasMetrics.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectGcBiasMetrics.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectMultipleMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectMultipleMetrics.scala index 022179b1d..7a18ed8ee 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectMultipleMetrics.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectMultipleMetrics.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectWgsMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectWgsMetrics.scala index 923ce0005..433ae67e5 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectWgsMetrics.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectWgsMetrics.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/FastqToSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/FastqToSam.scala index 24b88b185..002d38bbc 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/FastqToSam.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/FastqToSam.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala index 94b88c81d..95bdf959a 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MergeSamFiles.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MergeSamFiles.scala index e0d07b245..35ea1c8f8 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MergeSamFiles.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MergeSamFiles.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala index 2be93f04e..cc74417b5 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala index 2b0ef1a72..03602228e 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ReorderSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ReorderSam.scala index 482a6b57f..b068ac0a4 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ReorderSam.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ReorderSam.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/RevertSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/RevertSam.scala index d79ed96d6..e58ecfd9c 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/RevertSam.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/RevertSam.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SamToFastq.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SamToFastq.scala index 7a65d5e9e..26f60568b 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SamToFastq.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SamToFastq.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SortSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SortSam.scala index 663186e0c..38d6d172f 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SortSam.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SortSam.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ValidateSamFile.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ValidateSamFile.scala index 11f51356e..fd729fff0 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ValidateSamFile.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ValidateSamFile.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsCommandLineFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsCommandLineFunction.scala index 54400a01e..d3af6a5ec 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsCommandLineFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsCommandLineFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsIndexFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsIndexFunction.scala index 86a5a12e2..47b795720 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsIndexFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsIndexFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsMergeFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsMergeFunction.scala index a3a60b629..025f53638 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsMergeFunction.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsMergeFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/snpeff/SnpEff.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/snpeff/SnpEff.scala index fb8b8b8ee..94f1c0aa1 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/snpeff/SnpEff.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/snpeff/SnpEff.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervalsUnitTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervalsUnitTest.scala index bc7f85c6f..f61b5ab59 100644 --- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervalsUnitTest.scala +++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervalsUnitTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala index 010382233..f44e458c3 100644 --- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala +++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountLociQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountLociQueueTest.scala index 5e3474098..13db73b3b 100644 --- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountLociQueueTest.scala +++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountLociQueueTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountReadsQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountReadsQueueTest.scala index 189a88c21..3d4fcf5f8 100644 --- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountReadsQueueTest.scala +++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountReadsQueueTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala index 4829db78c..5edec76e3 100644 --- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala +++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleReadFilterQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleReadFilterQueueTest.scala index 39b74dcf0..92d49ff32 100644 --- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleReadFilterQueueTest.scala +++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleReadFilterQueueTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala index 46f630b57..51568f1e3 100644 --- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala +++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala index 1e51d75e2..7dd558a17 100644 --- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala +++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/QueueVersion.java b/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/QueueVersion.java index f3d5a7db5..a56594b05 100644 --- a/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/QueueVersion.java +++ b/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/QueueVersion.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/package-info.java b/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/package-info.java index 24722a083..4b3490ecf 100644 --- a/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/package-info.java +++ b/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala index 7994ae9a5..f8c998715 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandPlugin.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandPlugin.scala index 1e22d7ed9..27c8c6674 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandPlugin.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandPlugin.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QException.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QException.scala index 80ffe558a..bfa2439d6 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QException.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QException.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala index 541da93c9..7f9b926e1 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScriptManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScriptManager.scala index 8ffee1e08..3ab6f59f7 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScriptManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScriptManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala index b95e158bd..5cb91edbe 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobManager.scala index ab1fcbb43..c77d9c184 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobRunner.scala index 941126f35..078198ef1 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobRunner.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobRunner.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLinePluginManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLinePluginManager.scala index 37c50d09a..f2a0ed5dd 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLinePluginManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLinePluginManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/FunctionEdge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/FunctionEdge.scala index 9a567c60d..bb386fe77 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/FunctionEdge.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/FunctionEdge.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessJobManager.scala index 351b50c8a..d34b51d64 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessJobManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessJobManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessRunner.scala index b65a695d3..6417546b3 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessRunner.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessRunner.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobManager.scala index 16bc39c06..9d9ff9078 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunInfo.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunInfo.scala index 26713290c..1588dc709 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunInfo.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunInfo.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunner.scala index eca27e914..c36534e9c 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunner.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunner.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/MappingEdge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/MappingEdge.scala index e2b22561b..053c80be0 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/MappingEdge.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/MappingEdge.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QEdge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QEdge.scala index 6718dbb3b..30fb7b879 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QEdge.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QEdge.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala index b11652a84..2c18646ef 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala index bbe64525c..3ca80946a 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QNode.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QNode.scala index 82d22c22a..f4fe80259 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QNode.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QNode.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QStatusMessenger.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QStatusMessenger.scala index 912d3782b..c8bc134d5 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QStatusMessenger.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QStatusMessenger.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/RunnerStatus.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/RunnerStatus.scala index 5d5ac04e5..62d503876 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/RunnerStatus.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/RunnerStatus.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobManager.scala index fedf091ed..938db7ab3 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobRunner.scala index ea4fafee7..51abe17e3 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobRunner.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobRunner.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobManager.scala index 7b8e5231a..c8e0704e3 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala index b5b0121c0..62d2f13a9 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobManager.scala index 0b5a5ce49..093d9f70c 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobRunner.scala index d35c9c0c9..2e0de93f9 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobRunner.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobRunner.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobManager.scala index c200538c6..6b1b16e77 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobRunner.scala index 8afb80a25..a9a396535 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobRunner.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobRunner.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ThreadSafeProcessController.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ThreadSafeProcessController.scala index 4bf3f994c..3c74df88e 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ThreadSafeProcessController.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ThreadSafeProcessController.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobManager.scala index 31dfabec2..54fa415d8 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala index 5fa0d5bd6..814aafbcf 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobManager.scala index e97f69edd..ce0fc9e58 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobManager.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobManager.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobRunner.scala index 191867609..800dae28d 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobRunner.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobRunner.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/CommandLineFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/CommandLineFunction.scala index 998d4e564..52040e98c 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/CommandLineFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/CommandLineFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/InProcessFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/InProcessFunction.scala index a7d1363ba..80cbb76ad 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/InProcessFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/InProcessFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/JavaCommandLineFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/JavaCommandLineFunction.scala index 61aa43375..a7f06cdd7 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/JavaCommandLineFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/JavaCommandLineFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/ListWriterFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/ListWriterFunction.scala index 33aa1f463..bf8a0d3c2 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/ListWriterFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/ListWriterFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/QFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/QFunction.scala index 358b8c3f1..4976dfedc 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/QFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/QFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/RetryMemoryLimit.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/RetryMemoryLimit.scala index 1799c9a03..23ee635c1 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/RetryMemoryLimit.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/RetryMemoryLimit.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/CloneFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/CloneFunction.scala index 5eb581a8b..a7d7c2639 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/CloneFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/CloneFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ConcatenateLogsFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ConcatenateLogsFunction.scala index 35429c702..bd53dfc27 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ConcatenateLogsFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ConcatenateLogsFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GatherFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GatherFunction.scala index a94e86d2a..a8997f024 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GatherFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GatherFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GathererFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GathererFunction.scala index f5604522a..5a4997fc3 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GathererFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GathererFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterFunction.scala index e115667ec..967b50500 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterGatherableFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterGatherableFunction.scala index 6bb865bc2..d3374c192 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterGatherableFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterGatherableFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/SimpleTextGatherFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/SimpleTextGatherFunction.scala index 306872377..48245e8a3 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/SimpleTextGatherFunction.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/SimpleTextGatherFunction.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractIntervals.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractIntervals.scala index 4910e1df6..07d5904a9 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractIntervals.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractIntervals.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractSamples.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractSamples.scala index cd15b519d..508df71b3 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractSamples.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractSamples.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/SortByRef.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/SortByRef.scala index 6131f1684..624c783d7 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/SortByRef.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/SortByRef.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala index 1cba5f21f..00ff7d0d5 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSamples.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSamples.scala index f2cc999eb..f3bda45f1 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSamples.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSamples.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSites.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSites.scala index 31b43c2c8..5d36d13ed 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSites.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSites.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala index 3c4e02577..66684a6f5 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ClassFieldCache.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ClassFieldCache.scala index 27758454b..031db0715 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ClassFieldCache.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ClassFieldCache.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/CollectionUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/CollectionUtils.scala index e77ef47d8..9a836a000 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/CollectionUtils.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/CollectionUtils.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailMessage.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailMessage.scala index e8d2f22f2..5704b88a0 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailMessage.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailMessage.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailSettings.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailSettings.scala index 8ab5a1397..ec4dcbcc3 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailSettings.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailSettings.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Logging.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Logging.scala index a9b12d172..85f1a7a0d 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Logging.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Logging.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/PrimitiveOptionConversions.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/PrimitiveOptionConversions.scala index 66a7242a5..7c9c97479 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/PrimitiveOptionConversions.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/PrimitiveOptionConversions.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala index fd86d4d11..df84b634f 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala index 7b6dde65a..e7e08ab12 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala index 5627a46c1..b8923f212 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ReflectionUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ReflectionUtils.scala index c13f08833..2ba62b6f5 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ReflectionUtils.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ReflectionUtils.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFile.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFile.scala index 5ae4f7691..36c56c7b0 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFile.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFile.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFileConverter.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFileConverter.scala index 8f984f4cb..9441faadf 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFileConverter.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFileConverter.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Retry.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Retry.scala index 4f23f59d4..fe9753e75 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Retry.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Retry.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RetryException.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RetryException.scala index eb0d96bde..e1b25522d 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RetryException.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RetryException.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ScalaCompoundArgumentTypeDescriptor.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ScalaCompoundArgumentTypeDescriptor.scala index c6cf39c57..9f7c19f04 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ScalaCompoundArgumentTypeDescriptor.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ScalaCompoundArgumentTypeDescriptor.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ShellUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ShellUtils.scala index ff23690ad..7f22e1384 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ShellUtils.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ShellUtils.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/StringFileConversions.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/StringFileConversions.scala index f6e59317a..0dd37bf90 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/StringFileConversions.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/StringFileConversions.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/SystemUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/SystemUtils.scala index 440c15574..6e5b959a0 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/SystemUtils.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/SystemUtils.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/TextFormatUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/TextFormatUtils.scala index cea1b7722..4aeb3c409 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/TextFormatUtils.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/TextFormatUtils.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala index f722f66fb..099ab79e8 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/function/CommandLineFunctionUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/function/CommandLineFunctionUnitTest.scala index ab7ca2878..2fd544dbe 100644 --- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/function/CommandLineFunctionUnitTest.scala +++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/function/CommandLineFunctionUnitTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala index ed1c1c77f..2fb1c09d6 100644 --- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala +++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestEvalSpec.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestEvalSpec.scala index e0df4d9b5..b599442c0 100644 --- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestEvalSpec.scala +++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestEvalSpec.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestSpec.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestSpec.scala index ac1802e42..316c8bf1f 100644 --- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestSpec.scala +++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestSpec.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/ShellUtilsUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/ShellUtilsUnitTest.scala index 3f3acb56c..abf96aa5c 100644 --- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/ShellUtilsUnitTest.scala +++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/ShellUtilsUnitTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/StringFileConversionsUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/StringFileConversionsUnitTest.scala index 090ba8622..293fd3cd5 100644 --- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/StringFileConversionsUnitTest.scala +++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/StringFileConversionsUnitTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/SystemUtilsUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/SystemUtilsUnitTest.scala index e0950ceee..2ab20e7a8 100644 --- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/SystemUtilsUnitTest.scala +++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/SystemUtilsUnitTest.scala @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java index f11e01d20..b62f1717e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java index ccb4be7f8..ba8d4eb84 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java index fb7300809..7d6037bc9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java index df3944214..3e4be932a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java index 66ea8dff6..e13e9f1ed 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java index a89859fa3..8702c3b0f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java index 747e0fc23..64b770f47 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java index 34c58683f..27a98d825 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java index be3b40194..372ae5e34 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java index b4cafa8f7..015e466d2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java index 0c18bb187..bf998078d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java index ceb353bdc..836140bd5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java index adb2c4ab4..d558b289f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java index ca386e8d8..1063f1ed6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java index bddc020c9..d62029fb3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java index 8fd0abe05..667cb846b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java index 55c3e47cc..2589c6a0d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java index ee818ea34..91de64ce8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java index bb488679b..a9f7d3990 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java index 985774f51..07894c693 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java index 40a94cf70..a6ac476ad 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java index 363da058e..c65422a2f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java index 87954d221..1ad22b316 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java index 590c6b9c1..5cc4c55ad 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java index cc91cda52..b60d76718 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java index 25d2d8f41..225d556be 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java index c489d66bc..eb670d4d7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java index 70d7c9f25..86b1f5a45 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java index 72eecaa36..38578ab6a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java index 13fe48b66..b96a0d10e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java index 4bb9b28aa..ae7a5c516 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java index cc9a7d7b9..e911c34b2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java index bf2eddccb..a69cd1e3c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java index 1951a43c1..7e3079b65 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java index 6f0e5507f..f222380dc 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java index 96144ce13..2d6b3157f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageStats.java index aa7b5ae7e..43e8decbc 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageStats.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageStats.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DoCOutputType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DoCOutputType.java index f91c38574..c5789fc39 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DoCOutputType.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DoCOutputType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java index c4d1aef25..666e6b7e7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java index 6808d927b..1d241cecd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java index 86185b174..cd4d166aa 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java index 1f3d6c7f9..098d4d4ba 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java index f12d08a5e..b9356ba21 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java index d95fd2b46..4c345ad6e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java index 54db6f30e..69d0d5f2a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java index 5be2e8933..70354081f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java index 4eb8f3e23..52090b456 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java index 062297beb..7c0e04089 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java index 01d26c04e..35226f3a1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java index c0de7b9d7..dacc6fd65 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java index e48c8f45b..901991cb6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java index e47d54b6a..915825aa8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java index c4b6ea09e..ee2da20bd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java index 96586c030..1a7a47eee 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java index ac15e7439..1c1e71f1d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java index 8e3881cdb..79db163ba 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java index 53c155f0b..7ca62f75a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java index d38543c5b..4b2f88e81 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java index e0d2a3cd4..b309802ea 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java index 21f04271c..0aa3ab45a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java index 004906c46..8657aec96 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java index a8291418f..ac0f4034b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java index 78f194f9e..3dbfb486f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java index 8934fce68..fc08cff19 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java index 20d60a19f..37c68a614 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java index 17aa5bc69..387d1c6a0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java index 942e7c372..f004ae0fb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java index 579f43fa3..9a36e6ed1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java index 030c964e8..ff85c08d3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java index fee78877c..5e81b5479 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java index cd2c33630..2c00f06b0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java index 7873af930..6783a2857 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java index 93493544d..818489cca 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java index 1517ae73b..176ba38b5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java index 1043675cc..518b4d8c7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java index f8b46b62d..f0eaeb448 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java index 6aede1b75..49426a5ad 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java index 029d8b88a..9a671e760 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java index 782a6da35..b9f8a5591 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java index 120c4caf9..b1855ae4d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java index aef7d8b35..313a2cd7d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java index 1e634b718..1758b6acb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java index 2ab63c51b..7727611ce 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java index 21164ce36..0a00bf856 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java index 878d6fcbe..fb902516a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index 29d81ce96..cd419a3e1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java index ea7394461..1fbe7d513 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java index a45dfbcdc..e46fba144 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java index f9c67e872..519794804 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java index 9ee366c06..929b79202 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index ef91df2ee..ec62fbde9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index b60ed8445..2b8a10a8e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java index 74b280f0c..42db6023c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java index f1144a097..e1e767797 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java index a34ddeb4c..1b180d648 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java index 2ab005ae2..38363f7f4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java index d52ea8f41..352ee7494 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java index 72006196b..3c273de56 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java index 0645fd53f..4ac99d11f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java index f4c31a5d1..0a02efede 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java index 1e8368f91..e26651885 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java index 429396835..5222e756a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java index dddb20197..5e07ad1b0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java index e4acb9ea1..948c1f4fd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java @@ -1,6 +1,6 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. -* +* Copyright 2012-2016 Broad Institute, Inc. +* * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation * files (the "Software"), to deal in the Software without @@ -9,10 +9,10 @@ * copies of the Software, and to permit persons to whom the * Software is furnished to do so, subject to the following * conditions: -* +* * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. -* +* * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java index ac9b9e497..4178aed6a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java index 89ffe8691..d9b8dc33e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java index 48efe1ee4..64df04145 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java index 57ba0e7bb..7514ead14 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java index 7a1106241..c9c4f5f6e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java index 1faf818f1..3e783a661 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java index 9430d9faa..b6c81698c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java index 9a9313cca..fd18c6737 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java index c052dcaa5..3c03ca4db 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java index a09feae98..62ce8bd8c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java index de9388a5f..888867630 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java index 7349ccbfa..635ad50f4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java index 5b4e6c089..7a246337e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java index bc017db56..4dd4fcadf 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java index 4d3dcae43..2c7daaad7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java index 305f65c94..995f65310 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java index c9398a15b..c5ccb19b7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java index f206a30ab..5aeef7b5a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java index 035fabaa4..9ed84f4a8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java index d5f70a9a5..99cd79b14 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java index ac02b4d09..cf602ebe7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java index f18c381aa..2516bcbe5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java index f7a156673..9e2126c46 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java index 3b1c1424a..52b52813f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java index 15198dd53..74b03414f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java index 330a723c4..d1a743cf8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java index 090124882..f89509603 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java index 5019662f4..5361abc3f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java index 4ac6b9b0d..c495eae7a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java index 49aa15477..834c19753 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java index 41962bbcc..ce737178a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java index e95cbf379..28bce4803 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java index bd33c2cae..2ebdcb97b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java index a5b710acc..e34c78111 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java index a75491d67..7a316cbb5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java index 10f463727..57c0fe7ff 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java index ea1945e3c..ef4546181 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java index 051137009..3bf2c11b5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java index 9e6ad827f..1513fc5bf 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java index f26f6a90a..422bb8c33 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java index 4e11d0df3..f1746cb6d 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java index 521f4c237..a79555139 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java index 15279a0ad..5460291bc 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java index 3ac2a3d44..1889f6f4d 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java index e24564a4b..e9140c7cd 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java index 1f5e398fe..c78cd38d1 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java index f25ac3a94..578217059 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java index 92b3d862f..15020f8f0 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java index 4d3223f30..1e9a1dc81 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java index 2648ed81e..fb15c598d 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java index 889646017..dcd424f65 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java index f29cb80e8..f98cc4466 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java index e86c3301f..bc762de3d 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java index a64efaf26..0d9c7864a 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java index 53acd511c..44c0bc2fe 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java index cc436e1f9..fe5f47a58 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java index 5d1b6c056..c374e9de7 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java index c0aec4329..3b88a8e08 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java index 87589a50c..a316dffe7 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java index 7af19c538..62318967c 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java index df61b7c9a..f31b2cdf3 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java index 9e893a09f..397626023 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java index be38c06cb..b3b773d96 100644 --- a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java +++ b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java index d9698c38d..8ead6a56c 100644 --- a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java +++ b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java index 1a10819a8..34aed5a82 100644 --- a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java +++ b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java b/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java index f861ccbbe..aba557b98 100644 --- a/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java +++ b/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java index e77ff641a..59f29080b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java index f0ed568ab..3cf5e0873 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java index 20b602642..d0863f479 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java index a069415df..e0917d28f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java index 53613ca2a..9a951f994 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java index d41072adb..ec70eff8c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java index 6f2616c69..d6d5b02e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java index 6e777df29..dcb9476f8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java index d0309193f..6d9647f02 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java index b158794ad..fa84259df 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java index 83003d24a..a9d767285 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java index ed985c418..243ad95d9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java index b2c2d1a5a..df7e396e8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java index bb8866f34..9ddd62645 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java index fb8e8d987..374d43afc 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java index 948332209..6639818c4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java index 3dfe13c19..a90b0d02b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java index 1b3af7066..55800c4f9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java index f2a8340b7..b06b83017 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java index d67e5abc9..30aafde72 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java index 1ee279843..fda03c95f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java index 53ad3aca8..b493a7f26 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java index 56f80e3e2..d9c05b2ae 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java index 982cfa371..2b3ad5f42 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java index 8eaa8c42b..ef5004fa5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java index 466f42b9b..a08b8fd34 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java index 5101064fd..6e3a6af48 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java index 1b7ac79da..a284d6d6f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java index ce54e8f11..f4bbb48b2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java index c09ebe4cc..00ae68e02 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java index 8a4deb51d..1fc67d482 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java index 57fd35908..289a427b2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java index cdc7cb806..bf53ecd1b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java index a1df0baf6..544a4b6b4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java index 8458b3a96..76d035eca 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java index af61415aa..8c16c9702 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java index e8bd5d1ec..05030979e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java index 175ea369a..9d7a84445 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java index 91562b69e..b56305d86 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java index 329dfa19b..973002b3e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java index 7ef7a154c..b2b6c731b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java index 7a2b53696..80b18094f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java index dd2068bbd..d6d5a3640 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java index ad0de1da1..26147e2e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java index 8d556515b..e757e23d1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java index 3710698a2..d39ebedca 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java index 8eaa316c2..057e09bef 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java index 39908366c..57830f882 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java index 8f49dd063..dd6641427 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java index 2dc23fc55..fb84d7ae6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java index 4a2d15c31..78c5f5dff 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java index 62d4b05ba..15cceeb17 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java index b5bca03d4..922027d4d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java index 407cf8962..993aa5fae 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java index 1768c1328..8452b229a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java index 447aa4761..1078bf717 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java index fda2e692b..c95195704 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java index 84c071f19..23d8b843d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java index 9908ed632..b1d973b16 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java index 7960e1fdc..c6e8eef4c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java index 0ae22648b..456a735c4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java index 2f8adc392..add892555 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java index 671548e64..81df590a7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java index 746bb2c32..37e19fce1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java index 495f3dda7..764f38698 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java index 11229cbeb..955d58bee 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java index 522847e9a..1c0e805b2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java index 563578f0d..78cb83b78 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java index 634fb36fb..d87705716 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java index a7a98c7c9..58ecf9660 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java index 300d04c61..20c51fa78 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java index 30ba236ce..3a77144ae 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java index f5b542446..6ad8d4329 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java index d6e2cb504..8744fb3e6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java index 77c747f89..83151f0e4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java index e0985983c..ae3cfd8c8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java index b51023421..1db4dbf33 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java index bbabd5eea..23cf31f41 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java index db54fb505..a8d3c21cf 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java index 095ea9e99..7e79ede95 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java index 229af987a..ef7952eba 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java index d7990480c..b9acb6fc9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java index b663b5920..e6c2b611c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java index b6ebdcb8f..f49b017d5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java index 6edd75f18..3ead063a5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java index a8c4e3feb..66199b2dc 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java index c583fb93f..000c6d19f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java index 2753c8f6f..9fa736fbb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java index f29978ede..e77aefe54 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java index 62139fb48..1280990a0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java index be7a65b2a..ccbad6332 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java index e8e8cde7c..a52af7bb9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java index 158095adf..45f3b425a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java index f5a02021d..9ae15e653 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java index 9fd49782b..03d62de68 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java index 8d18177f3..555458f16 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java index da7fa6ee0..7de0a3ed9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java index f71aec78b..236590a2f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java index 199b71eb8..70a793765 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java index 643eae100..815087c78 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java index d7512f65a..1398604d7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java index ba403a1c6..0fdfba208 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java index 0265c8feb..ad9a8d883 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java index e0fc36156..65b544933 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java index 7d8788210..121cfebef 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java index b5d5add7a..ed09f38f3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java index 5a4c99c3f..a93b60e4c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java index 3221d21f6..68bb4da49 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java index 8f90f7d14..a6767acc9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java index 8ea28c881..6a697575e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java index 3dca4245f..da24c031a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java index 6add93bd2..a7b61add1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java index 92cfc74a1..93f3af659 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java index fca56dcc0..996b36231 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java index d06176e77..c423d78fe 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java index f9167ff00..c5d92d9e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java index 569934585..cfdec3cc5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java index f0e8476e6..036fcade1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java index 24f2a40f2..c2a4c518a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java index aef5e8c53..619f2cf61 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java index 9f67fd47f..b4757e1a2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java index 948fa2107..7318f0bd2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java index d5d305e20..eeded75a6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java index 37810ba00..20bd1f7a7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java index 41b59ccc5..536a31785 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java index 910409457..7aa92338c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java index 569eb709c..8d50f445a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java index 0435e7cd6..36cc36573 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java index d1a895b63..b9a047e01 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java index d480f23fc..d22163df7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java index 74037ea9f..ab4fa5945 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java index 89fbea0f1..222d57407 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java index e9161b739..5686ce0d8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java index fc7eb7719..d3ccf4890 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java index 455269b6c..2eedac4d1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java index ea7e6b079..5c066f3ad 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java index b7bf2be19..38d38c2cb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java index 50e89c2bc..bdf64aea9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java index 8a3da8a03..51722adaf 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java index bac785a91..1a65f6745 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java index 9ce7fc4be..64a32389f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java index 7aef3730a..26134a9a9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java index e39fd557d..7c9157569 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java index 3584b79ab..acb4c26ad 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java index d7595d0e5..bf336468c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java index e9c9a0777..859437fb7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java index cbf8c4259..d8b7b624b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java index a456008a5..a193eebf4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java index d0d7a6a56..7d1a027c9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java index 813d697aa..d922a90aa 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java index f3811333e..c81df70cc 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java index cbcce0b3d..d1c99a375 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java index 3d6c58113..49daae86d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java index a9423faa4..59e46871e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java index 249e270b3..bb6d28c0b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java index 0a57040cd..5eb2a0b31 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java index 8c3f04885..ccc4a417b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java index 95f2559aa..c1ba1b07a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java index f0a1d0be8..5b0a9d879 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java index c52278e9e..c19736b9f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java index a4c8ca90b..2fc250c84 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java index a171edd98..147762543 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java index 5a6364355..4955ec163 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java index 5a2735d50..c0eb5ad32 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java index 5b0ec5aae..28df151c9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java index d03f0b6bb..e23fa32ed 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java index f294076e4..19bd99291 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java index 241ac7294..1c5c97b34 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java index 56b39ebdf..563ee79f9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java index ef154246d..cfed7463e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java index f00fcebaa..c824407ff 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java index ce4ea5f88..3f7d4c8bb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java index 1d0186c6e..f0b659076 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java index 4a7853b6e..bbd9313a2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java index a1818dc0b..2d0c0762b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java index 75701d660..608a9803c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java index 89cdabbe1..3cdddebbb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java index 015f2d306..6aaa249f9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java index d08115601..0f1d8b93b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java index e9f2d4acd..a1290d8e3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java index 6dad68092..a06edb68b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java index 60aec0139..0f521f653 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java index 5a55f2792..f613b9431 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java index 83af1d9f1..c1610ed2c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java index c61d895f5..681954e26 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java index ba196a1b0..f357a04e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java index 424485adf..77fbf3d53 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java index e272eaca9..b2ff1708e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java index 22ec9fe8c..1782da6e2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java index 1a38ea089..bb65af037 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java index 98e1e62dd..543a0ee84 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java index bb5e80b7d..0cb5c163f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java index 9b8682a7f..3dc42dc20 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java index 61d8b9140..8480bd3fa 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java index 82aa8660b..3a94be46e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java index 836a14929..7f748068d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java index cebf5e4d6..8182e6cc6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java index 91baead01..4ec0957a6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java index ea5fd19d8..23f188aa5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java index 1afd96cb0..93460d044 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java index 0c0745c4f..58edb8c6e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java index d97be2b3a..1264170ea 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java index 73ff9cb6e..493def184 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java index 299b331a7..dbe5f2f17 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java index 9c8e563c6..262117f77 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java index 15b0e011e..3f2d2d1ea 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java index efbf33dcc..14f3ca629 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java index aaa518d36..55a4efe64 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java index 0d2893567..d9501b9ec 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java index c5bf32dd7..3ce8783b5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java index af9953eaf..b8fd1dfe6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java index 84912897b..586e0f1a7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java index 9ff3998d3..07c80999a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java index b0c9d8fd6..6e87ffb4e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java index 5676c75bd..50314e0a3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java index ab737f25c..79b6db82e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java index 3d6682312..2beba61da 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java index 31ad7e0aa..f29726c19 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java index 9b1c40626..30ddcf75a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java index 7f1027fce..b1ffb165f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java index 50139ddab..13fd921a6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java index cb3263c5b..b4cc8cea4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java index 25907ebd9..53f172fe4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java index 52b51c0cd..8794a458e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java index 4ee17c803..6b9a67eb1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java index 387171151..e76550c2c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java index dd1a41c1c..697777408 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java index 6644c2058..7fa82208a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java index a6fcb2bed..aab43cd62 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java index f078d76b0..3d0292792 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java index c90669877..a647de993 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java index 93f39ab1e..d1f62fe8f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java index b2a7e84ce..75710c65e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java index ad2108933..ee2b59da0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java index 5dd3c6a35..7bee0f92b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java index 07d5075c8..b68a5b9e0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java index 850b9f19b..eb18cb16c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java index 0b8e984eb..82ee659cc 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java index 5a74f7245..6e24dbcbb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java index 7b82ae236..b4915caff 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java index 680091662..5aa0fe4fe 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java index 72f61b20b..37633c628 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java index c54f9c55f..32d0c279b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java index 0e0bfda98..0fdbc6413 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java index 8b451780e..868106bc6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java index ea24c2b5a..5e9e8226a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java index a450fce8b..1b55d7d35 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java index 216be74f6..46dd48b5c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java index 76f2046af..9de109e3b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java index 93be5a8ef..9e48fa75f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java index 743ee95ae..8ea73f775 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java index 4f50460a5..4e61e6932 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java index 4f947d119..34e63b152 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java index 0bee072c2..7a89fab6e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java index dc35f7e01..de5df4148 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java index 4bba78dc9..8f4f2db68 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java index 70a7c6a33..5098bfdd2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java index 0dbeb3b8e..033c23dee 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java index 6249f4f21..10c8d0502 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java index a6e640feb..f5342d476 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java index f7f5196b3..c749a7999 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java index e40c3f37a..85d2386a0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java index cf985d5e5..a35c13108 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java index ee6dfbd96..788ee23c3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java index 2fdc5bee2..16ac91c71 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java index 25375edf1..35a8e2777 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java index 682c25800..ccfeeacd2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java index 71d90eb31..29553f802 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java index 52d2f0688..5e8f6b2bb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java index 241ebd212..404464017 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java index bd4298967..461568729 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java index e4a8b571d..0b76e26ff 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java index 8aac52dfa..ef43feee1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java index b64bbaccf..f8b2385d0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java index 04e3ccbe5..4cc189aea 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java index 371e0f326..b69794ed9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java index d430ab7c4..c4d586b21 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java index 3d7c3c784..4dea034e5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java index 99b317446..5921a0a59 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java index 74b953188..9491ed254 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java index aa035233c..2b218e3c2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java index e4f8b799a..16ab9434a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java index 29a051b36..1f565efb6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java index d3eb73dca..1fed6ec2c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java index 3c7b2aff8..6ad367d3a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java index 3017b56f2..ea2a58869 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java index e04787f22..25af04260 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java index 6d85d7d0b..f283dee8b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java index cb8616092..d0337638d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java index 1560dce92..9eec7b69f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java index d57238ef6..134b779e3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java index b3d945ec0..6c1925729 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java index 6b72d0c08..4e505eef0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java index 1338f7cda..e0697516a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java index c431528b1..97dd2ae83 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java index c41b5bfeb..20c3c136f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java index 66b897054..153432688 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java index f423a1ad1..f9c3b1be5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java index b750b35ca..3c79bdb75 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java index 40e45d93c..8d1f0fe6c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java index a5152735e..1a91b17be 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java index a913c5abe..8f60f11e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java index 91db56bf3..75a56b110 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java index 044a65783..06b313613 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java index 267ab5f0c..591080a31 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java index 97d280a64..c6c446deb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java index ceb238052..c6fac2d4f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java index 8d9bddd17..2470c4bd1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java index 61d4c0d4d..500509535 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java index 9af1b366b..f2a6b4e1b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java index 6865d11ac..527a417de 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java index 8b1aa1d44..62b4beb3a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java index eb1f13eea..5c7494d7d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java index ff2f6aa2d..e8f960bff 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java index 0ca4a341f..62f7d60ab 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java index db964663a..447409d25 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java index a8695fe84..216fe9d5a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java index 85f2ba3ec..0289e3937 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java index 4368ffd70..852b85ffd 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java index c7071f1dd..e1818ccd6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java index f0a1c9c17..ec14bb5f7 100644 --- a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java +++ b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java index 234bbcf7e..1e0a7ae07 100644 --- a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java +++ b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java index fb95d6777..41e8da95b 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java index e151541aa..4d11a43cd 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java index 92a412f93..6b4483e01 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java index 0124a0862..c5f629175 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java index 6f8a6789d..186f39f84 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java index 69e66fbda..76f26411a 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java index 402e3edaf..43af1502c 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java index c02bae7fd..5432e236f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java index cc6315df5..47c1f4d0f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java index c60356942..9f4b34c27 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java index 2f88c4e04..27ff55f61 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java index a85debde1..ff19686a6 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java index ef6ef7738..e5bebacdc 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java index 9cbfca59c..4e1bad337 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java index 283558256..022340177 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java index 74dfdb909..bf04176fa 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java index 998ef1d6f..1f8b1f49c 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java index 45bef5866..3f98c71f9 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java index 993878bf1..f42dadc90 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java index 98f973690..373a9c499 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java index ac3118ecb..282a1bc43 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java index 8e96d62f9..aab34be37 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java index 3d0a7b0a0..817dcc769 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java index 05203ad11..e2c455216 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java index e4772b3af..b05a4d8e0 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java index 22e534844..cc5172894 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java index 8fc6420a4..4a0b38215 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java index dfc30ae03..f83ddce49 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java index 7ee1040e7..cd0a44d73 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java index fa75e7163..1796940cf 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java index 1e9fd88b1..0f065eef6 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java index 96ec5f6b2..b67e7b17c 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java index 06b70b744..2ac2c6a81 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java index 69abeb2b5..43f7341bd 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java index 05632d6db..2b3f1be1a 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java index cf6bc20a7..f41f728ec 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java index 1f1f6b99e..86637d54a 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java index 301d671c9..a0e610a15 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java index f5c0f5ff5..42eaeba06 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java index 33ec130b4..71f01211d 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java index 78865bee0..ad2233c94 100755 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java index 78b19d6ff..41e9a5e7f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java index 32cec45b9..e2334a2e8 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java index 418bfe151..8628c8187 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java index 6b80ebd4b..7528eb46f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java index 7fdd7b835..31587b185 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java index efed9c195..6a466f727 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java index b5bea3247..93c4502c4 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java index ef8565dba..d55c3ad59 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java index 7dbf3472c..08d369e36 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java index decb8284a..ef87e35d6 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java index 1700baf12..1791f2274 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java index 2188dbce8..918f58d5e 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java index 42801a39c..988b93f76 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java index 0fbb0b2a8..07b49d480 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java index 66f619007..556616ae7 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java index 7d622868f..d1945356f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java index e2dc57b9c..15a65a6bb 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java index ecc0f9a8e..1faf1611f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java index 29b7ad015..00b6af45e 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java index df20a7e27..d10d151d8 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java index 60bbe6a87..f7e1dc67b 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java index ea7165b2f..224c43ba2 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java index e39045782..434086ec4 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java index 78185d817..3fecd369c 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java index 2522b8c35..33794f7e2 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java index ff4280e36..c1b50c3b5 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java index 2b6243745..3d399a5b7 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java index f45daa270..cd9126644 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java index 03c92a02d..c70c1dceb 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java index 5c4987401..c7f5fbf0d 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java index 70377e1c7..0e82ffc54 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java index 57ce9d956..720658715 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java index 2f11f2543..cf26b406e 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java index e514b670f..bee23d609 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java index 3dbfbfcd6..2345ce6ee 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java index 0194d4941..de14e0f43 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java index 7b25724ce..3131f92d6 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java index 191c68993..e928b9755 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java index 789ef1886..da12cf506 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java index 5ca887edf..42312c427 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java index 7b9a0feeb..21a83b044 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java index 436c4f422..bdfa4d487 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java index d67851771..97e498083 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java index 5d9478ab8..43285f5ab 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java index eeaac020a..b23935b4b 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java index 8f60ff0a8..0f2cf1955 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java index 6dca140ba..24351842f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java index d3a7c5c0b..c4dfdbe65 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java index b556c0eaf..d6daf677b 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java index 0df8bbf6d..88f63f2b9 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java index 19ef63f6e..db84ac631 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java index 70d25a585..431162985 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java index 5f6b36c1c..8f3e4664d 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java index 470671d09..d0698add5 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java index c6233f17d..211303945 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java index f6aff7ba4..b283c80fc 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java index aeb1101cf..1131fe9a3 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java index b8bf04b56..a7571a49f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java index bbd594d27..78480c9b7 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java index ecc611f7e..48eaff0c4 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java index c64c04dc1..6223a95df 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java index 79ee95611..3a7a88e72 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation