From 19bbe45cbc3960bcb70b6bfb74bdb4e73e762851 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Thu, 6 Aug 2015 14:30:38 -0400 Subject: [PATCH] Updated licenses for 2015 --- licensing/private_license.txt | 2 +- licensing/protected_license.txt | 2 +- licensing/public_license.txt | 2 +- .../ExampleFindCoveredIntervals.scala | 2 +- .../examples/ExampleHaplotypeCaller.scala | 24 ++++----- .../examples/ExampleUnifiedGenotyper.scala | 2 +- .../ExampleUnifiedGenotyperQueueTest.scala | 2 +- .../examples/UnmappedExcludedQueueTest.scala | 2 +- ...GenotypeCalculationArgumentCollection.java | 2 +- .../engine/recalibration/BQSRGatherer.java | 2 +- .../recalibration/BQSRReadTransformer.java | 2 +- .../recalibration/BaseRecalibration.java | 2 +- .../engine/recalibration/QualQuantizer.java | 2 +- .../recalibration/QuantizationInfo.java | 2 +- .../engine/recalibration/ReadCovariates.java | 2 +- .../gatk/engine/recalibration/RecalDatum.java | 2 +- .../engine/recalibration/RecalDatumNode.java | 2 +- .../gatk/engine/recalibration/RecalUtils.java | 2 +- .../RecalibrationArgumentCollection.java | 2 +- .../recalibration/RecalibrationReport.java | 2 +- .../recalibration/RecalibrationTables.java | 2 +- .../covariates/ContextCovariate.java | 2 +- .../recalibration/covariates/Covariate.java | 2 +- .../covariates/CycleCovariate.java | 2 +- .../covariates/ExperimentalCovariate.java | 2 +- .../covariates/QualityScoreCovariate.java | 2 +- .../covariates/ReadGroupCovariate.java | 2 +- .../covariates/RepeatCovariate.java | 2 +- .../covariates/RepeatLengthCovariate.java | 2 +- .../RepeatUnitAndLengthCovariate.java | 2 +- .../covariates/RepeatUnitCovariate.java | 2 +- .../covariates/RequiredCovariate.java | 2 +- .../covariates/StandardCovariate.java | 2 +- .../org/broadinstitute/gatk/package-info.java | 2 +- .../annotator/AlleleCountBySample.java | 2 +- .../walkers/annotator/AnnotationUtils.java | 24 ++++----- .../annotator/BaseQualityRankSumTest.java | 2 +- .../walkers/annotator/ChromosomeCounts.java | 2 +- .../annotator/ClippingRankSumTest.java | 2 +- .../tools/walkers/annotator/Coverage.java | 2 +- .../annotator/DepthPerAlleleBySample.java | 2 +- .../walkers/annotator/DepthPerSampleHC.java | 2 +- .../tools/walkers/annotator/FisherStrand.java | 2 +- .../tools/walkers/annotator/GCContent.java | 2 +- .../walkers/annotator/GenotypeSummaries.java | 2 +- .../walkers/annotator/HaplotypeScore.java | 2 +- .../walkers/annotator/HardyWeinberg.java | 2 +- .../walkers/annotator/HomopolymerRun.java | 2 +- .../walkers/annotator/InbreedingCoeff.java | 2 +- .../annotator/LikelihoodRankSumTest.java | 2 +- .../walkers/annotator/MVLikelihoodRatio.java | 2 +- .../annotator/MappingQualityRankSumTest.java | 2 +- .../walkers/annotator/MappingQualityZero.java | 2 +- .../walkers/annotator/PossibleDeNovo.java | 2 +- .../tools/walkers/annotator/QualByDepth.java | 2 +- .../walkers/annotator/RMSMappingQuality.java | 2 +- .../tools/walkers/annotator/RankSumTest.java | 2 +- .../walkers/annotator/ReadPosRankSumTest.java | 2 +- .../tools/walkers/annotator/SampleList.java | 2 +- .../walkers/annotator/SpanningDeletions.java | 2 +- .../annotator/StrandAlleleCountsBySample.java | 2 +- .../walkers/annotator/StrandBiasBySample.java | 2 +- .../walkers/annotator/StrandBiasTest.java | 2 +- .../walkers/annotator/StrandOddsRatio.java | 2 +- .../annotator/TandemRepeatAnnotator.java | 2 +- .../TransmissionDisequilibriumTest.java | 2 +- .../tools/walkers/annotator/VariantType.java | 2 +- .../tools/walkers/bqsr/AnalyzeCovariates.java | 2 +- .../tools/walkers/bqsr/BaseRecalibrator.java | 2 +- .../walkers/bqsr/ReadRecalibrationInfo.java | 2 +- .../walkers/bqsr/RecalibrationEngine.java | 2 +- .../diagnostics/BaseCoverageDistribution.java | 2 +- .../diagnostics/FindCoveredIntervals.java | 2 +- .../AbstractStratification.java | 2 +- .../diagnosetargets/CallableStatus.java | 2 +- .../diagnosetargets/DiagnoseTargets.java | 2 +- .../diagnosetargets/IntervalMetric.java | 2 +- .../IntervalStratification.java | 2 +- .../diagnosetargets/LocusMetric.java | 2 +- .../LocusMetricCoverageGap.java | 2 +- .../LocusMetricExcessiveCoverage.java | 2 +- .../LocusMetricLowCoverage.java | 2 +- .../LocusMetricPoorQuality.java | 2 +- .../diagnosetargets/LocusStratification.java | 2 +- .../diagnostics/diagnosetargets/Metric.java | 2 +- .../diagnosetargets/PluginUtils.java | 2 +- .../diagnosetargets/SampleMetric.java | 2 +- .../diagnosetargets/SampleMetricBadMates.java | 2 +- .../diagnosetargets/SampleMetricNoReads.java | 2 +- .../diagnosetargets/SampleStratification.java | 2 +- .../diagnosetargets/ThresHolder.java | 2 +- .../walkers/diagnostics/missing/Metrics.java | 2 +- .../missing/QualifyMissingIntervals.java | 2 +- .../walkers/genotyper/AFPriorProvider.java | 2 +- .../AlleleLikelihoodMatrixMapper.java | 2 +- .../walkers/genotyper/BaseMismatchModel.java | 2 +- .../genotyper/ConsensusAlleleCounter.java | 2 +- .../genotyper/CustomAFPriorProvider.java | 2 +- .../DiploidSNPGenotypeLikelihoods.java | 2 +- .../tools/walkers/genotyper/ErrorModel.java | 2 +- .../GeneralPloidyGenotypeLikelihoods.java | 2 +- ...dyGenotypeLikelihoodsCalculationModel.java | 2 +- ...GeneralPloidyIndelGenotypeLikelihoods.java | 2 +- ...elGenotypeLikelihoodsCalculationModel.java | 2 +- .../GeneralPloidySNPGenotypeLikelihoods.java | 2 +- ...NPGenotypeLikelihoodsCalculationModel.java | 2 +- .../genotyper/GenotypeAlleleCounts.java | 2 +- .../GenotypeLikelihoodCalculator.java | 2 +- .../GenotypeLikelihoodCalculators.java | 2 +- .../GenotypeLikelihoodsCalculationModel.java | 2 +- .../walkers/genotyper/GenotypePriors.java | 2 +- .../walkers/genotyper/GenotypingData.java | 2 +- .../walkers/genotyper/GenotypingEngine.java | 2 +- .../genotyper/GenotypingLikelihoods.java | 2 +- .../walkers/genotyper/GenotypingModel.java | 2 +- .../genotyper/GenotypingOutputMode.java | 2 +- .../HeterozygosityAFPriorProvider.java | 2 +- .../genotyper/HomogeneousPloidyModel.java | 2 +- ...elGenotypeLikelihoodsCalculationModel.java | 2 +- .../InfiniteRandomMatingPopulationModel.java | 2 +- .../tools/walkers/genotyper/OutputMode.java | 2 +- .../tools/walkers/genotyper/PloidyModel.java | 2 +- .../walkers/genotyper/PoolGenotypePriors.java | 2 +- .../walkers/genotyper/ProbabilityVector.java | 2 +- ...NPGenotypeLikelihoodsCalculationModel.java | 2 +- .../StandardCallerArgumentCollection.java | 2 +- .../genotyper/UnifiedArgumentCollection.java | 2 +- .../walkers/genotyper/UnifiedGenotyper.java | 2 +- .../genotyper/UnifiedGenotypingEngine.java | 2 +- .../walkers/genotyper/VariantCallContext.java | 2 +- .../genotyper/afcalc/AFCalculationResult.java | 2 +- .../genotyper/afcalc/AFCalculator.java | 2 +- .../genotyper/afcalc/AFCalculatorFactory.java | 2 +- .../afcalc/AFCalculatorImplementation.java | 2 +- .../afcalc/AFCalculatorPerformanceTest.java | 2 +- .../afcalc/AFCalculatorProvider.java | 2 +- .../afcalc/AFCalculatorTestBuilder.java | 2 +- .../ConcurrentAFCalculatorProvider.java | 2 +- .../afcalc/DiploidExactAFCalculator.java | 2 +- .../genotyper/afcalc/ExactACcounts.java | 2 +- .../walkers/genotyper/afcalc/ExactACset.java | 2 +- .../genotyper/afcalc/ExactAFCalculator.java | 2 +- .../genotyper/afcalc/ExactCallLogger.java | 2 +- .../afcalc/FixedAFCalculatorProvider.java | 2 +- .../GeneralPloidyExactAFCalculator.java | 2 +- ...ralPloidyFailOverAFCalculatorProvider.java | 2 +- ...endentAllelesDiploidExactAFCalculator.java | 2 +- .../OriginalDiploidExactAFCalculator.java | 2 +- .../ReferenceDiploidExactAFCalculator.java | 2 +- .../genotyper/afcalc/StateTracker.java | 2 +- .../haplotypecaller/ActiveRegionTrimmer.java | 2 +- ...AssemblyBasedCallerArgumentCollection.java | 2 +- .../haplotypecaller/AssemblyResult.java | 2 +- .../haplotypecaller/AssemblyResultSet.java | 2 +- .../walkers/haplotypecaller/EventBlock.java | 2 +- .../haplotypecaller/EventBlockFinder.java | 2 +- ...GraphBasedLikelihoodCalculationEngine.java | 2 +- ...edLikelihoodCalculationEngineInstance.java | 2 +- .../haplotypecaller/HaplotypeCaller.java | 2 +- .../HaplotypeCallerArgumentCollection.java | 2 +- .../HaplotypeCallerGenotypingEngine.java | 2 +- .../HaplotypeLDCalculator.java | 2 +- .../haplotypecaller/HaplotypeResolver.java | 2 +- .../haplotypecaller/HaplotypeRoute.java | 2 +- .../HeterogeneousKmerSizeResolution.java | 2 +- .../walkers/haplotypecaller/KMerCounter.java | 2 +- .../tools/walkers/haplotypecaller/Kmer.java | 2 +- .../walkers/haplotypecaller/KmerSequence.java | 2 +- .../haplotypecaller/KmerSequenceGraphMap.java | 2 +- .../walkers/haplotypecaller/LDMerger.java | 2 +- .../LikelihoodEngineArgumentCollection.java | 25 +++++----- .../haplotypecaller/LocalAssemblyEngine.java | 2 +- .../MergeVariantsAcrossHaplotypes.java | 2 +- .../PairHMMLikelihoodCalculationEngine.java | 2 +- .../RandomLikelihoodCalculationEngine.java | 2 +- .../haplotypecaller/ReadAnchoring.java | 2 +- .../walkers/haplotypecaller/ReadCost.java | 2 +- .../haplotypecaller/ReadErrorCorrector.java | 2 +- .../ReadLikelihoodCalculationEngine.java | 2 +- .../ReadSegmentComparator.java | 2 +- .../haplotypecaller/ReadSegmentCost.java | 2 +- ...dThreadingAssemblerArgumentCollection.java | 25 +++++----- .../haplotypecaller/RefVsAnyResult.java | 2 +- .../ReferenceConfidenceMode.java | 2 +- .../ReferenceConfidenceModel.java | 2 +- .../graphs/AggregatedSubHaplotypeFinder.java | 2 +- .../haplotypecaller/graphs/BaseEdge.java | 2 +- .../haplotypecaller/graphs/BaseGraph.java | 2 +- .../graphs/BaseGraphIterator.java | 2 +- .../haplotypecaller/graphs/BaseVertex.java | 2 +- .../graphs/CommonSuffixSplitter.java | 2 +- .../graphs/DeBruijnVertex.java | 2 +- .../DeadEndKBestSubHaplotypeFinder.java | 2 +- .../graphs/EmptyPathHaplotypeFinderNode.java | 2 +- .../haplotypecaller/graphs/GraphUtils.java | 2 +- .../graphs/KBestHaplotype.java | 2 +- .../graphs/KBestHaplotypeFinder.java | 2 +- .../graphs/KBestSubHaplotypeFinder.java | 2 +- .../graphs/KmerSearchableGraph.java | 2 +- .../graphs/LowWeightChainPruner.java | 2 +- .../graphs/MultiSampleEdge.java | 2 +- .../walkers/haplotypecaller/graphs/Path.java | 2 +- .../haplotypecaller/graphs/PathBuilder.java | 25 +++++----- .../graphs/RecursiveSubHaplotypeFinder.java | 2 +- .../walkers/haplotypecaller/graphs/Route.java | 2 +- .../haplotypecaller/graphs/RouteFinder.java | 2 +- .../haplotypecaller/graphs/SeqGraph.java | 2 +- .../haplotypecaller/graphs/SeqVertex.java | 2 +- .../graphs/SharedSequenceMerger.java | 2 +- .../graphs/SharedVertexSequenceSplitter.java | 2 +- .../haplotypecaller/graphs/TestGraph.java | 2 +- .../haplotypecaller/graphs/VertexOrder.java | 2 +- .../DanglingChainMergingGraph.java | 2 +- .../readthreading/HaplotypeGraph.java | 2 +- .../readthreading/MultiDeBruijnVertex.java | 2 +- .../readthreading/ReadThreadingAssembler.java | 2 +- .../readthreading/ReadThreadingGraph.java | 2 +- .../readthreading/SequenceForKmers.java | 2 +- .../indels/ConstrainedMateFixingManager.java | 2 +- .../indels/HaplotypeIndelErrorModel.java | 2 +- .../tools/walkers/indels/IndelRealigner.java | 2 +- .../tools/walkers/indels/LeftAlignIndels.java | 2 +- .../indels/PairHMMIndelErrorModel.java | 2 +- .../gatk/tools/walkers/indels/ReadBin.java | 2 +- .../indels/RealignerTargetCreator.java | 2 +- .../tools/walkers/phasing/AllelePair.java | 2 +- .../gatk/tools/walkers/phasing/BaseArray.java | 2 +- .../walkers/phasing/CardinalityCounter.java | 2 +- .../phasing/CloneableIteratorLinkedList.java | 2 +- .../tools/walkers/phasing/DisjointSet.java | 2 +- .../gatk/tools/walkers/phasing/Haplotype.java | 2 +- ...eSegregatingAlternateAllelesVCFWriter.java | 2 +- .../walkers/phasing/PhaseByTransmission.java | 2 +- .../tools/walkers/phasing/PhasingGraph.java | 2 +- .../walkers/phasing/PhasingGraphEdge.java | 2 +- .../tools/walkers/phasing/PhasingRead.java | 2 +- .../tools/walkers/phasing/PhasingUtils.java | 2 +- .../phasing/PreciseNonNegativeDouble.java | 2 +- .../walkers/phasing/ReadBackedPhasing.java | 2 +- .../gatk/tools/walkers/phasing/ReadBase.java | 2 +- .../walkers/phasing/ReadBasesAtPosition.java | 2 +- .../tools/walkers/phasing/SNPallelePair.java | 2 +- .../walkers/rnaseq/OverhangFixingManager.java | 2 +- .../walkers/rnaseq/SplitNCigarReads.java | 2 +- .../SimulateReadsForVariants.java | 2 +- .../validation/GenotypeAndValidate.java | 2 +- .../FrequencyModeSelector.java | 2 +- .../GLBasedSampleSelector.java | 2 +- .../GTBasedSampleSelector.java | 2 +- .../validationsiteselector/GenomeEvent.java | 2 +- .../KeepAFSpectrumFrequencySelector.java | 2 +- .../NullSampleSelector.java | 2 +- .../SampleSelector.java | 2 +- .../UniformSamplingFrequencySelector.java | 2 +- .../ValidationSiteSelector.java | 2 +- .../ApplyRecalibration.java | 2 +- .../GaussianMixtureModel.java | 2 +- .../MultivariateGaussian.java | 2 +- .../variantrecalibration/TrainingSet.java | 2 +- .../walkers/variantrecalibration/Tranche.java | 2 +- .../variantrecalibration/TrancheManager.java | 2 +- .../VariantDataManager.java | 2 +- .../variantrecalibration/VariantDatum.java | 2 +- .../VariantRecalibrator.java | 2 +- ...VariantRecalibratorArgumentCollection.java | 2 +- .../VariantRecalibratorEngine.java | 2 +- .../CalculateGenotypePosteriors.java | 2 +- .../walkers/variantutils/CombineGVCFs.java | 2 +- .../variantutils/FamilyLikelihoodsUtils.java | 2 +- .../walkers/variantutils/GenotypeGVCFs.java | 2 +- .../PosteriorLikelihoodsUtils.java | 2 +- ...ferenceConfidenceVariantContextMerger.java | 2 +- .../variantutils/RegenotypeVariants.java | 2 +- .../gatk/utils/SequenceComplexity.java | 2 +- .../gatk/utils/collections/CountSet.java | 2 +- .../gatk/utils/collections/IntMaxHeap.java | 2 +- .../gga/GenotypingGivenAllelesUtils.java | 2 +- .../gatk/utils/gvcf/GVCFWriter.java | 2 +- .../gatk/utils/gvcf/HomRefBlock.java | 2 +- .../AllHaplotypeBAMWriter.java | 2 +- .../CalledHaplotypeBAMWriter.java | 2 +- .../HaplotypeBAMWriter.java | 2 +- .../haplotypeBAMWriter/ReadDestination.java | 2 +- .../utils/pairhmm/ArrayLoglessPairHMM.java | 2 +- .../gatk/utils/pairhmm/CnyPairHMM.java | 2 +- .../utils/pairhmm/DebugJNILoglessPairHMM.java | 2 +- .../utils/pairhmm/FastLoglessPairHMM.java | 2 +- .../gatk/utils/pairhmm/FlexibleHMM.java | 2 +- .../gatk/utils/pairhmm/JNILoglessPairHMM.java | 2 +- .../gatk/utils/pairhmm/LoglessPairHMM.java | 2 +- .../utils/pairhmm/VectorLoglessPairHMM.java | 2 +- .../gatk/utils/sam/ClippedGATKSAMRecord.java | 2 +- .../utils/variant/TandemRepeatFinder.java | 25 +++++----- .../ContextCovariateUnitTest.java | 2 +- .../recalibration/CycleCovariateUnitTest.java | 2 +- .../recalibration/QualQuantizerUnitTest.java | 2 +- .../recalibration/ReadCovariatesUnitTest.java | 2 +- .../ReadGroupCovariateUnitTest.java | 2 +- .../recalibration/RecalDatumUnitTest.java | 2 +- .../recalibration/RecalUtilsUnitTest.java | 2 +- .../RecalibrationReportUnitTest.java | 2 +- .../RecalibrationTablesUnitTest.java | 2 +- .../recalibration/RecalibrationTestUtils.java | 2 +- .../RepeatCovariatesUnitTest.java | 2 +- .../walkers/WalkerTestIntegrationTest.java | 2 +- .../annotator/GenotypeSummariesUnitTest.java | 2 +- .../annotator/InbreedingCoeffUnitTest.java | 2 +- .../annotator/QualByDepthUnitTest.java | 2 +- .../walkers/annotator/RankSumUnitTest.java | 2 +- .../walkers/annotator/SnpEffUnitTest.java | 2 +- .../annotator/StrandOddsRatioUnitTest.java | 2 +- .../VariantAnnotatorIntegrationTest.java | 2 +- .../VariantOverlapAnnotatorUnitTest.java | 2 +- .../AnalyzeCovariatesIntegrationTest.java | 2 +- .../walkers/bqsr/BQSRGathererUnitTest.java | 2 +- .../walkers/bqsr/BQSRIntegrationTest.java | 2 +- .../bqsr/ReadRecalibrationInfoUnitTest.java | 2 +- ...seCoverageDistributionIntegrationTest.java | 2 +- .../ErrorRatePerCycleIntegrationTest.java | 2 +- .../ReadGroupPropertiesIntegrationTest.java | 2 +- .../DiagnoseTargetsIntegrationTest.java | 2 +- .../LocusStatisticsUnitTest.java | 2 +- .../QualifyMissingIntervalsUnitTest.java | 2 +- ...astaAlternateReferenceIntegrationTest.java | 2 +- .../VariantFiltrationIntegrationTest.java | 2 +- .../genotyper/AlleleListUnitTester.java | 2 +- .../genotyper/AlleleListUtilsUnitTest.java | 2 +- .../ArtificialReadPileupTestProvider.java | 2 +- ...eralPloidyGenotypeLikelihoodsUnitTest.java | 2 +- .../GenotypeAlleleCountsUnitTest.java | 2 +- .../GenotypeLikelihoodCalculatorUnitTest.java | 2 +- .../genotyper/GenotypingDataUnitTest.java | 2 +- .../genotyper/HeterogeneousPloidyModel.java | 2 +- .../HomogeneousPloidyModelUnitTest.java | 2 +- .../IndelGenotypeLikelihoodsUnitTest.java | 2 +- .../genotyper/IndexedAlleleListUnitTest.java | 2 +- .../genotyper/IndexedSampleListUnitTest.java | 2 +- ...teRandomMatingPopulationModelUnitTest.java | 2 +- .../NanoSchedulerIntegrationTest.java | 2 +- .../genotyper/ReadLikelihoodsUnitTest.java | 2 +- .../genotyper/ReadLikelihoodsUnitTester.java | 2 +- .../genotyper/SampleListUnitTester.java | 2 +- .../genotyper/SampleListUtilsUnitTest.java | 2 +- ...ndardCallerArgumentCollectionUnitTest.java | 2 +- .../UnifiedGenotyperEngineUnitTest.java | 2 +- ...perGeneralPloidySuite1IntegrationTest.java | 2 +- ...perGeneralPloidySuite2IntegrationTest.java | 2 +- ...iedGenotyperGeneralPloidyTestExecutor.java | 2 +- ...dGenotyperIndelCallingIntegrationTest.java | 2 +- .../UnifiedGenotyperIntegrationTest.java | 2 +- .../UnifiedGenotyperLargeScaleTest.java | 2 +- ...GenotyperNormalCallingIntegrationTest.java | 2 +- .../afcalc/AFCalculationUnitTest.java | 2 +- .../AFCalculatorPerformanceUnitTest.java | 2 +- .../afcalc/AFCalculatorResultUnitTest.java | 2 +- .../FixedAFCalculatorProviderUnitTest.java | 2 +- ...neralPloidyAFCalculationModelUnitTest.java | 2 +- ...yFailOverAFCalculatorProviderUnitTest.java | 2 +- ...lelesDiploidExactAFCalculatorUnitTest.java | 2 +- .../AFPriorProviderUnitTest.java | 2 +- .../ActiveRegionTestDataSet.java | 2 +- .../ActiveRegionTestDataSetUnitTest.java | 2 +- .../AssemblyResultSetUnitTest.java | 2 +- .../tools/walkers/haplotypecaller/Civar.java | 2 +- .../haplotypecaller/CivarUnitTest.java | 2 +- .../FastLoglessPairHMMUnitTest.java | 2 +- ...LikelihoodCalculationEnginesBenchmark.java | 2 +- .../HaplotypeBaseComparatorUnitTest.java | 2 +- ...lexAndSymbolicVariantsIntegrationTest.java | 2 +- .../HaplotypeCallerGVCFIntegrationTest.java | 2 +- ...plotypeCallerGenotypingEngineUnitTest.java | 2 +- .../HaplotypeCallerIntegrationTest.java | 2 +- .../HaplotypeCallerModesIntegrationTest.java | 2 +- ...aplotypeCallerParallelIntegrationTest.java | 2 +- .../HaplotypeLDCalculatorUnitTest.java | 2 +- .../HaplotypeScoreComparatorUnitTest.java | 2 +- ...aplotypeSizeAndBaseComparatorUnitTest.java | 2 +- .../KMerCounterCaseFixUnitTest.java | 2 +- .../walkers/haplotypecaller/KmerUnitTest.java | 2 +- .../haplotypecaller/LDMergerUnitTest.java | 2 +- .../LocalAssemblyEngineUnitTest.java | 2 +- ...MMLikelihoodCalculationEngineUnitTest.java | 2 +- .../PairHMMProbabilityBugIntegrationTest.java | 2 +- .../ReadErrorCorrectorUnitTest.java | 2 +- ...ngLikelihoodCalculationEngineUnitTest.java | 2 +- .../ReferenceConfidenceModelUnitTest.java | 2 +- .../graphs/BaseEdgeUnitTest.java | 2 +- .../graphs/BaseGraphUnitTest.java | 2 +- .../graphs/BaseVertexUnitTest.java | 2 +- .../graphs/CommonSuffixMergerUnitTest.java | 2 +- .../graphs/CommonSuffixSplitterUnitTest.java | 2 +- .../graphs/DeBruijnVertexUnitTest.java | 2 +- .../graphs/GraphUtilsUnitTest.java | 2 +- .../graphs/HaplotypeGraphUnitTest.java | 2 +- .../graphs/KBestHaplotypeFinderUnitTest.java | 2 +- .../graphs/LowWeightChainPrunerUnitTest.java | 2 +- .../graphs/MultiSampleEdgeUnitTest.java | 2 +- .../graphs/PathBuilderUnitTest.java | 25 +++++----- .../haplotypecaller/graphs/PathUnitTest.java | 2 +- .../haplotypecaller/graphs/RouteUnitTest.java | 2 +- .../graphs/SeqGraphUnitTest.java | 2 +- .../graphs/SeqVertexUnitTest.java | 2 +- .../SharedVertexSequenceSplitterUnitTest.java | 2 +- .../DanglingChainMergingGraphUnitTest.java | 2 +- .../ReadThreadingAssemblerUnitTest.java | 2 +- .../ReadThreadingGraphUnitTest.java | 2 +- .../SequenceForKmersUnitTest.java | 2 +- .../ConstrainedMateFixingManagerUnitTest.java | 2 +- .../indels/IndelRealignerIntegrationTest.java | 2 +- .../indels/IndelRealignerLargeScaleTest.java | 2 +- .../indels/IndelRealignerUnitTest.java | 2 +- .../PairHMMIndelErrorModelUnitTest.java | 2 +- .../tools/walkers/indels/ReadBinUnitTest.java | 2 +- ...RealignerTargetCreatorIntegrationTest.java | 2 +- .../RealignerTargetCreatorLargeScaleTest.java | 2 +- .../PhaseByTransmissionIntegrationTest.java | 2 +- .../walkers/phasing/PhasingUtilsUnitTest.java | 24 ++++----- .../ReadBackedPhasingIntegrationTest.java | 2 +- .../rnaseq/OverhangFixingManagerUnitTest.java | 2 +- .../SplitNCigarReadsIntegrationTest.java | 2 +- .../rnaseq/SplitNCigarReadsUnitTest.java | 2 +- ...mulateReadsForVariantsIntegrationTest.java | 2 +- ...ValidationSiteSelectorIntegrationTest.java | 2 +- .../VariantEvalIntegrationTest.java | 2 +- .../VariantEvalWalkerUnitTest.java | 2 +- .../StratificationManagerUnitTest.java | 2 +- .../ApplyRecalibrationUnitTest.java | 2 +- .../VariantDataManagerUnitTest.java | 2 +- .../VariantGaussianMixtureModelUnitTest.java | 2 +- ...ntRecalibrationWalkersIntegrationTest.java | 2 +- ...lateGenotypePosteriorsIntegrationTest.java | 2 +- .../CombineGVCFsIntegrationTest.java | 2 +- .../CombineVariantsIntegrationTest.java | 2 +- .../variantutils/CombineVariantsUnitTest.java | 2 +- .../ConcordanceMetricsUnitTest.java | 2 +- .../GenotypeConcordanceIntegrationTest.java | 2 +- .../GenotypeGVCFsIntegrationTest.java | 2 +- ...ftAlignAndTrimVariantsIntegrationTest.java | 2 +- .../LeftAlignAndTrimVariantsUnitTest.java | 2 +- .../LiftoverVariantsIntegrationTest.java | 2 +- .../PosteriorLikelihoodsUtilsUnitTest.java | 2 +- .../RegenotypeVariantsIntegrationTest.java | 2 +- .../SelectVariantsIntegrationTest.java | 2 +- ...SelectVariantsParallelIntegrationTest.java | 2 +- .../VCFStreamingIntegrationTest.java | 2 +- .../ValidateVariantsIntegrationTest.java | 2 +- .../VariantContextMergerUnitTest.java | 2 +- ...ntsToAllelicPrimitivesIntegrationTest.java | 2 +- .../VariantsToBinaryPedIntegrationTest.java | 2 +- .../VariantsToTableIntegrationTest.java | 2 +- .../VariantsToVCFIntegrationTest.java | 2 +- .../gatk/utils/ContigComparatorUnitTest.java | 2 +- .../broadinstitute/gatk/utils/RandomDNA.java | 2 +- .../utils/collections/CountSetUnitTest.java | 2 +- .../utils/collections/IndexedSetUnitTest.java | 2 +- .../utils/collections/IntMaxHeapUnitTest.java | 2 +- .../utils/diffengine/DiffEngineUnitTest.java | 2 +- .../utils/diffengine/DiffNodeUnitTest.java | 2 +- .../diffengine/DiffableReaderUnitTest.java | 2 +- .../utils/diffengine/DifferenceUnitTest.java | 2 +- .../genotyper/DiploidGenotypeUnitTest.java | 2 +- .../genotyper/MostLikelyAlleleUnitTest.java | 2 +- .../PerReadAlleleLikelihoodMapUnitTest.java | 2 +- .../gatk/utils/gvcf/GVCFWriterUnitTest.java | 2 +- .../gatk/utils/gvcf/HomRefBlockUnitTest.java | 2 +- .../HaplotypeBAMWriterUnitTest.java | 2 +- .../utils/pairhmm/CnyPairHMMUnitTest.java | 2 +- .../pairhmm/PairHMMEmpiricalBenchmark.java | 2 +- .../utils/pairhmm/PairHMMModelUnitTest.java | 2 +- .../pairhmm/PairHMMSyntheticBenchmark.java | 2 +- .../gatk/utils/pairhmm/PairHMMTestData.java | 2 +- .../gatk/utils/pairhmm/PairHMMUnitTest.java | 2 +- .../SWPairwiseAlignmentUnitTest.java | 2 +- .../VectorPairHMM/src/main/c++/Sandbox.java | 2 +- .../org/mycompany/app/MyExampleWalker.java | 2 +- .../app/MyExampleWalkerIntegrationTest.java | 2 +- .../app/MyExampleWalkerUnitTest.java | 2 +- .../gatk/engine/CommandLineExecutable.java | 2 +- .../gatk/engine/CommandLineGATK.java | 2 +- .../gatk/engine/GATKVCFUtils.java | 2 +- .../gatk/engine/GenomeAnalysisEngine.java | 2 +- .../gatk/engine/ReadMetrics.java | 2 +- .../gatk/engine/ReadProperties.java | 2 +- .../gatk/engine/SampleUtils.java | 2 +- .../gatk/engine/WalkerManager.java | 2 +- .../gatk/engine/alignment/Aligner.java | 2 +- .../gatk/engine/alignment/Alignment.java | 2 +- .../gatk/engine/alignment/bwa/BWAAligner.java | 2 +- .../alignment/bwa/BWAConfiguration.java | 2 +- .../gatk/engine/alignment/bwa/BWTFiles.java | 2 +- .../bwa/java/AlignerTestHarness.java | 2 +- .../bwa/java/AlignmentMatchSequence.java | 2 +- .../alignment/bwa/java/AlignmentState.java | 2 +- .../alignment/bwa/java/BWAAlignment.java | 2 +- .../alignment/bwa/java/BWAJavaAligner.java | 2 +- .../engine/alignment/bwa/java/LowerBound.java | 2 +- .../gatk/engine/alignment/package-info.java | 2 +- .../alignment/reference/bwt/AMBWriter.java | 2 +- .../alignment/reference/bwt/ANNWriter.java | 2 +- .../engine/alignment/reference/bwt/BWT.java | 2 +- .../alignment/reference/bwt/BWTReader.java | 2 +- .../bwt/BWTSupplementaryFileGenerator.java | 2 +- .../alignment/reference/bwt/BWTWriter.java | 2 +- .../engine/alignment/reference/bwt/Bases.java | 2 +- .../alignment/reference/bwt/Counts.java | 2 +- .../reference/bwt/CreateBWTFromReference.java | 2 +- .../reference/bwt/SequenceBlock.java | 2 +- .../alignment/reference/bwt/SuffixArray.java | 2 +- .../reference/bwt/SuffixArrayReader.java | 2 +- .../reference/bwt/SuffixArrayWriter.java | 2 +- .../packing/BasePackedInputStream.java | 2 +- .../packing/BasePackedOutputStream.java | 2 +- .../packing/CreatePACFromReference.java | 2 +- .../reference/packing/PackUtils.java | 2 +- .../packing/UnsignedIntPackedInputStream.java | 2 +- .../UnsignedIntPackedOutputStream.java | 2 +- .../arguments/DbsnpArgumentCollection.java | 2 +- .../arguments/GATKArgumentCollection.java | 2 +- ...VariantContextInputArgumentCollection.java | 2 +- .../gatk/engine/crypt/CryptUtils.java | 2 +- .../gatk/engine/crypt/GATKKey.java | 2 +- .../gatk/engine/datasources/package-info.java | 2 +- .../datasources/providers/AllLocusView.java | 2 +- .../providers/CoveredLocusView.java | 2 +- .../IntervalOverlappingRODsFromStream.java | 2 +- .../IntervalReferenceOrderedView.java | 2 +- .../providers/InvalidPositionException.java | 2 +- .../providers/LocusReferenceView.java | 2 +- .../providers/LocusShardDataProvider.java | 2 +- .../datasources/providers/LocusView.java | 2 +- .../ManagingReferenceOrderedView.java | 2 +- .../providers/RODMetaDataContainer.java | 2 +- .../ReadBasedReferenceOrderedView.java | 2 +- .../providers/ReadReferenceView.java | 2 +- .../providers/ReadShardDataProvider.java | 2 +- .../datasources/providers/ReadView.java | 2 +- .../providers/ReferenceOrderedView.java | 2 +- .../datasources/providers/ReferenceView.java | 2 +- .../datasources/providers/RodLocusView.java | 2 +- .../providers/ShardDataProvider.java | 2 +- .../engine/datasources/providers/View.java | 2 +- .../datasources/providers/package-info.java | 2 +- .../reads/ActiveRegionShardBalancer.java | 2 +- .../datasources/reads/BAMAccessPlan.java | 2 +- .../engine/datasources/reads/BAMSchedule.java | 2 +- .../datasources/reads/BAMScheduler.java | 2 +- .../reads/BGZFBlockLoadingDispatcher.java | 2 +- .../datasources/reads/BlockInputStream.java | 2 +- .../engine/datasources/reads/BlockLoader.java | 2 +- .../datasources/reads/FileHandleCache.java | 2 +- .../engine/datasources/reads/FilePointer.java | 2 +- .../datasources/reads/GATKBAMIndex.java | 2 +- .../datasources/reads/GATKBAMIndexData.java | 2 +- .../IntervalOverlapFilteringIterator.java | 2 +- .../datasources/reads/IntervalSharder.java | 2 +- .../engine/datasources/reads/LocusShard.java | 2 +- .../datasources/reads/LocusShardBalancer.java | 2 +- .../engine/datasources/reads/ReadShard.java | 2 +- .../datasources/reads/ReadShardBalancer.java | 2 +- .../datasources/reads/SAMDataSource.java | 2 +- .../gatk/engine/datasources/reads/Shard.java | 2 +- .../datasources/reads/ShardBalancer.java | 2 +- .../datasources/reads/package-info.java | 2 +- .../reads/utilities/BAMFileStat.java | 2 +- .../reads/utilities/BAMTagRenamer.java | 2 +- .../reads/utilities/FindLargeShards.java | 2 +- .../reads/utilities/PrintBAMRegion.java | 2 +- .../reads/utilities/PrintBGZFBounds.java | 2 +- .../reads/utilities/UnzipSingleBlock.java | 2 +- .../reads/utilities/package-info.java | 2 +- .../reference/ReferenceDataSource.java | 2 +- .../datasources/reference/package-info.java | 2 +- .../datasources/rmd/DataStreamSegment.java | 2 +- .../engine/datasources/rmd/EntireStream.java | 2 +- .../datasources/rmd/MappedStreamSegment.java | 2 +- .../rmd/ReferenceOrderedDataPool.java | 2 +- .../rmd/ReferenceOrderedDataSource.java | 2 +- .../engine/datasources/rmd/ResourcePool.java | 2 +- .../engine/datasources/rmd/package-info.java | 2 +- .../gatk/engine/executive/Accumulator.java | 2 +- .../executive/HierarchicalMicroScheduler.java | 2 +- .../HierarchicalMicroSchedulerMBean.java | 2 +- .../executive/LinearMicroScheduler.java | 2 +- .../gatk/engine/executive/MicroScheduler.java | 2 +- .../engine/executive/MicroSchedulerMBean.java | 2 +- .../engine/executive/OutputMergeTask.java | 2 +- .../gatk/engine/executive/ReduceTree.java | 2 +- .../gatk/engine/executive/ShardTraverser.java | 2 +- .../gatk/engine/executive/TreeReducer.java | 2 +- .../gatk/engine/executive/WindowMaker.java | 2 +- .../gatk/engine/executive/package-info.java | 2 +- .../engine/filters/BAQReadTransformer.java | 2 +- .../gatk/engine/filters/BadCigarFilter.java | 2 +- .../gatk/engine/filters/BadMateFilter.java | 2 +- .../filters/CountingFilteringIterator.java | 2 +- .../engine/filters/DisableableReadFilter.java | 2 +- .../engine/filters/DuplicateReadFilter.java | 2 +- .../FailsVendorQualityCheckFilter.java | 2 +- .../gatk/engine/filters/FilterManager.java | 2 +- .../engine/filters/LibraryReadFilter.java | 2 +- .../engine/filters/MalformedReadFilter.java | 2 +- .../engine/filters/MappingQualityFilter.java | 2 +- .../MappingQualityUnavailableFilter.java | 2 +- .../filters/MappingQualityZeroFilter.java | 2 +- .../engine/filters/MateSameStrandFilter.java | 2 +- .../engine/filters/MaxInsertSizeFilter.java | 2 +- .../filters/MissingReadGroupFilter.java | 2 +- .../filters/NDNCigarReadTransformer.java | 2 +- .../NoOriginalQualityScoresFilter.java | 2 +- .../filters/NotPrimaryAlignmentFilter.java | 2 +- .../engine/filters/OverclippedReadFilter.java | 2 +- .../engine/filters/Platform454Filter.java | 2 +- .../gatk/engine/filters/PlatformFilter.java | 2 +- .../engine/filters/PlatformUnitFilter.java | 50 +++++++++---------- .../filters/PlatformUnitFilterHelper.java | 2 +- .../gatk/engine/filters/ReadFilter.java | 2 +- .../filters/ReadGroupBlackListFilter.java | 2 +- .../gatk/engine/filters/ReadLengthFilter.java | 2 +- .../gatk/engine/filters/ReadNameFilter.java | 2 +- .../gatk/engine/filters/ReadStrandFilter.java | 2 +- .../filters/ReassignMappingQualityFilter.java | 2 +- .../ReassignOneMappingQualityFilter.java | 2 +- .../gatk/engine/filters/SampleFilter.java | 2 +- .../engine/filters/SingleReadGroupFilter.java | 2 +- .../engine/filters/UnmappedReadFilter.java | 2 +- .../gatk/engine/filters/package-info.java | 2 +- .../gatk/engine/io/BySampleSAMFileWriter.java | 2 +- .../gatk/engine/io/DirectOutputTracker.java | 2 +- .../gatk/engine/io/FastqFileWriter.java | 2 +- .../gatk/engine/io/NWaySAMFileWriter.java | 2 +- .../gatk/engine/io/OutputTracker.java | 2 +- .../engine/io/ThreadGroupOutputTracker.java | 2 +- .../io/storage/OutputStreamStorage.java | 2 +- .../io/storage/SAMFileWriterStorage.java | 2 +- .../gatk/engine/io/storage/Storage.java | 2 +- .../engine/io/storage/StorageFactory.java | 2 +- .../storage/VariantContextWriterStorage.java | 2 +- .../OutputStreamArgumentTypeDescriptor.java | 2 +- .../engine/io/stubs/OutputStreamStub.java | 2 +- .../SAMFileWriterArgumentTypeDescriptor.java | 2 +- .../engine/io/stubs/SAMFileWriterStub.java | 2 +- .../SAMReaderArgumentTypeDescriptor.java | 2 +- .../gatk/engine/io/stubs/Stub.java | 2 +- .../VCFWriterArgumentTypeDescriptor.java | 2 +- .../io/stubs/VariantContextWriterStub.java | 2 +- .../engine/iterators/BoundedReadIterator.java | 2 +- .../engine/iterators/GenomeLocusIterator.java | 2 +- .../engine/iterators/IterableIterator.java | 2 +- .../MalformedBAMErrorReformatingIterator.java | 2 +- .../MisencodedBaseQualityReadTransformer.java | 2 +- .../engine/iterators/NullSAMIterator.java | 2 +- .../engine/iterators/PeekingIterator.java | 2 +- .../iterators/PositionTrackingIterator.java | 2 +- .../engine/iterators/RNAReadTransformer.java | 2 +- .../iterators/ReadFormattingIterator.java | 2 +- .../engine/iterators/ReadTransformer.java | 2 +- .../iterators/ReadTransformersMode.java | 2 +- .../iterators/ReadTransformingIterator.java | 2 +- .../iterators/VerifyingSamIterator.java | 2 +- .../gatk/engine/iterators/package-info.java | 2 +- .../gatk/engine/package-info.java | 2 +- .../gatk/engine/phonehome/GATKRunReport.java | 2 +- .../phonehome/GATKRunReportException.java | 2 +- .../engine/recalibration/BQSRArgumentSet.java | 2 +- .../gatk/engine/recalibration/BQSRMode.java | 2 +- .../resourcemanagement/ThreadAllocation.java | 2 +- .../gatk/engine/samples/Affection.java | 2 +- .../gatk/engine/samples/Gender.java | 2 +- .../engine/samples/MendelianViolation.java | 2 +- .../gatk/engine/samples/PedReader.java | 2 +- .../samples/PedigreeValidationType.java | 2 +- .../gatk/engine/samples/Sample.java | 2 +- .../gatk/engine/samples/SampleDB.java | 2 +- .../gatk/engine/samples/SampleDBBuilder.java | 2 +- .../gatk/engine/samples/Trio.java | 2 +- .../traversals/ArtificialReadsTraversal.java | 2 +- .../traversals/TAROrderedReadCache.java | 2 +- .../engine/traversals/TraversalEngine.java | 2 +- .../traversals/TraverseActiveRegions.java | 2 +- .../engine/traversals/TraverseDuplicates.java | 2 +- .../engine/traversals/TraverseLociNano.java | 2 +- .../engine/traversals/TraverseReadPairs.java | 2 +- .../engine/traversals/TraverseReadsNano.java | 2 +- .../gatk/engine/traversals/package-info.java | 2 +- .../ActiveRegionTraversalParameters.java | 2 +- .../engine/walkers/ActiveRegionWalker.java | 2 +- .../gatk/engine/walkers/Allows.java | 2 +- .../gatk/engine/walkers/Attribution.java | 2 +- .../gatk/engine/walkers/BAQMode.java | 2 +- .../gatk/engine/walkers/By.java | 2 +- .../gatk/engine/walkers/DataSource.java | 2 +- .../engine/walkers/DisabledReadFilters.java | 2 +- .../gatk/engine/walkers/Downsample.java | 2 +- .../gatk/engine/walkers/DuplicateWalker.java | 2 +- .../gatk/engine/walkers/FailMethod.java | 2 +- .../gatk/engine/walkers/LocusWalker.java | 2 +- .../gatk/engine/walkers/NanoSchedulable.java | 2 +- .../gatk/engine/walkers/PartitionBy.java | 2 +- .../gatk/engine/walkers/PartitionType.java | 2 +- .../gatk/engine/walkers/RMD.java | 2 +- .../gatk/engine/walkers/ReadFilters.java | 2 +- .../gatk/engine/walkers/ReadPairWalker.java | 2 +- .../gatk/engine/walkers/ReadWalker.java | 2 +- .../gatk/engine/walkers/RefWalker.java | 2 +- .../gatk/engine/walkers/Reference.java | 2 +- .../engine/walkers/RemoveProgramRecords.java | 2 +- .../gatk/engine/walkers/Requires.java | 2 +- .../gatk/engine/walkers/RodWalker.java | 2 +- .../gatk/engine/walkers/TreeReducible.java | 2 +- .../gatk/engine/walkers/Walker.java | 2 +- .../gatk/engine/walkers/WalkerName.java | 2 +- .../gatk/engine/walkers/Window.java | 2 +- .../gatk/engine/CommandLineGATKUnitTest.java | 2 +- .../engine/EngineFeaturesIntegrationTest.java | 2 +- .../gatk/engine/GATKVCFUtilsUnitTest.java | 2 +- .../engine/GenomeAnalysisEngineUnitTest.java | 2 +- .../gatk/engine/InstantiableWalker.java | 2 +- .../engine/MaxRuntimeIntegrationTest.java | 2 +- .../gatk/engine/ReadMetricsUnitTest.java | 2 +- .../gatk/engine/SampleUtilsUnitTest.java | 2 +- .../gatk/engine/UninstantiableWalker.java | 2 +- .../gatk/engine/WalkerManagerUnitTest.java | 2 +- .../engine/arguments/CramIntegrationTest.java | 2 +- .../arguments/IntervalIntegrationTest.java | 2 +- .../InvalidArgumentIntegrationTest.java | 2 +- .../arguments/LoggingIntegrationTest.java | 2 +- .../gatk/engine/crypt/CryptUtilsUnitTest.java | 2 +- .../engine/crypt/GATKKeyIntegrationTest.java | 2 +- .../gatk/engine/crypt/GATKKeyUnitTest.java | 2 +- .../providers/AllLocusViewUnitTest.java | 2 +- .../providers/CoveredLocusViewUnitTest.java | 2 +- .../IntervalReferenceOrderedViewUnitTest.java | 2 +- .../providers/LocusReferenceViewUnitTest.java | 2 +- .../providers/LocusViewTemplate.java | 2 +- .../providers/ReadReferenceViewUnitTest.java | 2 +- .../ReferenceOrderedViewUnitTest.java | 2 +- .../providers/ReferenceViewTemplate.java | 2 +- .../providers/ShardDataProviderUnitTest.java | 2 +- .../ActiveRegionShardBalancerUnitTest.java | 2 +- .../reads/DownsamplerBenchmark.java | 2 +- .../reads/FilePointerUnitTest.java | 2 +- .../reads/GATKBAMIndexUnitTest.java | 2 +- .../reads/GATKWalkerBenchmark.java | 2 +- ...ervalOverlapFilteringIteratorUnitTest.java | 2 +- .../datasources/reads/MockLocusShard.java | 2 +- .../reads/PicardBaselineBenchmark.java | 2 +- .../reads/ReadProcessingBenchmark.java | 2 +- .../reads/ReadShardBalancerUnitTest.java | 2 +- .../reads/SAMDataSourceUnitTest.java | 2 +- .../reads/SAMReaderIDUnitTest.java | 2 +- .../reads/SeekableBufferedStreamUnitTest.java | 2 +- .../reads/TheoreticalMinimaBenchmark.java | 2 +- .../ReferenceDataSourceIntegrationTest.java | 2 +- .../rmd/ReferenceOrderedDataPoolUnitTest.java | 2 +- ...ReferenceOrderedQueryDataPoolUnitTest.java | 2 +- .../DownsamplingIntegrationTest.java | 2 +- .../DownsamplingReadsIteratorUnitTest.java | 2 +- .../FractionalDownsamplerUnitTest.java | 2 +- .../LevelingDownsamplerUnitTest.java | 2 +- ...mpleDownsamplingReadsIteratorUnitTest.java | 2 +- ...ificialSingleSampleReadStreamAnalyzer.java | 2 +- .../ReservoirDownsamplerUnitTest.java | 2 +- .../SimplePositionalDownsamplerUnitTest.java | 2 +- .../engine/executive/ReduceTreeUnitTest.java | 2 +- ...llowNCigarMalformedReadFilterUnitTest.java | 2 +- .../filters/BadCigarFilterUnitTest.java | 2 +- .../filters/BadReadGroupsIntegrationTest.java | 2 +- .../filters/MalformedReadFilterUnitTest.java | 2 +- .../NDNCigarReadTransformerUnitTest.java | 2 +- .../OverclippedReadFilterUnitTest.java | 2 +- .../gatk/engine/filters/ReadFilterTest.java | 2 +- .../ReadGroupBlackListFilterUnitTest.java | 2 +- .../UnsafeMalformedReadFilterUnitTest.java | 2 +- .../gatk/engine/io/OutputTrackerUnitTest.java | 2 +- .../stubs/ArgumentTypeDescriptorUnitTest.java | 2 +- .../BoundedReadIteratorUnitTest.java | 2 +- .../GATKSAMIteratorAdapterUnitTest.java | 2 +- .../MisencodedBaseQualityUnitTest.java | 2 +- .../ReadFormattingIteratorUnitTest.java | 2 +- .../VerifyingSamIteratorUnitTest.java | 2 +- .../phonehome/GATKRunReportUnitTest.java | 2 +- .../engine/samples/PedReaderUnitTest.java | 2 +- .../gatk/engine/samples/SampleDBUnitTest.java | 2 +- .../gatk/engine/samples/SampleUnitTest.java | 2 +- .../traversals/DummyActiveRegionWalker.java | 2 +- .../TAROrderedReadCacheUnitTest.java | 2 +- .../TraverseActiveRegionsUnitTest.java | 2 +- .../TraverseDuplicatesUnitTest.java | 2 +- .../traversals/TraverseReadsUnitTest.java | 2 +- .../engine/walkers/TestCountLociWalker.java | 2 +- .../engine/walkers/TestCountReadsWalker.java | 2 +- .../walkers/TestErrorThrowingWalker.java | 2 +- .../engine/walkers/TestPrintReadsWalker.java | 2 +- .../walkers/TestPrintVariantsWalker.java | 2 +- .../gatk/engine/walkers/WalkerTest.java | 2 +- .../gatk/ArgumentDefinitionField.java | 2 +- .../queue/extensions/gatk/ArgumentField.java | 2 +- .../gatk/GATKExtensionsGenerator.java | 2 +- .../extensions/gatk/ReadFilterField.java | 2 +- .../CNV/ONLY_GENOTYPE_xhmmCNVpipeline.scala | 2 +- .../queue/qscripts/CNV/xhmmCNVpipeline.scala | 2 +- .../queue/qscripts/GATKResourcesBundle.scala | 2 +- .../qscripts/examples/ExampleCountLoci.scala | 2 +- .../qscripts/examples/ExampleCountReads.scala | 2 +- .../examples/ExampleCustomWalker.scala | 2 +- .../qscripts/examples/ExamplePrintReads.scala | 2 +- .../qscripts/examples/ExampleReadFilter.scala | 2 +- .../examples/ExampleRetryMemoryLimit.scala | 2 +- .../queue/qscripts/examples/HelloWorld.scala | 2 +- .../gatk/queue/qscripts/lib/ChunkVCF.scala | 2 +- .../gatk/queue/qscripts/lib/Vcf2Table.scala | 2 +- .../gatk/queue/qscripts/lib/VcfToPed.scala | 2 +- .../gatk/queue/extensions/cancer/MuTect.scala | 2 +- .../extensions/gatk/BamGatherFunction.scala | 2 +- .../extensions/gatk/CatVariantsGatherer.scala | 2 +- .../gatk/ContigScatterFunction.scala | 2 +- .../gatk/DistributedScatterFunction.scala | 2 +- .../queue/extensions/gatk/DoC/package.scala | 2 +- .../queue/extensions/gatk/GATKIntervals.scala | 2 +- .../extensions/gatk/GATKScatterFunction.scala | 2 +- .../gatk/IntervalScatterFunction.scala | 2 +- .../gatk/LocusScatterFunction.scala | 2 +- .../extensions/gatk/ReadScatterFunction.scala | 2 +- .../queue/extensions/gatk/TaggedFile.scala | 2 +- .../extensions/gatk/VcfGatherFunction.scala | 2 +- .../gatk/WriteFlankingIntervalsFunction.scala | 2 +- .../queue/extensions/gatk/XHMM/package.scala | 2 +- .../picard/AddOrReplaceReadGroups.scala | 2 +- .../picard/CalculateHsMetrics.scala | 2 +- .../picard/CollectGcBiasMetrics.scala | 2 +- .../picard/CollectMultipleMetrics.scala | 2 +- .../queue/extensions/picard/FastqToSam.scala | 2 +- .../extensions/picard/MarkDuplicates.scala | 2 +- .../extensions/picard/MergeSamFiles.scala | 2 +- .../extensions/picard/PicardBamFunction.scala | 2 +- .../picard/PicardMetricsFunction.scala | 2 +- .../queue/extensions/picard/ReorderSam.scala | 2 +- .../queue/extensions/picard/RevertSam.scala | 2 +- .../queue/extensions/picard/SamToFastq.scala | 2 +- .../queue/extensions/picard/SortSam.scala | 2 +- .../extensions/picard/ValidateSamFile.scala | 2 +- .../SamtoolsCommandLineFunction.scala | 2 +- .../samtools/SamtoolsIndexFunction.scala | 2 +- .../samtools/SamtoolsMergeFunction.scala | 2 +- .../gatk/queue/extensions/snpeff/SnpEff.scala | 2 +- .../gatk/GATKIntervalsUnitTest.scala | 2 +- .../gatk/QueueFeaturesQueueTest.scala | 2 +- .../examples/ExampleCountLociQueueTest.scala | 2 +- .../examples/ExampleCountReadsQueueTest.scala | 2 +- .../examples/ExamplePrintReadsQueueTest.scala | 2 +- .../examples/ExampleReadFilterQueueTest.scala | 2 +- .../ExampleRetryMemoryLimitQueueTest.scala | 2 +- .../examples/HelloWorldQueueTest.scala | 2 +- .../gatk/queue/QueueVersion.java | 2 +- .../gatk/queue/package-info.java | 2 +- .../gatk/queue/QCommandLine.scala | 2 +- .../gatk/queue/QCommandPlugin.scala | 2 +- .../gatk/queue/QException.scala | 2 +- .../broadinstitute/gatk/queue/QScript.scala | 2 +- .../gatk/queue/QScriptManager.scala | 2 +- .../broadinstitute/gatk/queue/QSettings.scala | 2 +- .../queue/engine/CommandLineJobManager.scala | 2 +- .../queue/engine/CommandLineJobRunner.scala | 2 +- .../engine/CommandLinePluginManager.scala | 2 +- .../gatk/queue/engine/FunctionEdge.scala | 2 +- .../queue/engine/InProcessJobManager.scala | 2 +- .../gatk/queue/engine/InProcessRunner.scala | 2 +- .../gatk/queue/engine/JobManager.scala | 2 +- .../gatk/queue/engine/JobRunInfo.scala | 2 +- .../gatk/queue/engine/JobRunner.scala | 2 +- .../gatk/queue/engine/MappingEdge.scala | 2 +- .../gatk/queue/engine/QEdge.scala | 2 +- .../gatk/queue/engine/QGraph.scala | 2 +- .../gatk/queue/engine/QGraphSettings.scala | 2 +- .../gatk/queue/engine/QNode.scala | 2 +- .../gatk/queue/engine/QStatusMessenger.scala | 2 +- .../gatk/queue/engine/RunnerStatus.scala | 2 +- .../queue/engine/drmaa/DrmaaJobManager.scala | 2 +- .../queue/engine/drmaa/DrmaaJobRunner.scala | 2 +- .../gridengine/GridEngineJobManager.scala | 2 +- .../gridengine/GridEngineJobRunner.scala | 2 +- .../queue/engine/lsf/Lsf706JobManager.scala | 2 +- .../queue/engine/lsf/Lsf706JobRunner.scala | 2 +- .../pbsengine/PbsEngineJobManager.scala | 2 +- .../engine/pbsengine/PbsEngineJobRunner.scala | 2 +- .../queue/engine/shell/ShellJobManager.scala | 2 +- .../queue/engine/shell/ShellJobRunner.scala | 2 +- .../queue/function/CommandLineFunction.scala | 2 +- .../queue/function/InProcessFunction.scala | 2 +- .../function/JavaCommandLineFunction.scala | 2 +- .../queue/function/ListWriterFunction.scala | 2 +- .../gatk/queue/function/QFunction.scala | 2 +- .../queue/function/RetryMemoryLimit.scala | 2 +- .../scattergather/CloneFunction.scala | 2 +- .../ConcatenateLogsFunction.scala | 2 +- .../scattergather/GatherFunction.scala | 2 +- .../scattergather/GathererFunction.scala | 2 +- .../scattergather/ScatterFunction.scala | 2 +- .../ScatterGatherableFunction.scala | 2 +- .../SimpleTextGatherFunction.scala | 2 +- .../library/clf/vcf/VCFExtractIntervals.scala | 2 +- .../library/clf/vcf/VCFExtractSamples.scala | 2 +- .../gatk/queue/library/ipf/SortByRef.scala | 2 +- .../library/ipf/vcf/VCFExtractIntervals.scala | 2 +- .../library/ipf/vcf/VCFExtractSamples.scala | 2 +- .../library/ipf/vcf/VCFExtractSites.scala | 2 +- .../library/ipf/vcf/VCFSimpleMerge.scala | 2 +- .../gatk/queue/util/ClassFieldCache.scala | 2 +- .../gatk/queue/util/CollectionUtils.scala | 2 +- .../gatk/queue/util/EmailMessage.scala | 2 +- .../gatk/queue/util/EmailSettings.scala | 2 +- .../gatk/queue/util/Logging.scala | 2 +- .../util/PrimitiveOptionConversions.scala | 2 +- .../gatk/queue/util/QJobReport.scala | 2 +- .../gatk/queue/util/QJobsReporter.scala | 2 +- .../gatk/queue/util/QScriptUtils.scala | 2 +- .../gatk/queue/util/ReflectionUtils.scala | 2 +- .../gatk/queue/util/RemoteFile.scala | 2 +- .../gatk/queue/util/RemoteFileConverter.scala | 2 +- .../gatk/queue/util/Retry.scala | 2 +- .../gatk/queue/util/RetryException.scala | 2 +- .../ScalaCompoundArgumentTypeDescriptor.scala | 2 +- .../gatk/queue/util/ShellUtils.scala | 2 +- .../queue/util/StringFileConversions.scala | 2 +- .../gatk/queue/util/SystemUtils.scala | 2 +- .../gatk/queue/util/TextFormatUtils.scala | 2 +- .../gatk/queue/util/VCF_BAM_utilities.scala | 2 +- .../CommandLineFunctionUnitTest.scala | 2 +- .../gatk/queue/pipeline/QueueTest.scala | 2 +- .../queue/pipeline/QueueTestEvalSpec.scala | 2 +- .../gatk/queue/pipeline/QueueTestSpec.scala | 2 +- .../gatk/queue/util/ShellUtilsUnitTest.scala | 2 +- .../util/StringFileConversionsUnitTest.scala | 2 +- .../gatk/queue/util/SystemUtilsUnitTest.scala | 2 +- .../gatk/tools/CatVariants.java | 2 +- .../gatk/tools/ListAnnotations.java | 2 +- .../walkers/annotator/AlleleBalance.java | 2 +- .../annotator/AlleleBalanceBySample.java | 2 +- .../tools/walkers/annotator/BaseCounts.java | 2 +- .../gatk/tools/walkers/annotator/LowMQ.java | 2 +- .../annotator/MappingQualityZeroBySample.java | 2 +- .../tools/walkers/annotator/NBaseCount.java | 2 +- .../gatk/tools/walkers/annotator/SnpEff.java | 2 +- .../tools/walkers/annotator/SnpEffUtil.java | 2 +- .../walkers/annotator/VariantAnnotator.java | 2 +- .../annotator/VariantAnnotatorEngine.java | 2 +- .../annotator/VariantOverlapAnnotator.java | 2 +- .../ActiveRegionBasedAnnotation.java | 2 +- .../interfaces/AnnotationHelpUtils.java | 2 +- .../AnnotationInterfaceManager.java | 2 +- .../annotator/interfaces/AnnotationType.java | 2 +- .../interfaces/AnnotatorCompatible.java | 2 +- .../interfaces/ExperimentalAnnotation.java | 2 +- .../interfaces/GenotypeAnnotation.java | 2 +- .../interfaces/InfoFieldAnnotation.java | 2 +- .../interfaces/RodRequiringAnnotation.java | 2 +- .../interfaces/StandardAnnotation.java | 2 +- .../interfaces/StandardUGAnnotation.java | 8 +-- .../VariantAnnotatorAnnotation.java | 2 +- .../interfaces/WorkInProgressAnnotation.java | 2 +- .../tools/walkers/coverage/CallableLoci.java | 2 +- .../walkers/coverage/CompareCallableLoci.java | 2 +- .../tools/walkers/coverage/CoverageUtils.java | 2 +- .../walkers/coverage/DepthOfCoverage.java | 2 +- .../coverage/DepthOfCoverageStats.java | 2 +- .../tools/walkers/coverage/DoCOutputType.java | 2 +- .../walkers/coverage/GCContentByInterval.java | 2 +- .../diagnostics/CoveredByNSamplesSites.java | 2 +- .../diagnostics/ErrorRatePerCycle.java | 2 +- .../diagnostics/ReadGroupProperties.java | 2 +- .../diagnostics/ReadLengthDistribution.java | 2 +- .../tools/walkers/diffengine/DiffObjects.java | 2 +- .../walkers/examples/GATKDocsExample.java | 2 +- .../walkers/examples/GATKPaperGenotyper.java | 2 +- .../fasta/FastaAlternateReferenceMaker.java | 2 +- .../walkers/fasta/FastaReferenceMaker.java | 2 +- .../tools/walkers/fasta/FastaSequence.java | 2 +- .../gatk/tools/walkers/fasta/FastaStats.java | 2 +- .../tools/walkers/filters/ClusteredSnps.java | 2 +- .../walkers/filters/FiltrationContext.java | 2 +- .../filters/FiltrationContextWindow.java | 2 +- .../walkers/filters/VariantFiltration.java | 2 +- .../HCMappingQualityFilter.java | 2 +- .../gatk/tools/walkers/help/WalkerDoclet.java | 2 +- .../help/WalkerDocumentationHandler.java | 2 +- .../gatk/tools/walkers/package-info.java | 2 +- .../gatk/tools/walkers/qc/CheckPileup.java | 2 +- .../gatk/tools/walkers/qc/CountBases.java | 2 +- .../gatk/tools/walkers/qc/CountIntervals.java | 2 +- .../gatk/tools/walkers/qc/CountLoci.java | 2 +- .../gatk/tools/walkers/qc/CountMales.java | 2 +- .../gatk/tools/walkers/qc/CountRODs.java | 2 +- .../gatk/tools/walkers/qc/CountRODsByRef.java | 2 +- .../tools/walkers/qc/CountReadEvents.java | 2 +- .../gatk/tools/walkers/qc/CountReads.java | 2 +- .../tools/walkers/qc/CountTerminusEvent.java | 2 +- .../tools/walkers/qc/DocumentationTest.java | 2 +- .../gatk/tools/walkers/qc/ErrorThrowing.java | 2 +- .../gatk/tools/walkers/qc/FlagStat.java | 2 +- .../gatk/tools/walkers/qc/Pileup.java | 2 +- .../gatk/tools/walkers/qc/PrintRODs.java | 2 +- .../gatk/tools/walkers/qc/QCRef.java | 2 +- .../tools/walkers/qc/ReadClippingStats.java | 2 +- .../tools/walkers/qc/RodSystemValidation.java | 2 +- .../tools/walkers/readutils/ClipReads.java | 2 +- .../tools/walkers/readutils/PrintReads.java | 2 +- .../walkers/readutils/ReadAdaptorTrimmer.java | 2 +- .../tools/walkers/readutils/SplitSamFile.java | 2 +- .../tools/walkers/rnaseq/ASEReadCounter.java | 2 +- .../walkers/varianteval/VariantEval.java | 2 +- .../varianteval/VariantEvalReportWriter.java | 2 +- .../varianteval/evaluators/CompOverlap.java | 2 +- .../varianteval/evaluators/CountVariants.java | 2 +- .../evaluators/IndelLengthHistogram.java | 2 +- .../varianteval/evaluators/IndelSummary.java | 2 +- .../MendelianViolationEvaluator.java | 2 +- .../evaluators/MultiallelicSummary.java | 2 +- .../evaluators/PrintMissingComp.java | 2 +- .../varianteval/evaluators/StandardEval.java | 2 +- .../evaluators/ThetaVariantEvaluator.java | 2 +- .../evaluators/TiTvVariantEvaluator.java | 2 +- .../evaluators/ValidationReport.java | 2 +- .../evaluators/VariantEvaluator.java | 2 +- .../evaluators/VariantSummary.java | 2 +- .../stratifications/AlleleCount.java | 2 +- .../stratifications/AlleleFrequency.java | 2 +- .../varianteval/stratifications/CompRod.java | 2 +- .../varianteval/stratifications/Contig.java | 2 +- .../varianteval/stratifications/CpG.java | 2 +- .../stratifications/Degeneracy.java | 2 +- .../DynamicStratification.java | 2 +- .../varianteval/stratifications/EvalRod.java | 2 +- .../varianteval/stratifications/Filter.java | 2 +- .../stratifications/FunctionalClass.java | 2 +- .../stratifications/IndelSize.java | 2 +- .../IntervalStratification.java | 2 +- .../stratifications/JexlExpression.java | 2 +- .../varianteval/stratifications/Novelty.java | 2 +- .../stratifications/OneBPIndel.java | 2 +- .../RequiredStratification.java | 2 +- .../varianteval/stratifications/Sample.java | 2 +- .../SnpEffPositionModifier.java | 2 +- .../StandardStratification.java | 2 +- .../stratifications/TandemRepeat.java | 2 +- .../stratifications/VariantStratifier.java | 2 +- .../stratifications/VariantType.java | 2 +- .../stratifications/manager/StratNode.java | 2 +- .../manager/StratNodeIterator.java | 2 +- .../manager/StratificationManager.java | 2 +- .../stratifications/manager/Stratifier.java | 2 +- .../walkers/varianteval/util/Analysis.java | 2 +- .../util/AnalysisModuleScanner.java | 2 +- .../walkers/varianteval/util/DataPoint.java | 2 +- .../varianteval/util/EvaluationContext.java | 2 +- .../walkers/varianteval/util/Molten.java | 2 +- .../util/SortableJexlVCMatchExp.java | 2 +- .../varianteval/util/VariantEvalUtils.java | 2 +- .../VQSRCalibrationCurve.java | 2 +- .../walkers/variantutils/CombineVariants.java | 2 +- .../variantutils/ConcordanceMetrics.java | 2 +- .../variantutils/FilterLiftedVariants.java | 2 +- .../variantutils/GenotypeConcordance.java | 2 +- .../LeftAlignAndTrimVariants.java | 2 +- .../variantutils/LiftoverVariants.java | 2 +- .../variantutils/RandomlySplitVariants.java | 2 +- .../walkers/variantutils/SelectHeaders.java | 2 +- .../walkers/variantutils/SelectVariants.java | 2 +- .../variantutils/ValidateVariants.java | 2 +- .../VariantValidationAssessor.java | 2 +- .../VariantsToAllelicPrimitives.java | 2 +- .../variantutils/VariantsToBinaryPed.java | 2 +- .../walkers/variantutils/VariantsToTable.java | 2 +- .../walkers/variantutils/VariantsToVCF.java | 2 +- .../tools/CatVariantsIntegrationTest.java | 2 +- .../tools/walkers/BAQIntegrationTest.java | 2 +- .../CNV/SymbolicAllelesIntegrationTest.java | 2 +- .../walkers/annotator/SnpEffUtilUnitTest.java | 2 +- .../coverage/CallableLociIntegrationTest.java | 2 +- ...pareCallableLociWalkerIntegrationTest.java | 2 +- .../DepthOfCoverageB36IntegrationTest.java | 2 +- .../DepthOfCoverageIntegrationTest.java | 2 +- .../DiffObjectsIntegrationTest.java | 2 +- .../filters/VariantFiltrationUnitTest.java | 8 +-- .../qc/CheckPileupIntegrationTest.java | 2 +- .../tools/walkers/qc/CountReadsUnitTest.java | 2 +- .../DictionaryConsistencyIntegrationTest.java | 2 +- .../walkers/qc/FlagStatIntegrationTest.java | 2 +- .../qc/PileupWalkerIntegrationTest.java | 2 +- .../ClipReadsWalkersIntegrationTest.java | 2 +- .../readutils/PrintReadsIntegrationTest.java | 2 +- .../readutils/PrintReadsLargeScaleTest.java | 2 +- .../walkers/readutils/PrintReadsUnitTest.java | 2 +- .../ReadAdaptorTrimmerIntegrationTest.java | 2 +- .../SplitSamFileIntegrationTest.java | 2 +- .../rnaseq/ASEReadCounterIntegrationTest.java | 2 +- .../FilterLiftedVariantsUnitTest.java | 2 +- .../variantutils/SelectVariantsUnitTest.java | 2 +- .../variantutils/VCFIntegrationTest.java | 2 +- .../java/htsjdk/samtools/GATKBAMFileSpan.java | 2 +- .../main/java/htsjdk/samtools/GATKBin.java | 2 +- .../main/java/htsjdk/samtools/GATKChunk.java | 2 +- .../htsjdk/samtools/PicardNamespaceUtils.java | 2 +- .../gatk/utils/AutoFormattingTime.java | 2 +- .../broadinstitute/gatk/utils/BaseUtils.java | 2 +- .../gatk/utils/BitSetUtils.java | 2 +- .../gatk/utils/ContigComparator.java | 2 +- .../gatk/utils/DeprecatedToolChecks.java | 2 +- .../broadinstitute/gatk/utils/GenomeLoc.java | 2 +- .../gatk/utils/GenomeLocParser.java | 2 +- .../gatk/utils/GenomeLocSortedSet.java | 2 +- .../gatk/utils/HasGenomeLocation.java | 2 +- .../gatk/utils/HeapSizeMonitor.java | 2 +- .../broadinstitute/gatk/utils/IndelUtils.java | 2 +- .../broadinstitute/gatk/utils/LRUCache.java | 2 +- .../MRUCachingSAMSequenceDictionary.java | 2 +- .../gatk/utils/MannWhitneyU.java | 2 +- .../broadinstitute/gatk/utils/MathUtils.java | 2 +- .../org/broadinstitute/gatk/utils/Median.java | 2 +- .../gatk/utils/MultiThreadedErrorTracker.java | 2 +- .../gatk/utils/NGSPlatform.java | 2 +- .../broadinstitute/gatk/utils/PathUtils.java | 2 +- .../gatk/utils/QualityUtils.java | 2 +- .../gatk/utils/R/RScriptExecutor.java | 2 +- .../utils/R/RScriptExecutorException.java | 2 +- .../gatk/utils/R/RScriptLibrary.java | 2 +- .../broadinstitute/gatk/utils/R/RUtils.java | 2 +- .../gatk/utils/SequenceDictionaryUtils.java | 2 +- .../gatk/utils/SequencerFlowClass.java | 2 +- .../gatk/utils/SimpleTimer.java | 2 +- .../gatk/utils/UnvalidatingGenomeLoc.java | 2 +- .../org/broadinstitute/gatk/utils/Utils.java | 2 +- .../gatk/utils/ValidationExclusion.java | 2 +- .../gatk/utils/activeregion/ActiveRegion.java | 2 +- .../activeregion/ActiveRegionReadState.java | 2 +- .../utils/activeregion/ActivityProfile.java | 2 +- .../activeregion/ActivityProfileState.java | 2 +- .../activeregion/BandPassActivityProfile.java | 2 +- .../gatk/utils/analysis/AminoAcid.java | 2 +- .../gatk/utils/analysis/AminoAcidTable.java | 2 +- .../gatk/utils/analysis/AminoAcidUtils.java | 2 +- .../broadinstitute/gatk/utils/baq/BAQ.java | 2 +- .../gatk/utils/classloader/JVMUtils.java | 2 +- .../gatk/utils/classloader/PluginManager.java | 2 +- .../classloader/ProtectedPackageSource.java | 2 +- .../classloader/PublicPackageSource.java | 2 +- .../gatk/utils/clipping/ClippingOp.java | 2 +- .../clipping/ClippingRepresentation.java | 2 +- .../gatk/utils/clipping/ReadClipper.java | 2 +- .../gatk/utils/codecs/beagle/BeagleCodec.java | 2 +- .../utils/codecs/beagle/BeagleFeature.java | 2 +- .../utils/codecs/hapmap/RawHapMapCodec.java | 2 +- .../utils/codecs/hapmap/RawHapMapFeature.java | 2 +- .../gatk/utils/codecs/refseq/RefSeqCodec.java | 2 +- .../utils/codecs/refseq/RefSeqFeature.java | 2 +- .../gatk/utils/codecs/refseq/Transcript.java | 2 +- .../codecs/sampileup/SAMPileupCodec.java | 2 +- .../codecs/sampileup/SAMPileupFeature.java | 2 +- .../utils/codecs/samread/SAMReadCodec.java | 2 +- .../utils/codecs/samread/SAMReadFeature.java | 2 +- .../utils/codecs/table/BedTableCodec.java | 2 +- .../gatk/utils/codecs/table/TableCodec.java | 2 +- .../gatk/utils/codecs/table/TableFeature.java | 2 +- .../utils/collections/DefaultHashMap.java | 2 +- .../utils/collections/ExpandingArrayList.java | 2 +- .../gatk/utils/collections/IndexedSet.java | 2 +- .../LoggingNestedIntegerArray.java | 2 +- .../utils/collections/NestedIntegerArray.java | 2 +- .../gatk/utils/collections/Pair.java | 2 +- .../gatk/utils/collections/Permutation.java | 2 +- .../gatk/utils/collections/PrimitivePair.java | 2 +- .../utils/collections/RODMergingIterator.java | 2 +- .../gatk/utils/commandline/Advanced.java | 2 +- .../gatk/utils/commandline/Argument.java | 2 +- .../utils/commandline/ArgumentCollection.java | 2 +- .../utils/commandline/ArgumentDefinition.java | 2 +- .../commandline/ArgumentDefinitionGroup.java | 2 +- .../commandline/ArgumentDefinitions.java | 2 +- .../utils/commandline/ArgumentException.java | 2 +- .../utils/commandline/ArgumentIOType.java | 2 +- .../gatk/utils/commandline/ArgumentMatch.java | 2 +- .../commandline/ArgumentMatchFileValue.java | 2 +- .../utils/commandline/ArgumentMatchSite.java | 2 +- .../commandline/ArgumentMatchSource.java | 2 +- .../commandline/ArgumentMatchSourceType.java | 2 +- .../commandline/ArgumentMatchStringValue.java | 2 +- .../utils/commandline/ArgumentMatchValue.java | 2 +- .../utils/commandline/ArgumentMatches.java | 2 +- .../utils/commandline/ArgumentSource.java | 2 +- .../commandline/ArgumentTypeDescriptor.java | 2 +- .../gatk/utils/commandline/ClassType.java | 2 +- .../utils/commandline/CommandLineProgram.java | 2 +- .../utils/commandline/CommandLineUtils.java | 2 +- .../EnumerationArgumentDefault.java | 2 +- .../gatk/utils/commandline/Gather.java | 2 +- .../gatk/utils/commandline/Gatherer.java | 2 +- .../gatk/utils/commandline/Hidden.java | 2 +- .../gatk/utils/commandline/Input.java | 2 +- .../IntervalArgumentCollection.java | 2 +- .../utils/commandline/IntervalBinding.java | 2 +- .../MissingArgumentValueException.java | 2 +- .../gatk/utils/commandline/Multiplex.java | 2 +- .../gatk/utils/commandline/Multiplexer.java | 2 +- .../gatk/utils/commandline/Output.java | 2 +- .../gatk/utils/commandline/ParsedArgs.java | 2 +- .../utils/commandline/ParsedListArgs.java | 2 +- .../gatk/utils/commandline/ParsingEngine.java | 2 +- .../ParsingEngineArgumentFiles.java | 2 +- .../ParsingEngineArgumentProvider.java | 2 +- .../gatk/utils/commandline/ParsingMethod.java | 2 +- .../gatk/utils/commandline/RodBinding.java | 2 +- .../commandline/RodBindingCollection.java | 2 +- .../gatk/utils/commandline/Tags.java | 2 +- .../gatk/utils/commandline/package-info.java | 2 +- .../gatk/utils/contexts/AlignmentContext.java | 2 +- .../utils/contexts/AlignmentContextUtils.java | 2 +- .../gatk/utils/contexts/ReferenceContext.java | 2 +- .../utils/diffengine/BAMDiffableReader.java | 2 +- .../gatk/utils/diffengine/DiffElement.java | 2 +- .../gatk/utils/diffengine/DiffEngine.java | 2 +- .../gatk/utils/diffengine/DiffNode.java | 2 +- .../gatk/utils/diffengine/DiffValue.java | 2 +- .../gatk/utils/diffengine/DiffableReader.java | 2 +- .../gatk/utils/diffengine/Difference.java | 2 +- .../diffengine/GATKReportDiffableReader.java | 2 +- .../utils/diffengine/VCFDiffableReader.java | 2 +- .../AlleleBiasedDownsamplingUtils.java | 2 +- .../utils/downsampling/DownsampleType.java | 2 +- .../gatk/utils/downsampling/Downsampler.java | 2 +- .../downsampling/DownsamplingMethod.java | 2 +- .../DownsamplingReadsIterator.java | 2 +- .../utils/downsampling/DownsamplingUtils.java | 2 +- .../downsampling/FractionalDownsampler.java | 2 +- .../FractionalDownsamplerFactory.java | 2 +- .../downsampling/LevelingDownsampler.java | 2 +- .../downsampling/PassThroughDownsampler.java | 2 +- .../PerSampleDownsamplingReadsIterator.java | 2 +- .../utils/downsampling/ReadsDownsampler.java | 2 +- .../downsampling/ReadsDownsamplerFactory.java | 2 +- .../downsampling/ReservoirDownsampler.java | 2 +- .../ReservoirDownsamplerFactory.java | 2 +- .../SimplePositionalDownsampler.java | 2 +- .../SimplePositionalDownsamplerFactory.java | 2 +- .../gatk/utils/duplicates/DupUtils.java | 2 +- .../gatk/utils/duplicates/DuplicateComp.java | 2 +- .../DynamicClassResolutionException.java | 2 +- .../gatk/utils/exceptions/GATKException.java | 2 +- .../exceptions/ReviewedGATKException.java | 2 +- .../gatk/utils/exceptions/UserException.java | 2 +- .../utils/fasta/ArtificialFastaUtils.java | 2 +- .../CachingIndexedFastaSequenceFile.java | 2 +- .../gatk/utils/fasta/package-info.java | 2 +- .../gatk/utils/file/FSLockWithShared.java | 2 +- .../utils/fragments/FragmentCollection.java | 2 +- .../gatk/utils/fragments/FragmentUtils.java | 2 +- .../gatk/utils/genotyper/AlleleList.java | 2 +- .../genotyper/AlleleListPermutation.java | 2 +- .../gatk/utils/genotyper/AlleleListUtils.java | 2 +- .../gatk/utils/genotyper/DiploidGenotype.java | 2 +- .../utils/genotyper/IndexedAlleleList.java | 2 +- .../utils/genotyper/IndexedSampleList.java | 2 +- .../utils/genotyper/MostLikelyAllele.java | 2 +- .../genotyper/PerReadAlleleLikelihoodMap.java | 2 +- .../gatk/utils/genotyper/ReadLikelihoods.java | 2 +- .../gatk/utils/genotyper/SampleList.java | 2 +- .../gatk/utils/genotyper/SampleListUtils.java | 2 +- .../gatk/utils/haplotype/EventMap.java | 2 +- .../gatk/utils/haplotype/Haplotype.java | 2 +- .../haplotype/HaplotypeBaseComparator.java | 2 +- .../haplotype/HaplotypeScoreComparator.java | 2 +- .../HaplotypeSizeAndBaseComparator.java | 2 +- .../gatk/utils/help/ApplicationDetails.java | 2 +- .../gatk/utils/help/DocletUtils.java | 2 +- .../utils/help/DocumentedGATKFeature.java | 2 +- .../help/DocumentedGATKFeatureHandler.java | 2 +- .../help/DocumentedGATKFeatureObject.java | 2 +- .../gatk/utils/help/ForumAPIUtils.java | 2 +- .../gatk/utils/help/ForumDiscussion.java | 2 +- .../gatk/utils/help/GATKDocUtils.java | 2 +- .../gatk/utils/help/GATKDocWorkUnit.java | 2 +- .../gatk/utils/help/GATKDoclet.java | 2 +- .../gatk/utils/help/GSONArgument.java | 2 +- .../gatk/utils/help/GSONWorkUnit.java | 2 +- .../help/GenericDocumentationHandler.java | 2 +- .../gatk/utils/help/HelpConstants.java | 2 +- .../gatk/utils/help/HelpFormatter.java | 2 +- .../help/ResourceBundleExtractorDoclet.java | 2 +- .../gatk/utils/instrumentation/Sizeof.java | 2 +- .../utils/interval/IntervalMergingRule.java | 2 +- .../gatk/utils/interval/IntervalSetRule.java | 2 +- .../gatk/utils/interval/IntervalUtils.java | 2 +- .../gatk/utils/io/FileExtension.java | 2 +- .../io/HardThresholdingOutputStream.java | 2 +- .../broadinstitute/gatk/utils/io/IOUtils.java | 2 +- .../gatk/utils/io/ReferenceBacked.java | 2 +- .../gatk/utils/io/Resource.java | 2 +- .../gatk/utils/iterators/GATKSAMIterator.java | 2 +- .../iterators/GATKSAMIteratorAdapter.java | 2 +- .../utils/iterators/PushbackIterator.java | 2 +- .../gatk/utils/jna/clibrary/JNAUtils.java | 2 +- .../gatk/utils/jna/clibrary/LibC.java | 2 +- .../gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java | 2 +- .../utils/jna/drmaa/v1_0/JnaJobTemplate.java | 2 +- .../gatk/utils/jna/drmaa/v1_0/JnaSession.java | 2 +- .../jna/drmaa/v1_0/JnaSessionFactory.java | 2 +- .../gatk/utils/jna/drmaa/v1_0/LibDrmaa.java | 2 +- .../gatk/utils/jna/lsf/v7_0_6/LibBat.java | 2 +- .../gatk/utils/jna/lsf/v7_0_6/LibLsf.java | 2 +- .../locusiterator/AlignmentStateMachine.java | 2 +- .../locusiterator/LIBSDownsamplingInfo.java | 2 +- .../utils/locusiterator/LIBSPerformance.java | 2 +- .../utils/locusiterator/LocusIterator.java | 2 +- .../locusiterator/LocusIteratorByState.java | 2 +- .../PerSampleReadStateManager.java | 2 +- .../utils/locusiterator/ReadStateManager.java | 2 +- .../locusiterator/SamplePartitioner.java | 2 +- .../utils/nanoScheduler/EOFMarkedValue.java | 2 +- .../utils/nanoScheduler/InputProducer.java | 2 +- .../gatk/utils/nanoScheduler/MapResult.java | 2 +- .../utils/nanoScheduler/MapResultsQueue.java | 2 +- .../utils/nanoScheduler/NSMapFunction.java | 2 +- .../nanoScheduler/NSProgressFunction.java | 2 +- .../utils/nanoScheduler/NSReduceFunction.java | 2 +- .../utils/nanoScheduler/NanoScheduler.java | 2 +- .../gatk/utils/nanoScheduler/Reducer.java | 2 +- .../gatk/utils/package-info.java | 2 +- .../gatk/utils/pairhmm/BatchPairHMM.java | 2 +- .../gatk/utils/pairhmm/Log10PairHMM.java | 2 +- .../gatk/utils/pairhmm/N2MemoryPairHMM.java | 2 +- .../gatk/utils/pairhmm/PairHMM.java | 2 +- .../gatk/utils/pairhmm/PairHMMModel.java | 2 +- .../utils/pairhmm/PairHMMReadyHaplotypes.java | 2 +- .../pileup/MergingPileupElementIterator.java | 2 +- .../gatk/utils/pileup/PileupElement.java | 2 +- .../utils/pileup/PileupElementFilter.java | 2 +- .../utils/pileup/PileupElementTracker.java | 2 +- .../gatk/utils/pileup/ReadBackedPileup.java | 2 +- .../utils/pileup/ReadBackedPileupImpl.java | 2 +- .../utils/progressmeter/ProgressMeter.java | 2 +- .../progressmeter/ProgressMeterDaemon.java | 2 +- .../progressmeter/ProgressMeterData.java | 2 +- .../gatk/utils/recalibration/EventType.java | 2 +- .../gatk/utils/refdata/RODRecordListImpl.java | 2 +- .../utils/refdata/RefMetaDataTracker.java | 2 +- .../ReferenceDependentFeatureCodec.java | 2 +- .../utils/refdata/ReferenceOrderedDatum.java | 2 +- .../utils/refdata/SeekableRODIterator.java | 50 +++++++++---------- .../utils/refdata/VariantContextAdaptors.java | 2 +- .../gatk/utils/refdata/package-info.java | 2 +- .../utils/refdata/tracks/FeatureManager.java | 2 +- .../refdata/tracks/IndexDictionaryUtils.java | 2 +- .../gatk/utils/refdata/tracks/RMDTrack.java | 2 +- .../utils/refdata/tracks/RMDTrackBuilder.java | 2 +- .../utils/FeatureToGATKFeatureIterator.java | 2 +- .../refdata/utils/FlashBackIterator.java | 2 +- .../gatk/utils/refdata/utils/GATKFeature.java | 2 +- .../LocationAwareSeekableRODIterator.java | 2 +- .../gatk/utils/refdata/utils/RMDTriplet.java | 2 +- .../utils/refdata/utils/RODRecordList.java | 2 +- .../gatk/utils/report/GATKReport.java | 2 +- .../gatk/utils/report/GATKReportColumn.java | 2 +- .../utils/report/GATKReportColumnFormat.java | 2 +- .../gatk/utils/report/GATKReportDataType.java | 2 +- .../gatk/utils/report/GATKReportGatherer.java | 2 +- .../gatk/utils/report/GATKReportTable.java | 2 +- .../gatk/utils/report/GATKReportVersion.java | 2 +- .../utils/runtime/CapturedStreamOutput.java | 2 +- .../utils/runtime/InputStreamSettings.java | 2 +- .../utils/runtime/OutputStreamSettings.java | 2 +- .../gatk/utils/runtime/ProcessController.java | 2 +- .../gatk/utils/runtime/ProcessOutput.java | 2 +- .../gatk/utils/runtime/ProcessSettings.java | 2 +- .../gatk/utils/runtime/RuntimeUtils.java | 2 +- .../gatk/utils/runtime/StreamLocation.java | 2 +- .../gatk/utils/runtime/StreamOutput.java | 2 +- .../utils/sam/AlignmentStartComparator.java | 2 +- .../AlignmentStartWithNoTiesComparator.java | 2 +- .../gatk/utils/sam/AlignmentUtils.java | 2 +- .../gatk/utils/sam/ArtificialBAMBuilder.java | 2 +- .../sam/ArtificialGATKSAMFileWriter.java | 2 +- .../sam/ArtificialMultiSampleReadStream.java | 2 +- .../sam/ArtificialPatternedSAMIterator.java | 2 +- .../utils/sam/ArtificialSAMFileReader.java | 2 +- .../gatk/utils/sam/ArtificialSAMIterator.java | 2 +- .../utils/sam/ArtificialSAMQueryIterator.java | 2 +- .../gatk/utils/sam/ArtificialSAMUtils.java | 2 +- .../sam/ArtificialSingleSampleReadStream.java | 2 +- ...ificialSingleSampleReadStreamAnalyzer.java | 2 +- .../gatk/utils/sam/CigarUtils.java | 2 +- .../gatk/utils/sam/GATKSAMFileWriter.java | 2 +- .../utils/sam/GATKSAMReadGroupRecord.java | 2 +- .../gatk/utils/sam/GATKSAMRecord.java | 2 +- .../gatk/utils/sam/GATKSAMRecordIterator.java | 2 +- ...eadUnclippedStartWithNoTiesComparator.java | 2 +- .../gatk/utils/sam/ReadUtils.java | 2 +- .../gatk/utils/sam/SAMReaderBuilder.java | 2 +- .../gatk/utils/sam/SAMReaderID.java | 2 +- .../utils/sam/SimplifyingSAMFileWriter.java | 2 +- .../gatk/utils/sam/package-info.java | 2 +- .../GlobalEdgeGreedySWPairwiseAlignment.java | 2 +- .../gatk/utils/smithwaterman/Parameters.java | 2 +- .../smithwaterman/SWPairwiseAlignment.java | 2 +- .../SWPairwiseAlignmentMain.java | 2 +- .../utils/smithwaterman/SWParameterSet.java | 2 +- .../utils/smithwaterman/SmithWaterman.java | 2 +- .../gatk/utils/text/ListFileUtils.java | 2 +- .../gatk/utils/text/TextFormattingUtils.java | 2 +- .../gatk/utils/text/XReadLines.java | 2 +- .../EfficiencyMonitoringThreadFactory.java | 2 +- .../utils/threading/NamedThreadFactory.java | 2 +- .../threading/ThreadEfficiencyMonitor.java | 2 +- .../utils/threading/ThreadLocalArray.java | 2 +- .../utils/threading/ThreadPoolMonitor.java | 2 +- .../gatk/utils/threading/package-info.java | 2 +- .../variant/ChromosomeCountConstants.java | 2 +- .../gatk/utils/variant/GATKVCFConstants.java | 2 +- .../utils/variant/GATKVCFHeaderLines.java | 2 +- .../gatk/utils/variant/GATKVCFIndexType.java | 2 +- .../variant/GATKVariantContextUtils.java | 2 +- .../utils/variant/HomoSapiensConstants.java | 2 +- .../gatk/utils/variant/VCIterable.java | 2 +- .../gatk/utils/wiggle/WiggleHeader.java | 2 +- .../gatk/utils/wiggle/WiggleWriter.java | 2 +- .../samtools/GATKBAMFileSpanUnitTest.java | 2 +- .../htsjdk/samtools/GATKChunkUnitTest.java | 2 +- .../utils/AutoFormattingTimeUnitTest.java | 2 +- .../broadinstitute/gatk/utils/BaseTest.java | 2 +- .../gatk/utils/BaseUtilsUnitTest.java | 2 +- .../gatk/utils/BitSetUtilsUnitTest.java | 2 +- .../gatk/utils/ExampleToCopyUnitTest.java | 2 +- .../gatk/utils/GATKTextReporter.java | 2 +- .../gatk/utils/GenomeLocParserBenchmark.java | 2 +- .../gatk/utils/GenomeLocParserUnitTest.java | 2 +- .../utils/GenomeLocSortedSetUnitTest.java | 2 +- .../gatk/utils/GenomeLocUnitTest.java | 2 +- .../org/broadinstitute/gatk/utils/MD5DB.java | 2 +- .../gatk/utils/MD5Mismatch.java | 2 +- ...achingSAMSequencingDictionaryUnitTest.java | 2 +- .../broadinstitute/gatk/utils/MWUnitTest.java | 2 +- .../gatk/utils/MathUtilsUnitTest.java | 2 +- .../gatk/utils/MedianUnitTest.java | 2 +- .../gatk/utils/NGSPlatformUnitTest.java | 2 +- .../gatk/utils/PathUtilsUnitTest.java | 2 +- .../gatk/utils/QualityUtilsUnitTest.java | 2 +- .../gatk/utils/R/RScriptExecutorUnitTest.java | 2 +- .../gatk/utils/R/RScriptLibraryUnitTest.java | 2 +- .../gatk/utils/R/RUtilsUnitTest.java | 2 +- .../SequenceDictionaryUtilsUnitTest.java | 2 +- .../gatk/utils/SimpleTimerUnitTest.java | 2 +- .../gatk/utils/TestNGTestTransformer.java | 2 +- .../gatk/utils/UtilsUnitTest.java | 2 +- .../activeregion/ActiveRegionUnitTest.java | 2 +- .../ActivityProfileStateUnitTest.java | 2 +- .../activeregion/ActivityProfileUnitTest.java | 2 +- .../BandPassActivityProfileUnitTest.java | 2 +- .../gatk/utils/baq/BAQUnitTest.java | 2 +- .../utils/classloader/JVMUtilsUnitTest.java | 2 +- .../utils/clipping/ReadClipperTestUtils.java | 2 +- .../utils/clipping/ReadClipperUnitTest.java | 2 +- .../utils/codecs/hapmap/HapMapUnitTest.java | 2 +- .../collections/DefaultHashMapUnitTest.java | 2 +- .../ExpandingArrayListUnitTest.java | 2 +- .../ArgumentMatchSiteUnitTest.java | 2 +- .../ArgumentMatchSourceUnitTest.java | 2 +- .../commandline/ParsingEngineUnitTest.java | 2 +- .../RodBindingCollectionUnitTest.java | 2 +- .../utils/commandline/RodBindingUnitTest.java | 2 +- ...AlleleBiasedDownsamplingUtilsUnitTest.java | 2 +- ...chingIndexedFastaSequenceFileUnitTest.java | 2 +- .../utils/file/FSLockWithSharedUnitTest.java | 2 +- .../fragments/FragmentUtilsBenchmark.java | 2 +- .../fragments/FragmentUtilsUnitTest.java | 2 +- .../utils/haplotype/EventMapUnitTest.java | 2 +- .../utils/haplotype/HaplotypeUnitTest.java | 2 +- .../utils/interval/IntervalUtilsUnitTest.java | 2 +- .../gatk/utils/io/IOUtilsUnitTest.java | 2 +- .../gatk/utils/jna/clibrary/LibCUnitTest.java | 2 +- .../jna/drmaa/v1_0/JnaSessionQueueTest.java | 2 +- .../jna/drmaa/v1_0/LibDrmaaQueueTest.java | 2 +- .../utils/jna/lsf/v7_0_6/LibBatQueueTest.java | 2 +- .../AlignmentStateMachineUnitTest.java | 2 +- .../utils/locusiterator/LIBS_position.java | 2 +- .../locusiterator/LocusIteratorBenchmark.java | 2 +- .../LocusIteratorByStateBaseTest.java | 2 +- .../LocusIteratorByStateUnitTest.java | 2 +- .../PerSampleReadStateManagerUnitTest.java | 2 +- .../nanoScheduler/InputProducerUnitTest.java | 2 +- .../nanoScheduler/MapResultUnitTest.java | 2 +- .../nanoScheduler/NanoSchedulerUnitTest.java | 2 +- .../utils/nanoScheduler/ReducerUnitTest.java | 2 +- .../utils/pileup/PileupElementUnitTest.java | 2 +- .../pileup/ReadBackedPileupUnitTest.java | 2 +- .../ProgressMeterDaemonUnitTest.java | 2 +- .../ProgressMeterDataUnitTest.java | 2 +- .../recalibration/EventTypeUnitTest.java | 2 +- .../refdata/RefMetaDataTrackerUnitTest.java | 2 +- .../tracks/FeatureManagerUnitTest.java | 2 +- .../tracks/RMDTrackBuilderUnitTest.java | 2 +- .../CheckableCloseableTribbleIterator.java | 2 +- .../FeatureToGATKFeatureIteratorUnitTest.java | 2 +- .../utils/FlashBackIteratorUnitTest.java | 2 +- .../refdata/utils/TestFeatureReader.java | 2 +- .../refdata/utils/TestRMDTrackBuilder.java | 2 +- .../gatk/utils/report/GATKReportUnitTest.java | 2 +- .../report/ReportMarshallerUnitTest.java | 2 +- .../runtime/ProcessControllerUnitTest.java | 2 +- .../utils/runtime/RuntimeUtilsUnitTest.java | 2 +- .../utils/sam/AlignmentUtilsUnitTest.java | 2 +- .../sam/ArtificialBAMBuilderUnitTest.java | 2 +- ...rtificialPatternedSAMIteratorUnitTest.java | 2 +- .../sam/ArtificialSAMFileWriterUnitTest.java | 2 +- .../ArtificialSAMQueryIteratorUnitTest.java | 2 +- .../utils/sam/ArtificialSAMUtilsUnitTest.java | 2 +- ...ificialSingleSampleReadStreamUnitTest.java | 2 +- .../gatk/utils/sam/GATKSAMRecordUnitTest.java | 2 +- .../gatk/utils/sam/ReadUtilsUnitTest.java | 2 +- .../smithwaterman/SmithWatermanBenchmark.java | 2 +- .../utils/text/ListFileUtilsUnitTest.java | 2 +- .../text/TextFormattingUtilsUnitTest.java | 2 +- ...ciencyMonitoringThreadFactoryUnitTest.java | 2 +- .../threading/ThreadPoolMonitorUnitTest.java | 2 +- .../GATKVariantContextUtilsUnitTest.java | 2 +- .../variant/VariantContextBenchmark.java | 2 +- 1522 files changed, 1669 insertions(+), 1664 deletions(-) diff --git a/licensing/private_license.txt b/licensing/private_license.txt index a9d39041c..bbb8dcf9e 100644 --- a/licensing/private_license.txt +++ b/licensing/private_license.txt @@ -24,7 +24,7 @@ LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic 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 2012-2014 Broad Institute, Inc. +Copyright 2012-2015 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 a9d39041c..bbb8dcf9e 100644 --- a/licensing/protected_license.txt +++ b/licensing/protected_license.txt @@ -24,7 +24,7 @@ LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic 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 2012-2014 Broad Institute, Inc. +Copyright 2012-2015 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 648ec8fc3..c53c5b34a 100644 --- a/licensing/public_license.txt +++ b/licensing/public_license.txt @@ -1,4 +1,4 @@ -Copyright (c) 2012 The Broad Institute +Copyright 2012-2015 Broad 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 48a393cb6..00b42a871 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 @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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 de7cdd4c6..2f592bcb6 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 @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * 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”). -* +* * 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. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 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. -* +* * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive 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 5f4d7dc0b..3120995ec 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 @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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 d49bee6a5..33066ffb0 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 @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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 997f0e9ef..3bb34de38 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 @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/arguments/GenotypeCalculationArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java index 5974ff3f4..3ffefcf0e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/BQSRGatherer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java index 9ad2282ea..8e663a73b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/BQSRReadTransformer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java index b524ad08a..4c8e1b16c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/BaseRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java index 9095f695e..3e0a27adb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/QualQuantizer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java index b01359fca..d9998596d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/QuantizationInfo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java index e054805af..2f2151672 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/ReadCovariates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java index c02dd4881..a21878740 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/RecalDatum.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java index c92ef1773..43a1d0826 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/RecalDatumNode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java index 14b4c762b..d9ad4a7e1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/RecalUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java index f2f33ee59..c60b1bf1f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/RecalibrationArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java index dcf7ed737..88ea9496a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/RecalibrationReport.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java index a9b401c2b..b9ca005a8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/RecalibrationTables.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java index ad227f9bd..70323ad14 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/ContextCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java index f1ef944dc..fa3dc4045 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/Covariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java index 4c984c10b..2879efb35 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/CycleCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java index a76a13e4a..23560b627 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/ExperimentalCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java index c276f43ec..4cc1d5b98 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/QualityScoreCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java index 889e00b9a..6b5243b44 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/ReadGroupCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java index 9f4c34463..9fffce30a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/RepeatCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java index f5d3e24b8..7a876db8c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/RepeatLengthCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java index fb6aeaf85..96cd80d91 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java index 10a7f6672..ff70758b5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/RepeatUnitCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java index d961b1460..56da591f2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/RequiredCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java index 8f2155ff2..a064bd32b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/engine/recalibration/covariates/StandardCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java index 82e2bd199..9330ae724 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/package-info.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java index 8cc6647b6..8e1822f2a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/AlleleCountBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java index f66390fc1..b83178f3d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/AnnotationUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java index aa736b2d1..c500c1b3c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * 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”). -* +* * 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. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 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. -* +* * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java index 7bdc365f1..9605c94eb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/ChromosomeCounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java index 6f0bba28e..c990ffd20 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/ClippingRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java index 3e70eea57..4963555b4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/Coverage.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java index f8404800e..bbdd10530 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/DepthPerAlleleBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java index 536f196c4..e5d6942d6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/DepthPerSampleHC.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java index 50a640482..318309b57 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/FisherStrand.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java index eb8b17ee4..61cba0875 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/GCContent.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java index 6dc097583..94a1ddb7b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/GenotypeSummaries.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java index 7f01f56db..445a90615 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/HaplotypeScore.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java index 44c38e757..e68696844 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/HardyWeinberg.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java index 9bf17a721..1762560df 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/HomopolymerRun.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java index 4bc2151fe..85c83fa1f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/InbreedingCoeff.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java index 458a1b696..a4ddd71db 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/LikelihoodRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java index d18302e25..e05a31f57 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/MVLikelihoodRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java index 1cc87240b..7cfc34b58 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/MappingQualityRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java index 883c878b6..f93954258 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/MappingQualityZero.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java index 2b81d45c4..af0d0ceef 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/PossibleDeNovo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java index 6471488a5..5208c34ea 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/QualByDepth.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java index adff9dc33..4b544709d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/RMSMappingQuality.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java index 038545cf4..534357d43 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/RankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java index c257a05ff..999ebb8cd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/ReadPosRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java index 2c49355f9..c39f872f9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/SampleList.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java index c1c226a81..dae9ab9b2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/SpanningDeletions.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java index 1aeb79a6b..1e87377d2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/StrandAlleleCountsBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandAlleleCountsBySample.java index 21632b5eb..abe330883 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandAlleleCountsBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandAlleleCountsBySample.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/StrandBiasBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java index fdfa06241..115a68d20 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/StrandBiasTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java index 40d8cecf6..8978759fb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/StrandOddsRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java index 96913ceb9..35986bdc7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/TandemRepeatAnnotator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java index 9d5ec3608..80ea1ab4c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/TransmissionDisequilibriumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java index a96878a0f..2ff64073c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/annotator/VariantType.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java index c92cac17c..a1191bda9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/bqsr/AnalyzeCovariates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java index cd68e028a..1419180a9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/bqsr/BaseRecalibrator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java index 2c6744f97..5626ce7a1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/bqsr/ReadRecalibrationInfo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java index c3914216d..6a2603cef 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/bqsr/RecalibrationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java index aa20c9656..94ee44f3e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/BaseCoverageDistribution.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java index 81c080d17..dadd5a5fc 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/FindCoveredIntervals.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java index 6f1718430..cd87a845a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/AbstractStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/AbstractStratification.java index 1d52c4558..643c7ec2b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/AbstractStratification.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/AbstractStratification.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/CallableStatus.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/CallableStatus.java index ae56cd3e9..9a7f635a5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/CallableStatus.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/CallableStatus.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/DiagnoseTargets.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java index 56097e625..5a4c2e122 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/IntervalMetric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalMetric.java index 71249233d..5cd19038e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalMetric.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalMetric.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/IntervalStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java index 4261eee4c..53cdc11da 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/LocusMetric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetric.java index 20828854a..411fc9e49 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetric.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetric.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/LocusMetricCoverageGap.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java index 69b297dc0..b088b2184 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java index 33b32df73..33b1f9adc 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/LocusMetricLowCoverage.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java index d7f0f01b1..fbfca4146 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/LocusMetricPoorQuality.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java index e6aed49b7..5c22a57ea 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/LocusStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStratification.java index d8af7e846..b20cf8250 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStratification.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStratification.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/Metric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/Metric.java index b5ac8eaf1..6b219c30b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/Metric.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/Metric.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/PluginUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/PluginUtils.java index d7550b389..3d9aaaebd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/PluginUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/PluginUtils.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/SampleMetric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetric.java index 09325b706..b92f727bd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetric.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetric.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/SampleMetricBadMates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java index dc32b36e8..05e95e105 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/SampleMetricNoReads.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java index dea34836b..0a517bfaa 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/SampleStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleStratification.java index e4c8830f7..1d0d233da 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleStratification.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleStratification.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/diagnosetargets/ThresHolder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/ThresHolder.java index 7201b29ab..9bb5da08d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/ThresHolder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/ThresHolder.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/missing/Metrics.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/Metrics.java index 53c33c122..490343940 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/Metrics.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/Metrics.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/diagnostics/missing/QualifyMissingIntervals.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java index 36cf28696..6674faca6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/AFPriorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AFPriorProvider.java index 6bc7ea732..7e988e69b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AFPriorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AFPriorProvider.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/AlleleLikelihoodMatrixMapper.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java index 54ea7da0a..c14540bb0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/BaseMismatchModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/BaseMismatchModel.java index 3614de7b4..c2722c277 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/BaseMismatchModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/BaseMismatchModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/ConsensusAlleleCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java index 96f432dc1..90caf37a3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/CustomAFPriorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java index dd29ee205..caa264a00 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java index a2ce9a24d..fb2a22e8f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/ErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java index 71587fe3e..1935ebe66 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GeneralPloidyGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java index 984215df3..6a80c7b92 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java index 49e49d82d..5c30fc6a0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java index 3a65a3a9e..cd2986747 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java index c0e2ea95e..10e409309 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GeneralPloidySNPGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java index 6c9a9c7a5..8da146fe2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java index 93b7524db..bbf3511ac 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GenotypeAlleleCounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java index c7762996d..9c1e72edb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GenotypeLikelihoodCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java index 9922483cc..c4dc9520b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GenotypeLikelihoodCalculators.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java index 058c744fb..cb2578a20 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index b32f291f9..550817d2b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GenotypePriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypePriors.java index 5f4fbb894..2e66ff201 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypePriors.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypePriors.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GenotypingData.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java index c73690a84..024f15556 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java index b144170a7..ab6bc3b77 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GenotypingLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java index f06a40b73..d016f19fd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GenotypingModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java index 4dfb8d312..983c81f07 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/GenotypingOutputMode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingOutputMode.java index e7669971f..683c74d9b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingOutputMode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingOutputMode.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/HeterozygosityAFPriorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterozygosityAFPriorProvider.java index 3466c2a94..187923cc4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterozygosityAFPriorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterozygosityAFPriorProvider.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/HomogeneousPloidyModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java index dee370eec..79f2725e4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 7ee4a9aca..a3d6abb07 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/InfiniteRandomMatingPopulationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java index 1589e8374..a1aa8b66d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/OutputMode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/OutputMode.java index c3a2e3b63..d6410fd86 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/OutputMode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/OutputMode.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/PloidyModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java index 1ad1a2241..902b89466 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/PoolGenotypePriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PoolGenotypePriors.java index eb6b061e3..80da4cb10 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PoolGenotypePriors.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PoolGenotypePriors.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/ProbabilityVector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ProbabilityVector.java index 3767aa676..7f728db14 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ProbabilityVector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ProbabilityVector.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 9f8e88fac..7497a22d0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/StandardCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java index b2bd306fc..873752bdd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/UnifiedArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java index 08e13da1b..da04daca7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/UnifiedGenotyper.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java index bfcfd91c2..6a96d4b9f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/UnifiedGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java index 989905705..7abbd432e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/VariantCallContext.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/VariantCallContext.java index c02d0552c..ec9d048f1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/VariantCallContext.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/VariantCallContext.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/AFCalculationResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java index 9e4bd3e09..8f38456d2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/AFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculator.java index 0f243aed9..33c5114e7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/AFCalculatorFactory.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorFactory.java index a44c2a0c6..68e10f746 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorFactory.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorFactory.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/AFCalculatorImplementation.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorImplementation.java index b3c274ef1..9058edce4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorImplementation.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorImplementation.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/AFCalculatorPerformanceTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java index e97b9ca79..727b1b32d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/AFCalculatorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorProvider.java index 5a0e4c1c7..9025c3481 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorProvider.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/AFCalculatorTestBuilder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorTestBuilder.java index 108aeb8f6..21cb74d40 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorTestBuilder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorTestBuilder.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/ConcurrentAFCalculatorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ConcurrentAFCalculatorProvider.java index 64c38ca24..ae1e07b96 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ConcurrentAFCalculatorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ConcurrentAFCalculatorProvider.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/DiploidExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalculator.java index 3bdc53f1e..fee15363e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalculator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/ExactACcounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACcounts.java index 5696b6667..64e0199ee 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACcounts.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACcounts.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/ExactACset.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACset.java index e5879dfa1..402e6b257 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACset.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACset.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/ExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalculator.java index 3437c6da3..876eb1af5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalculator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/ExactCallLogger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactCallLogger.java index 5927b7561..dee29073b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactCallLogger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactCallLogger.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/FixedAFCalculatorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java index 53bfbcbe6..58f2b8763 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/GeneralPloidyExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalculator.java index 56859e540..d4c26b7e5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalculator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProvider.java index 13d9b0e20..afa4501f6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProvider.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java index 4ca9d7a56..2c9cb2a36 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/OriginalDiploidExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalculator.java index 4f61d438d..4f2b1cb35 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalculator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/ReferenceDiploidExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalculator.java index 05a90fd64..1b6b7aa39 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalculator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/genotyper/afcalc/StateTracker.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java index 9347ad2b5..66e9417d5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/ActiveRegionTrimmer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTrimmer.java index 6a8564b28..4644a779b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTrimmer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTrimmer.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/AssemblyBasedCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java index 6ab211cb9..42432c9ae 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/AssemblyResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResult.java index 291d6da7a..201aa5aa1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResult.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResult.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/AssemblyResultSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSet.java index b910ba2f4..c32e814bb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSet.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSet.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/EventBlock.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlock.java index 34536a5fe..4ea2bd579 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlock.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlock.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/EventBlockFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlockFinder.java index b87be5e0f..4fbd027ae 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlockFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlockFinder.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java index b70765402..88864a3af 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java index 91120f43d..5e3556bda 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java index 242e5b867..e2a1ba850 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/HaplotypeCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java index 1a4b4af39..b2210cd25 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java index e1e449409..1ca9e6c9d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/HaplotypeLDCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java index cf202bf5f..47706085b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/HaplotypeResolver.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java index 8bf383240..77a77ba38 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/HaplotypeRoute.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeRoute.java index 4e09a52e3..3b7f5cac0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeRoute.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeRoute.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/HeterogeneousKmerSizeResolution.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java index 4eeef5504..f8f1fa52e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/KMerCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounter.java index 53e47941b..afdb5cd0e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounter.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/Kmer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Kmer.java index 574ac416c..b51f130e1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Kmer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Kmer.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/KmerSequence.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequence.java index eaae1f74c..411c33871 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequence.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequence.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/KmerSequenceGraphMap.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequenceGraphMap.java index cdfddf56c..a74430951 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequenceGraphMap.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequenceGraphMap.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/LDMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java index 7d17e7502..a5b1c233e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/LikelihoodEngineArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java index f3ec62a31..8daffb915 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * 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”). -* +* * 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. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 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. -* +* * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. @@ -48,6 +48,7 @@ * 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ + package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.broadinstitute.gatk.utils.commandline.Advanced; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngine.java index 6081b511d..9651d4533 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngine.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/MergeVariantsAcrossHaplotypes.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java index 7e42a8742..1cd949014 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java index be7bdd98a..fc1ed6a16 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/RandomLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java index 7a134a380..6e14466d2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/ReadAnchoring.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadAnchoring.java index ef6cea2c7..5ad254b79 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadAnchoring.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadAnchoring.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/ReadCost.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadCost.java index 261dfbe87..60db1fc46 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadCost.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadCost.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/ReadErrorCorrector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrector.java index df0d37266..b307fc47e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrector.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/ReadLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java index 6dbcd161e..42961f812 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/ReadSegmentComparator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentComparator.java index 012d3c621..c6dd5c9c1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentComparator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentComparator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/ReadSegmentCost.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentCost.java index 8abfed1a5..bb51c7e37 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentCost.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentCost.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/ReadThreadingAssemblerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingAssemblerArgumentCollection.java index 14b6b4361..743b92ce7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingAssemblerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingAssemblerArgumentCollection.java @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * 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”). -* +* * 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. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 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. -* +* * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. @@ -48,6 +48,7 @@ * 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ + package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RefVsAnyResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RefVsAnyResult.java index 2a404dac0..3e25e6794 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RefVsAnyResult.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RefVsAnyResult.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/ReferenceConfidenceMode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceMode.java index b18ae19aa..74df4872a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceMode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceMode.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/ReferenceConfidenceModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java index 6f62457ec..18dec15c3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java index 04788e25e..fb397963a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/BaseEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java index a11331502..63cb82174 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/BaseGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java index be049fa3f..973c9ca27 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/BaseGraphIterator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java index 2c07ff48f..daa9b48f1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/BaseVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java index 8d4e4d6d5..5fd4f8fff 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/CommonSuffixSplitter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java index 8cbca1aad..03c8c1424 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/DeBruijnVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java index 658ac42ba..4d436282e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java index 9a5b62015..ecb5b4b87 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java index dc086dc68..e0d084c75 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/GraphUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java index 1a8514f23..7dfbb1b0e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/KBestHaplotype.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java index 1943765f8..2f9717757 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/KBestHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java index 16546b39c..343b6b1c7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/KBestSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java index 92ebbe1af..2a2ea9a1d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/KmerSearchableGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java index 2d208f919..171aa70e6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/LowWeightChainPruner.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java index 18be20f22..6f6c00b6f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/MultiSampleEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java index 067ab49d0..d63d88fb8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/Path.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java index 7a4b3caee..1a990e0a1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/PathBuilder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilder.java index cd72c899d..64a60ab3b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilder.java @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * 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”). -* +* * 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. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 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. -* +* * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. @@ -48,6 +48,7 @@ * 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ + package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import java.util.ArrayList; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java index 355897e96..aedfd127f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/Route.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java index 6ba820721..69166699f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/RouteFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java index 7194a2670..a4e59005b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/SeqGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java index e6b4c297a..7c8d45086 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/SeqVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java index 85c04fe42..ec5fd5fbe 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/SharedSequenceMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java index 80fdb148d..66452e229 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/SharedVertexSequenceSplitter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java index 5b5d5bcd9..48cf29ebe 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/TestGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java index 674a36afb..96040a64d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/graphs/VertexOrder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java index eb9055163..27e413cf2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/readthreading/DanglingChainMergingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java index 1dd1c4c3e..9ceed6b15 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/readthreading/HaplotypeGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java index b5c334e0b..79ceeffb5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/readthreading/MultiDeBruijnVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java index fbe4c874c..6053ac550 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/readthreading/ReadThreadingAssembler.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java index f9de3173a..8985ede87 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/readthreading/ReadThreadingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java index 5669d65ed..ace1b80a1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/haplotypecaller/readthreading/SequenceForKmers.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java index 0c9feb746..3ae440b1b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/indels/ConstrainedMateFixingManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java index cd4f359b4..10c118c31 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/indels/HaplotypeIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java index f5639a982..1195c9bb5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/indels/IndelRealigner.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java index 75df30550..9c03a9bb4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/indels/LeftAlignIndels.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java index a6afa812a..7421311ff 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/indels/PairHMMIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java index ba9c985db..dd502a354 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/indels/ReadBin.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java index f1b68f3d8..9d9975cea 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/indels/RealignerTargetCreator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java index a81af2e5a..06a4cea91 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/AllelePair.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/AllelePair.java index e57d0a97a..47c80c9f3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/AllelePair.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/AllelePair.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/BaseArray.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/BaseArray.java index 1eef64f1c..100c31d36 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/BaseArray.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/BaseArray.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/CardinalityCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CardinalityCounter.java index fc43b538f..db9162fe4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CardinalityCounter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CardinalityCounter.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/CloneableIteratorLinkedList.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CloneableIteratorLinkedList.java index 008f3aaf9..cfbd823b7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CloneableIteratorLinkedList.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CloneableIteratorLinkedList.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/DisjointSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/DisjointSet.java index d7ad6a8b7..f3dad23e0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/DisjointSet.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/DisjointSet.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/Haplotype.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/Haplotype.java index 726e98a1a..1a96368e2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/Haplotype.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/Haplotype.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java index f65379907..5aca8268e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/PhaseByTransmission.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java index 4ff278755..9f80b66f4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/PhasingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java index cfd6d5a4c..d2e4f95c2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/PhasingGraphEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java index f1955f251..6151e5706 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/PhasingRead.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java index 696c9840f..f68955b40 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/PhasingUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java index 0dc151895..24060876b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/PreciseNonNegativeDouble.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java index a5c121e5e..81d16670a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/ReadBackedPhasing.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java index ad46e191b..d5250a480 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/ReadBase.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java index 4df7cda30..416dc538b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/ReadBasesAtPosition.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java index 98c069b75..1fd05ed0f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/phasing/SNPallelePair.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java index d91f68b4c..3c38794c3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/rnaseq/OverhangFixingManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java index c1693c95d..809f97214 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/rnaseq/SplitNCigarReads.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java index 4aaaf9c77..ced1e9ce5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/simulatereads/SimulateReadsForVariants.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java index d2ad91e97..616b36a4b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/validation/GenotypeAndValidate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java index 09346919a..ca3da994c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/validation/validationsiteselector/FrequencyModeSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java index 3d96ea4e5..b9228f23c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/validation/validationsiteselector/GLBasedSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java index cc8611c06..6d2cf5296 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/validation/validationsiteselector/GTBasedSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java index 54f4888a3..a7d716c24 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/validation/validationsiteselector/GenomeEvent.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java index 40eb9fc31..78bc3b5f9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java index 6e4de0860..897ef9a81 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/validation/validationsiteselector/NullSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java index b7f44063f..dc6c1ba58 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/validation/validationsiteselector/SampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java index 470c59157..c2e86faa9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java index 8ec51c3ed..7e459c021 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/validation/validationsiteselector/ValidationSiteSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java index 01572780d..c64070cff 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/ApplyRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java index 2361ca64e..b6ef38ade 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/GaussianMixtureModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java index 1eb555f2c..624b6c062 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/MultivariateGaussian.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java index 3c8c48a4e..7365340f2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/TrainingSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java index 3135a390c..55a26bc42 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/Tranche.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java index c9383758c..f6167e8c4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/TrancheManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java index 636dd8ece..2290f3c76 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/VariantDataManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java index febef6138..a2c49df4d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/VariantDatum.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java index 3133d4336..8fe785769 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/VariantRecalibrator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java index dfbc3dc0a..c641c8ea7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java index 577560580..1547bbf2a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantrecalibration/VariantRecalibratorEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java index c2569d038..ddaf5d400 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantutils/CalculateGenotypePosteriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java index 9d92a4b8a..884193184 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantutils/CombineGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java index 50b4c98d2..94af8530e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantutils/FamilyLikelihoodsUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FamilyLikelihoodsUtils.java index d4c3c4ed0..05baa6e06 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FamilyLikelihoodsUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FamilyLikelihoodsUtils.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantutils/GenotypeGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java index b0bbe02ec..4757258e0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantutils/PosteriorLikelihoodsUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java index beb2451ee..c96fec979 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantutils/ReferenceConfidenceVariantContextMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java index 1bce6000c..5fa4e5d14 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/variantutils/RegenotypeVariants.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java index 134f5e514..069c52177 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/SequenceComplexity.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java index 666190960..c56cba9af 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/collections/CountSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java index 0d29e0ee6..55c4b43b5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/collections/IntMaxHeap.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java index 9484676c2..91b08a61b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/gga/GenotypingGivenAllelesUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java index 134842bcc..c386272e7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/gvcf/GVCFWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java index fd8a98775..7d9e533ba 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/gvcf/HomRefBlock.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java index 6e27a5a63..eba6d6771 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java index dd756a5aa..9824e08fa 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java index 53fcc2e57..97aacb559 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java index 4edfd4f0f..026a249e7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/haplotypeBAMWriter/ReadDestination.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java index 567a3635e..f8d8ead57 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/pairhmm/ArrayLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java index 18fd5a4fc..a03ea8303 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/pairhmm/CnyPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java index d01fb9fa7..7beb8b04a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/pairhmm/DebugJNILoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java index eaaf1798f..0e6f92510 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/pairhmm/FastLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java index 28add0f64..e27856c40 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/pairhmm/FlexibleHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java index 18ba8e315..654b36e23 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/pairhmm/JNILoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java index 3f4641cd0..a73f20edd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/pairhmm/LoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java index 23187b5af..ad9fa20f0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java index 63cce9881..368150335 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/sam/ClippedGATKSAMRecord.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java index 5f6ee422d..40bdb12c6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/utils/variant/TandemRepeatFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/TandemRepeatFinder.java index 9f6756dd6..965ef04fc 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/TandemRepeatFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/TandemRepeatFinder.java @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * 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”). -* +* * 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. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 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. -* +* * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. @@ -48,6 +48,7 @@ * 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ + package org.broadinstitute.gatk.utils.variant; import org.broadinstitute.gatk.utils.Utils; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java index 25748f70e..1cf60d688 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java index f40152e94..681f001c1 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java index b8d5c5303..c200701f3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java index f263345e7..8229d2586 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java index 34548aee3..65ce02cc8 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumUnitTest.java index 3c9048fae..77cd87a08 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java index 0e95122da..54ed375e0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java index d16f718be..e6d3d9444 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java index f40ef2602..675e10b87 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java index ce374b047..8f29d42c3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java index 66c12a55a..90474319a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java index e2cbcc6a5..d20b08b2f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java index dd18b9d08..b2f758cd9 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java index d76a5351d..3d5148c1f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java index cbc429837..a3259dd14 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java index 5242414d7..5bacc7450 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java index 4fa913cdc..7cc76a199 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java index e7398c393..4be0bbebf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java index 333175938..d4439a70d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java index d403dc6fa..d356c629d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java index 116e2efde..dcbe80446 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java index ca10b9a1a..3daffaa3e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java index e3bfde076..4d90bcaf0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java index 3b4243831..2adaec781 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java index dd2f3bd55..916bb68a9 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java index e78b3d3fc..e754c3aaf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java index 9a1e6d799..b65fbc1fd 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java index 8b5e42109..389adbad6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java index 6a08859a4..5fd8e8562 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java index 0fbd950f6..8604e05ea 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java index 765deb0e5..9916196b4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java index 6c139b2e9..e71527ff9 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java index 585bb2f8d..32080e3c4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java index 7c3a85d53..367d1810c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java index d65770d7b..d163ccae5 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java index 830f3681d..44bf0acc3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java index 3ee0a79ed..545ead5e9 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java index d3a0864da..65d56cc2a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java index a96302d0a..b185db532 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java index e918602da..2d10c6a66 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java index 1b5d97994..d5a26fee0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java index 778b38093..d3e681e84 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java index 151a2325f..de44779b9 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java index 098c39c66..f9e4ad05f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java index 70fdf5245..464e94ab8 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java index bae62b6c5..9297e88be 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java index 32ad71f4b..1a795edd8 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java index 0aededd99..a894d26bc 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java index c79acccbc..e3ef6e58b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java index 4575e62c1..659832d10 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java index 4781488a9..6c24cb1e1 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java index 4d7b1568b..a2c0e06ce 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java index a3458305b..17aa46088 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java index a2f2262fa..b19314824 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java index 7eb913997..9930d80ac 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java index 8475cbd18..51195d9ed 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index de8ac514c..f364bdbe6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java index 1a19b5e91..98f9cad32 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java index b97d108c7..cd0a00749 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java index 7cddf67ea..65529093c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java index b7427a181..c3e6936b7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java index 9a869a5cc..f414311b5 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java index 9fddd1722..0ded6f8ca 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java index ef0a46027..d5f0b7625 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java index e97be921a..5b8bdafbf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java index 1f588ff0f..aa2c3976f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java index 366b90bb7..8844eb783 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java index 3a12ee99c..cce9708bd 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java index 3f0cb94f3..11921ee3b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java index b1174e22a..908198cbb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java index 8771866ff..6d34f7693 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java index cbaea15c6..607bdc985 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java index 8773bbc63..fc6efae37 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java index c46a2a2de..2ba09aa9f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java index dfd91ab24..336775aac 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java index 136b656f2..85ea843af 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java index 6f5634b56..36d7d4a64 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java index b9c005554..c07ff16cb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 0b6bfd201..7a9d141ea 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java index f5894b84f..76c7cfc3e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java index ed3413364..2a786248e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java index 2ef8b7332..8eae1588d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java index b137c3c20..69138bd65 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java index 593b3a833..ffc3ed72f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java index 3609af77a..d84483615 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java index 55a3106a5..b5fa37df9 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java index 826666d43..4819c7f21 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java index 3e73bd024..08dc468da 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java index 40e3aa30e..963a7da61 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java index 4ec4c4cbf..a07e815a6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java index e82c84b22..d230ed7b6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java index 119cf45fd..b240e5ffb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java index 078177f4a..8973eb9ba 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java index b8310e024..dad8d8e2d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java index edaf56ee3..61d568d57 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java index ec4238d10..e633ca39c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java index a1baa298e..5c73ce2fe 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java index 314ba5c02..b94cc75cf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java index 19105eeed..8a9cedfb3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java index 68a298f0c..b2a530d6c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java index 9255ef96d..1f28f6b97 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java index 33d091953..60065ea92 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java index facf6a08e..c0093c275 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java index c929d2c0b..caeafd16e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java index fafba50aa..a0675e428 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * 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”). -* +* * 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. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 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. -* +* * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. @@ -48,6 +48,7 @@ * 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ + package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import org.testng.Assert; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java index 951272633..cbec4b9b2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java index a39a73f63..8f7513be7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java index 60796c4dc..9fb138613 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java index 89e9a8543..2086234c7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java index 8c80b7839..8fa4f4ae8 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java index 1e4bc4f9d..ade84cbf6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java index f51838369..cacf2ba2a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java index 13891ed92..83a00412a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java index 955857b04..c17b8d1b4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java index d35536df3..1ef0db5d4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java index c08420fa2..2342a6aff 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java index 165e611a4..4dc1b23e4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java index ec5b681a8..a706d3182 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java index 91fa5ed46..ce78b68f6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java index 7fac51266..97e658a5d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java index ff1ebe32a..6f2647201 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java index 39d38aebc..4d2a628e4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java index 3bc03f539..461ea519c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java index 740f2759c..08be802f2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * 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”). -* +* * 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. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 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. -* +* * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java index 8933314c8..d54c9ded0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java index c511e5994..7e707479f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java index c615315a9..87fffd2e6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java index f92afc6f2..f5b4264dd 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java index d4eb17c29..7d4ab9763 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java index cbe3408de..b15f3b375 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java index 1c79501fa..1a37d8069 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java index 964d6c151..d862de991 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java index 724f5e129..a01355e65 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java index a3f2f9eac..e4b1dc4eb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java index 14b13e23c..f5b92941e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java index 872f5f399..103d25b67 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index 473ab8cd4..ae4f6de9e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java index 7f860f343..397fcad12 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java index 8ac40aa74..1062073ac 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java index b6d05eefb..7092ddeb5 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java index d3a145be6..1df099b00 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java index c7043bad9..f0b6d33da 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java index 32603d084..eb9f56899 100755 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java index ee1e10d46..7ab8b2598 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java index aa117ef9f..6310f2c4e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java index b9cfc0949..440582438 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariantsIntegrationTest.java index c6ae7ea64..19720dd85 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariantsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java index d6213ccde..9b78c08aa 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java index e8afa6250..88ce59f3d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java index 8bba6d980..925e9d27a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java index 8116b6b11..54e3c8b14 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java index 33b04a175..9a65b7616 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java index 2721b5d47..64f87fe5f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java index 642733d8f..d34859b07 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java index 874cfa928..abb64795a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java index 387c26021..61ef9991c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java index fd7cf737a..8d4474473 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java index ff9b45b98..39fe67fed 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java index 77d61eb5c..1509655cf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/RandomDNA.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java index 3a678c437..49477f01d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java index f56e970a4..b7a76d1c8 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java index 2dafcb70d..36acb38e7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java index aeab35ad4..d62c00a12 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java index e00ac7e8e..d4056f927 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java index 38252223a..e65fe4b27 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java index e20ba1625..620b0f190 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java index cee923476..e55b51a24 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java index 502f4d1c3..360955cb2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java index bb816b11d..13972ae90 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java index c62586753..5fddfdd1d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java index 28fe83d6c..b32019cba 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java index 88b5b6bbc..7b1f5c756 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java index e2f703e01..93a5393de 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java index 8e6958f9d..4393d134c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java index 456daf365..fe6042771 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java index 3d4865e38..3181b43c0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java index 34ac9d983..21bd5670d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java index 0fba905f7..aefd8dff2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java index 1c34405b0..8cef47ea1 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java index 7ec12397b..e499d6139 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java @@ -25,7 +25,7 @@ * * 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 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 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 ae8497ea7..99c91d23b 100644 --- a/public/VectorPairHMM/src/main/c++/Sandbox.java +++ b/public/VectorPairHMM/src/main/c++/Sandbox.java @@ -1,5 +1,5 @@ /* -* Copyright (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, 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 8dedbdd59..c6188df7d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, 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 c3461f23e..9f866bf08 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, 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 56335f1f0..3c8ca6c81 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a2bb4afd9..ceb2eda3d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 328960390..9f6c16edc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4d05d824e..c1daca1e7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3117d3c57..c92111c7b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0f00bd668..f391b45f5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0f6aee60c..5e4a3559d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 eb98e0bb4..838a4ae24 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0660cb015..c0008c32f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e9622c931..eb403c610 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 02bc06fa0..2b2c6b12a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2668b8ce7..d9924c70d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b533a0d33..54e63e4cc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 16cc4adac..f5a337bfa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 91e41e5b3..50981a355 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f1148c6c2..f3ba0e4fe 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f4ba1bb9e..4331b9667 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 88ef4a557..34be0f885 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 09a5b4584..40dfc030b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e5e292bd8..04e165e28 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 5a6d70d21..0daa83e79 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b090bab0e..90e6b97d1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 123b3ca1f..7619d4102 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7d0c43b4a..dedb71d48 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 9b28e2a42..956f1e9bb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e60a78bd4..551cf1a7e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4f2a15945..636412dbd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d0cd84994..d6fa7bd70 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c6684b5ad..66ff7e392 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 baa5ebefc..b9775b274 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 555e7ccb4..f4d13024e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d1edfe5cb..f052ee3c7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 dc8cdc0c1..9bc95e173 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 df152b90a..b98da8cee 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 727a378d6..f94c351a7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b3dbba893..e14ce625b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fac3d92ff..057342c50 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e60780a64..4b64c03a6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 060050047..5eed18d5e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 44c462b89..b9d94b640 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 05ebffa07..39247f5b4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4fec3e240..42adde781 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 331029f52..ff8da29db 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 cbbbe47e1..d7696d6ca 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 42a88b9d0..3260476eb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 680da25bb..71a1af2a1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4bcecbcad..865a72b7b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 777e23cb8..6d961a370 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 1525c381a..1eb58a1d0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4dfc31d86..659a2c7ed 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 997435d84..b00d1c664 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d4278c9b2..a39ceeae1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7dc589da7..bcb148b92 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 11437cf2c..78262b560 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 17e8c4290..bb5fcdd92 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 197abd49a..419898581 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 dea8acf5f..ae555c3ee 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c7b2575be..6687ee658 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f9629f5c8..541787f49 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ec879fdfd..5c6bf31e4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3be983d4a..93a2e0aec 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2eade15e2..870d5bafa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 297ccbedd..269cb6f0a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a36bee579..99ad5a577 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f628bb47c..1611778d9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 bc8a60251..db2aabe1c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 efe6336ad..cc3fcd185 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 178d440bf..259c77b3c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 aca33e411..71db6022c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f916bc185..047477905 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 cc1d9e9a4..acb931130 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 125d4f731..84c55e434 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 09a0cab2a..b26297d02 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7f6653888..1765b7b78 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4ea4aabf9..78b6eab68 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3b94e438a..eba6c017f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f1d6203d6..80d5ba0ce 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c272e0acd..f992cf111 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e355c7ee2..fd5b73be7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4714df9b7..d84aa5dd8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 6fb4d48ed..cf4286d35 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d8ae3bf55..399e4bc73 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4a27219e4..5b52c8f29 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 79b853e6b..e946f3e72 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 eb9ec480a..a8f46fabb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 237a38021..fee842db9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f3506f22c..399737b5a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 95e0341fc..69ba13ce9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 bde44a08c..5c601ef45 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b6869f0b9..5aaba79c0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b0842e161..95454122e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 807e0380d..01299aec1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d65b779e5..399ea3803 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 65a909a21..e50a770c8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 6b7bf2187..21d1c7c2f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 581d213dd..77bea8969 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2543c42b7..c12933c85 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 eba5b534e..389f2c6fa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0344ff032..c4904818d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 6920ba242..3ed14bb9f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e90cb8047..1dd8e8fb9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7d6e9c010..213ab28a6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 41b7e53b7..402087d7c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 9276331e1..8d166e1c8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f7e3dbcda..0f01f76ce 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 30e03c6a8..b0fd074a6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fc68b9c7a..04516da45 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f9660a94a..27e0859ff 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 772fe01dd..06fcfef5e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4e5ef9ff0..846657ab3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e02b846b7..b1ab50b41 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 443fdf7e7..5753b0fbb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 270b06f33..67a5fabbd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 496178d88..e2f870d55 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c0d6e9dcc..400f02881 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f0e889a63..c3ff6ae16 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0b7d1a905..d4f6cb8a8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 562e50ea9..317322da9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8717f1ff3..de49247a7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 9c44be3de..2898ca1cf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 310f1dee3..bb1d7e82b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fc5cdcb53..1834be5ee 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 90d8a3fd8..b0dcae564 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d6e78a616..e56dc27b4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 05c6f564e..4e267167e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 58ec76660..85dda8ece 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ff1542e41..f006a3ccf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b0d40c074..46f044b69 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 20dda5427..a8a02dafa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c7b512f2b..0407d8591 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0a7a2cdbf..7acc34e7f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e01827723..aa449a105 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4e8a1dc2b..482a54117 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 55a697d3e..841a139e2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 07c7bfc8e..f7f56f337 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f1b375835..22822dd3a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7ca07d35d..8c7fcc630 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b0e0bbebb..c00d52124 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 @@ -1,28 +1,28 @@ -/* -* Copyright (c) 2012 The Broad Institute -* -* 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 -* restriction, including without limitation the rights to use, -* copy, modify, merge, publish, distribute, sublicense, and/or sell -* 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 -* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR -* THE USE OR OTHER DEALINGS IN THE SOFTWARE. -*/ - +/* +* Copyright 2012-2015 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 +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* 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 +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMReadGroupRecord; 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 428806d6a..d92ffe73c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a2102a838..1720fdc76 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 9f815cf72..7c57b0d60 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f9a6fab57..b0fc108e6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 cdee7e14b..94548ab3a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 292803d1c..6cfcdac8a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 89be38db7..dffd8662e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2ff1d5a4e..0a4eeaf8e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ab63e1e00..df582abb5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 58cf9183d..b5f7e4418 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d5f8d30ff..e448068cd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7e36ffbdf..c5ba1d96e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 6dd8833b8..15b6f2dff 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 96c9cb24d..d5c6695ab 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 772c327bd..ec9b5ee2b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 74ed19d3e..87a8b6629 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d5925900c..693d70954 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fdb5fd2cb..70a94a65f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ac348a2ab..7ed538b4d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 68943f887..9d5712c38 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 363b70f15..e28548413 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3396006d7..ac79c367d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a54d2ffac..2512bfccb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 89b8b5907..dd1d691e0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2f64dc236..5c8274751 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 dc4824c08..27b59b202 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 50435eb53..3dca0e84c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3a440488d..8b9b6217f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8a000077b..a8b8c3fea 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 68163850d..4219930f3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 548bee887..409209dd2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ecce811f9..7ab11e3e5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c76a07e36..3a21d5a32 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 bf8b69741..7ef375b93 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d3a6bdc4b..d04ddaa4e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ea2e081c7..f7c408004 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ca53fcf1d..743847e59 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f46fb0cce..8db59fbe2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a79d592f7..dfeb73921 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4cc2a82be..2b92758e0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7a3ca935f..223c2faec 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b7db50594..575aebfe5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3fa18c496..fc7e77364 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ed5c4b3b9..e3d676b47 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8721779bf..6c0004c71 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 338789022..e450d451c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 bd34a1792..51722e707 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3bd174442..d81c27088 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4de344eb6..46158825b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 497eafe68..9d3b6d100 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 de6500e19..13e97f810 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 034413520..867647625 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0e5833b99..2dac6e111 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0f26bc630..fd721edbc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a37eb8d88..0e37cb4bb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8946d2808..0bbc3c8a9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 14fefd2be..1a373e114 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0d60c39a1..acc8f2295 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 141f01b3a..c0502da06 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2744bec61..2b5427f76 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b5a698b9a..3bbf7bfb6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ac34b7594..91ba863ea 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f84824a59..858a557fd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 25abafd2d..3671ded82 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b3a0603f4..9eb732cc3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a8c88aace..41738a09f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 1c16c0e19..0c2676b5a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c68e10908..4387436fe 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e392041f0..ccc81599a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 72d10994d..b203e39c3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 bcae8ecdc..f017cfb27 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 eb964c826..3e92ff73b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7188fd01c..ef2251e50 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ded2941f3..613b6b2e4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 931381efb..8a500c180 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3962c98e0..903f5bd13 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fab984084..e6deb7635 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ccf09fd40..5708e2664 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f85123ab6..19929988c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 42398ec33..46691e44a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3f8862975..a2d12dc46 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3c6268de3..66f34b3a0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 5852b77cf..329aaaca3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 200614e50..5078d4ea7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2c738e109..eb6b6040b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a2ee8d0bd..8a221cb35 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 eac57155e..3438232bc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 67eae69ac..9b8e3be01 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8c59bc8eb..81731315a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 90c10c50a..0535acaff 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3598cf505..c3cee866f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ad945f277..8f6f5e3c1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 5a16a6767..9dec898aa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 88a1eaacf..ef94e7e2d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c170f3d19..a0411484a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 88c4ff388..c21289722 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 9e02bf182..2c8dca90b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 66205b93f..f613607c6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 dc3e99653..a5ddd0654 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fb498412a..4e94d855c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3881eb719..439c7e5ab 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 424083a11..79fdb9253 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4c6e35d0c..7258e4d86 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2d48487e4..9ae72597b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 50c7f8222..6a1c3407d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7de5f0dbf..972816ca6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 11a3c3d6d..32fcee33d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0a940ef22..5173dcb89 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 644b5ed1c..07d61fabe 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 1229ecfff..cb817dd1e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ca9682747..985c3444a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 73c177688..abb5fb61d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 beac3ace8..51d4c2434 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 350ba7b75..53e33bde1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 89ef0b26e..2d1579501 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 99d7559c4..02751f664 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 6665b7481..2c45ebc8c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 791046a77..27936b5fe 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3f620f900..4115b97b1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 72f2bb1ee..fc7857d84 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8bf4f4103..342c9ca14 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 dbc2f5518..ec26ba2b4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 bffd23da1..68ecabc10 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 251eec49a..3ada2445f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 258e61b49..afa700116 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7df9bc2cb..553ca998f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a54237bfb..7c016c3fa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 289a10cf1..8e7f86de1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 aa66d6636..1a42dd067 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 90ac7549e..817fcc112 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 bed203b3d..d006fcaba 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f96a35a79..90c75598e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 71fc81aeb..a8973e16b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c4f6159a1..20a99f754 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8be72a22c..16f43f98e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c975fb166..b8bf0eadb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c67cadb8d..201d9c41d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 aa66f179f..039ca4d5e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a544d716a..36cbb58bf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a77c0961c..15bc5b731 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 514b85737..0f6f9e384 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c98243adc..8dac72faa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 27804c6d1..4fbb02a92 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8e3ac5f49..af7e5716c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 74a936782..e3f2fee1a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fdc8587ba..219307802 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b8a57e791..d23fb1b7c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 88a1c5d5c..87e2ac868 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c22a3eaed..47a1179b2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 50f21a62e..44432cfac 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d3fb18896..c0e48a974 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f774af092..109c64c72 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f4232067d..870277d1d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 405610011..aec599099 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 beb4123fe..6a35f0b3e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3400b61e9..68fa13d18 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d997f3758..9c3e3904d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3a0fc6ebd..8f11220ac 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 343ad656e..38b1cb7c2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 479e19ebe..1e00065a4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 60e529281..ecffcfc55 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b295e1230..3c5d84cf0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fc7465de3..9f2589d70 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 994de2b28..d743d0021 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c12bb1551..a931bcb18 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c7e7d05d5..4e3c20590 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3042e3082..bcfb60c38 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 cd6014bcd..b059f8d50 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fc934ef06..5184a7f84 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b1b09db01..4e63d5dbe 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b32a3db63..e17ff3e73 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 75c669c1d..88421abc0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 5b710a10d..c69774b7b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a332be127..10f6801f3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a03802635..099d9e20c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8b7a8d758..8bf453300 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 cc0162fc1..7362c4d3c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 00774f7b7..d5308a375 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 bbf653ac1..e3c852eae 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8af514693..89d630d9f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ff6b1242f..e19f6c8dd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1a6cda658..849d994ae 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9c93efd5d..d4e0aea36 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 3b7f7db17..90adfc206 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b23f1aafa..581aef077 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 83379787f..c2ff1c4b6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 d031f5d4d..fd7698f09 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ccc0cb56a..ef6baffbb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e988a42a5..0900b369f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 55711c026..65da43863 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e38ba3ef7..9826494f7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f3c4bf382..8d300f988 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f736406d1..20798a38e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 71e009469..34a25562e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c095169b7..7564da943 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ab687c020..2cf5b765c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 eb57d2e5f..aaa071d28 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 962d495d3..85bb70f0c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f116af51a..d8ade79a5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 53885109e..e502bb701 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 fd91e5352..e111e1984 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e1da454f5..d7d79bc27 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f4ad99390..49d51ef69 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 fc999d04a..4df0ac7cb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c1d71e281..72e73956e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 12fea171b..afe465563 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 99454d459..8fd76224d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5d71d3585..7983f56e2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 01e9eed2d..4a7deeac1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e1612091f..967a00d5a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 68664c34b..6ba815b8e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 290eff973..0f89fe38e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 36fcdc74d..153cf4b95 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 6b70d2f58..e02863f20 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 68c4ca730..28c1c31f1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f0d2300c4..f36d14afd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 15073668a..022179b1d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 44e10af86..24b88b185 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 fe7739093..94b88c81d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1b25a8e6c..e0d07b245 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 80a60c502..2be93f04e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b9885a969..2b0ef1a72 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1813694a3..482a6b57f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 2012b543e..d79ed96d6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e5624fcd6..7a65d5e9e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 847ed9238..663186e0c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e9ad0970f..11f51356e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 a7e603074..54400a01e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 cb55c06fb..86a5a12e2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 4d7c0c6fd..a3a60b629 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ae316bcc2..fb8b8b8ee 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f2ec8a929..bc7f85c6f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f1db69e1c..7a7b4e856 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f6cc7465f..5e3474098 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e79ea8a9f..189a88c21 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 fcaf0d7cf..4829db78c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 af701740e..39b74dcf0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 dddccaa83..46f630b57 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 cef77f961..f72bdee22 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e5e9dcb08..f3d5a7db5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 755b69683..24722a083 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 843743e48..7994ae9a5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 6df8b3c36..1e22d7ed9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1ae41e950..80ffe558a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 d4ee1ad70..541da93c9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 8df12c25f..8ffee1e08 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 7574518ef..b95e158bd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 a3b004ce6..ab1fcbb43 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e5c2594b5..941126f35 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 3931c5f0c..37c50d09a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1b02f5dde..9a567c60d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 aa7d06955..351b50c8a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 bb8896d48..b65a695d3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e8fb1f08d..16bc39c06 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 20a536e91..26713290c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 d7e4868e7..eca27e914 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 af5160216..e2b22561b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 d3f2f4ba6..6718dbb3b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 31cdef904..6a3e600bb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1345e79ba..eb610aa28 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5751a723d..82d22c22a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 14e40821b..912d3782b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 93c9fde91..5d5ac04e5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 02cf34e85..fedf091ed 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 aa19bfa26..ea4fafee7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 eb60cb324..7b8e5231a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 8ddda6c97..b5b0121c0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 dbe25366a..0b5a5ce49 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 eeb82a333..d35c9c0c9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 fb68231d2..31dfabec2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 092152f3b..5fa0d5bd6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5645590e2..e97f69edd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 327be225e..191867609 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e1cb7d037..998d4e564 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5525eeb91..a7d1363ba 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 80027a02d..61aa43375 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c7450b1c0..33aa1f463 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f7e26718e..358b8c3f1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9202c2aa2..1799c9a03 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ccc9dcfbe..5eb581a8b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b97cee157..35429c702 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 704426524..a94e86d2a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 4fcc19f90..f5604522a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 29f8c41c1..e115667ec 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 50ad3cf9a..6bb865bc2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 2c6aa58d2..306872377 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e3b936f0b..4910e1df6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 799061abc..cd15b519d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 0ee38e99b..6131f1684 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 8abcf5bc0..1cba5f21f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 99571e9f2..f2cc999eb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5bd25bf55..31b43c2c8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b3093c8f2..3c4e02577 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 82b8ca572..27758454b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5c0be04a0..e77ef47d8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e38183af6..e8d2f22f2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 d31541060..8ab5a1397 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 3a83a2f50..a9b12d172 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 edaf80229..66a7242a5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ddc11eb34..fd86d4d11 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 082062364..7b6dde65a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9d029133e..5627a46c1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 d172e976a..c13f08833 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 141081385..5ae4f7691 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b38b27a5a..8f984f4cb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 8d1c1cfca..4f23f59d4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ffd69cc7f..eb0d96bde 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 80ab0683b..c6cf39c57 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 02d767a6d..ff23690ad 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ee21380ee..f6e59317a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 cf8537224..440c15574 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c776dd531..cea1b7722 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9de4b288f..f722f66fb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 351fb71e0..ab7ca2878 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 024fcb6f1..eb5b14f27 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 764449cff..e0df4d9b5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 4fdcb08da..ac1802e42 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 944cc851a..3f3acb56c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 160e04036..090ba8622 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 2fd78e363..e0950ceee 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5f4e1b516..f11e01d20 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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/ListAnnotations.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java index 4bc91d6e3..bd7b78899 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java @@ -1,5 +1,5 @@ /* -* Copyright (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5de5d6656..ccb4be7f8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1c99fa8fc..fb7300809 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 a01c945ac..66ea8dff6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1d4b7a002..34c58683f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 728fa3fa3..be3b40194 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 465fa285f..b4cafa8f7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9da3de861..ceb353bdc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c82a013b6..adb2c4ab4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9fe3934bc..8bc532183 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f064bd4de..ff7a9643b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e7e0b5431..8fd0abe05 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 8a32ae150..ee818ea34 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 d8e3c8c3c..bb488679b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 56c4087c3..985774f51 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 0051c978f..40a94cf70 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f1aeedeaf..363da058e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9ed24db69..87954d221 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 41c2650ca..590c6b9c1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 32f6b90f7..cc91cda52 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 04e545ad0..c489d66bc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 247af00b2..70d7c9f25 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 06927f8d4..13fe48b66 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 @@ -1,6 +1,6 @@ /* -* Copyright (c) 2012 The Broad Institute -* +* Copyright 2012-2015 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/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java index 0c689558e..4bb9b28aa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9daab4345..cc9a7d7b9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 cc12172a1..bf2eddccb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e02a10ee6..1951a43c1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e027464d4..6f0e5507f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 098e81c94..96144ce13 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c8a43567f..aa7b5ae7e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 6e2266d48..f91c38574 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 441f920f7..c4d1aef25 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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/CoveredByNSamplesSites.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java index 4e3e91fc8..432c7d095 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java @@ -1,5 +1,5 @@ /* -* Copyright (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 129fa00ad..6808d927b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 987d1a0e1..86185b174 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 cfebdd29a..1f3d6c7f9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 dc71d58ee..f12d08a5e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e026b286b..d95fd2b46 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 bdddc5040..54db6f30e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 8ec22e5ea..f9c2eb9d5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9df4579e2..4eb8f3e23 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 013e356a7..062297beb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 7215e2b7b..01d26c04e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 97bde83b1..c0de7b9d7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c5302b9a2..e48c8f45b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 731b1a361..e47d54b6a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 4c4d6f02d..3c61235e3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f82985fd0..96586c030 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 831655f56..ac15e7439 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b4e586fb3..8bdcfb502 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 4201ef0dc..53c155f0b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b76b9ff9c..d38543c5b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 023d103e7..e0d2a3cd4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 443196cff..21f04271c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5a0ec3370..004906c46 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 55424f67b..a8291418f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c81f7b9ac..78f194f9e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c359bf1c3..8934fce68 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 d5f424b6f..20d60a19f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 369a5878e..17aa5bc69 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b569a0a6c..942e7c372 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9679baac3..579f43fa3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 7def2e0e3..030c964e8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 57cf4d59a..fee78877c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 db6199951..cd2c33630 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9c71f0934..7873af930 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 0a0b9b6cd..93493544d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 a2c3f796e..1517ae73b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 4e4d131a2..1043675cc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 cafaa82c5..f8b46b62d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 2f609facf..6aede1b75 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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/ReadAdaptorTrimmer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java index 0e23fac95..0944cf675 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java @@ -1,5 +1,5 @@ /* -* Copyright (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b015e6dc8..029d8b88a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 a5622d570..3f80ffae6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 dea80d112..1b6b01beb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 281d8d346..aef7d8b35 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1732b6d8d..1e634b718 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 3ef087e51..2ab63c51b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b0d1bbeee..21164ce36 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 6d2982c1c..878d6fcbe 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 7adcc05c8..b78ef2ddf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e52923db6..a45dfbcdc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 8beda5c56..1a2251921 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c3b75c1e6..9ee366c06 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c972d9a91..ef91df2ee 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 c5fa247ec..b60ed8445 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 337056fb0..74b280f0c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 a1c5b21f3..f1144a097 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 3309b815c..a34ddeb4c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 54cc06cfb..9b3a94eae 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b0108aa58..50597067f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 72bfa4b8c..7eb781d1b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 cb64651ef..6bcd06856 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 72ea18718..2566ceea5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 2cf50e38f..ddfdef600 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1c428982c..429396835 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1f01fc611..695d48c87 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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/Filter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java index 1ee8d0294..ddeb2e75a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 abb517a01..628e938be 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 6efc332a8..3bff75529 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5b6a3e078..d00783f70 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 746e4967d..7a4a113e1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 349535dc8..bebebec59 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 9884952fa..b4f27e477 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 946c723fc..9a9313cca 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 90a6ece92..c563e92c6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 549738ad7..99be53fa3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 41c52c2f0..de9388a5f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 493f4fe36..6f349851c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 a7a0543ce..b5bd4aabf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 46a9ab97b..e3fed5de4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 0db937052..4d3dcae43 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 a789b70e1..305f65c94 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 729001677..c9398a15b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b096db93d..f206a30ab 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 67dc18701..035fabaa4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 411394bf4..d5f70a9a5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 0805cb5e7..ac02b4d09 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e8b7fe2ec..f18c381aa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 57c4fbc06..f7a156673 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 a759eb258..3b1c1424a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 53b143b80..f03ee2b61 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 355441d5b..330a723c4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 61db1efb0..090124882 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 7085b515b..5019662f4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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/FilterLiftedVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java index d04e14ceb..9c5e3b4cd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java @@ -1,5 +1,5 @@ /* -* Copyright (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 5597a4c67..4ac6b9b0d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 099293cc2..70f73ac51 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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/LiftoverVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java index 15981d19a..4bed885f1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java @@ -1,5 +1,5 @@ /* -* Copyright (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 7b08bef53..41962bbcc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 a55c2215e..e95cbf379 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 d44fbc84f..5d7986eca 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 82a201091..751b1cd1f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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/VariantValidationAssessor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java index 307b78289..fd3aef8e9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java @@ -1,5 +1,5 @@ /* -* Copyright (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 0873d5b94..a75491d67 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 8618d816d..b215bb3a5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 bd228f323..a2651ef29 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f2386d088..051137009 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 0e9c80451..5c32d8c0c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 68451ef49..ea53eae53 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 16e47cda5..cf736072f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ec10d7d02..15279a0ad 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 b59794740..3ac2a3d44 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ccfd743ee..e24564a4b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 447515d0e..1f5e398fe 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 f000513d2..f25ac3a94 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 feefd5f60..92b3d862f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ab972a119..4d3223f30 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 @@ -1,6 +1,6 @@ /* -* Copyright (c) 2012 The Broad Institute -* +* Copyright 2012-2015 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/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 eae4decad..2648ed81e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 e79edfdde..889646017 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 69e623e5e..f29cb80e8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 7a8868198..e86c3301f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 38154bd6d..a64efaf26 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 29f4621f0..3143876b0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 ee179a765..2e5da9436 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 956d70f61..5d1b6c056 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 bb6d5bc1a..c0aec4329 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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/ReadAdaptorTrimmerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java index 65ca2e7f7..dd5f05099 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 1c2e6bbac..eef29b197 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 238ce93c7..d656abae7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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/FilterLiftedVariantsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariantsUnitTest.java index 847c8f1c6..7074d81b7 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariantsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariantsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 91f1a7931..df61b7c9a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * 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 bbbcbdd1b..0b7cd440c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, 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 c2a5e8042..be38c06cb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, 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 a4a7c7246..d9698c38d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, 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 aed7aecde..1a10819a8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, 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 00f65e54c..f861ccbbe 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 31032e3f6..e77ff641a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 ecb8bbde5..f0ed568ab 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a9ab00de3..20b602642 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f3f93b411..a069415df 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 bbd5d24f9..d7585970e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 101796bc0..c913e6efd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 55e66244c..9cac5d536 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 694c27187..6e777df29 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d080d5bc0..d0309193f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 041bf76ba..b158794ad 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3c6b48cc3..83003d24a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 df2e829ab..ed985c418 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2f9a3b028..b2c2d1a5a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 61261f217..a768a1c55 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 614cb927e..fb8e8d987 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 40e41f28d..948332209 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 edbf25dca..3dfe13c19 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 829728835..1b3af7066 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 ef6d5a05b..f2a8340b7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e97f31321..d67e5abc9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c6c4fba02..1ee279843 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 233ff73a0..53ad3aca8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 390edc73e..56f80e3e2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 80f73139d..982cfa371 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d0eb0b9f8..160abd38d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7290292e7..466f42b9b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 39d6fa67b..5101064fd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2c3d24b7f..1b7ac79da 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 883143a14..ce54e8f11 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 0dfce0e99..08d84b084 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 86a89c1c9..8a4deb51d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 76b4eb6ca..57fd35908 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2d97f69f7..cdc7cb806 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 915db6189..a1df0baf6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 52437a846..8458b3a96 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 041660944..af61415aa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7cd89336d..e8bd5d1ec 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 9213e8263..175ea369a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c679ec248..91562b69e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d695543c4..329dfa19b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2aa2f76d5..7ef7a154c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7c7a776a0..7a2b53696 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 5321466d4..dd2068bbd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f4ca70e84..ad0de1da1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 5d86e0bf7..8d556515b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c31784fa4..3710698a2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a8ac99def..77ee61752 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 673885a1b..39908366c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 ac50853e0..e24841639 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e760aaa83..2dc23fc55 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 379fba036..46e5ede2e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 0e7b80d75..62d4b05ba 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 1671c79fc..b5bca03d4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8c4385448..3dd277be7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 501a7b597..1768c1328 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d0e69db9f..159ea0984 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 857871cfd..fda2e692b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 cf6cefeb8..84c071f19 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 09af2f7a5..4b481469e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 680c13f92..7960e1fdc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2c543dd4a..0ae22648b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 b2b23d36d..2f8adc392 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2bedb9296..671548e64 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3117852f5..746bb2c32 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 02dd15a17..495f3dda7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 b09c9dfc9..11229cbeb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 53eafe704..522847e9a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2b759ced7..563578f0d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e5c7fad4e..634fb36fb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3995ff71c..a7a98c7c9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 66c562934..300d04c61 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c142f06e3..30ba236ce 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f2e7e6ef0..f5b542446 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 b6bb16ca3..d6e2cb504 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8bc17d78d..77c747f89 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a55da890a..e0985983c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 27b816324..b51023421 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e372b4e02..bbabd5eea 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3b9c8d3d8..db54fb505 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 967d4c60a..095ea9e99 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a7ce7bad7..229af987a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 9dee5be28..d7990480c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 9f772bc89..b663b5920 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f37d5382b..b6ebdcb8f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e58d8888f..6edd75f18 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 79e07a6bd..a8c4e3feb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 944858f55..c583fb93f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d57d32668..2753c8f6f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 70c06e24a..c2142b8eb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 70f5532a4..62139fb48 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3bbdedb01..be7a65b2a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 b29166352..e8e8cde7c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 761611f97..158095adf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 02325a767..f5a02021d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8ec048389..9fd49782b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 717a07708..8d18177f3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 815b02d6b..da7fa6ee0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f8f3895ad..f71aec78b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d00206b90..199b71eb8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3a6fb2f71..643eae100 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 88057a235..d7512f65a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 45cc055a8..ba403a1c6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 aa9e186d0..0265c8feb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 6244b8652..e0fc36156 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 0361c4cc0..7d8788210 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d53a36ca1..b5d5add7a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a93974231..5a4c99c3f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2c557872c..3221d21f6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 faf456538..8f90f7d14 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2b1c7f7ce..8ea28c881 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f572d3485..3dca4245f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 bbbb61778..6add93bd2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 82e1b0eb0..92cfc74a1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 ae70402de..fca56dcc0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 29a08cc9e..d06176e77 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 0e0b79741..f9167ff00 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 4960e6bfa..569934585 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 651af07ba..f0e8476e6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c84842dab..24f2a40f2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 43d947329..aef5e8c53 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 25ebc032e..9f67fd47f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 9dc5e2e5e..948fa2107 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a60209ad3..d5d305e20 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 fd81e4ba7..37810ba00 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 52ece95c1..41b59ccc5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 cdaec016c..910409457 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 5cb32386d..569eb709c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d7106b76a..0435e7cd6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 9bfc13a13..d1a895b63 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 11d28c7d6..d480f23fc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c2113c4a3..74037ea9f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 537a9f8c0..89fbea0f1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 313a432d3..e9161b739 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f289960ee..fc7eb7719 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 ed6b4394a..455269b6c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7cae97be5..ea7e6b079 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e4a6ee464..b7bf2be19 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2e6207410..50e89c2bc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f150636f1..8a3da8a03 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 cdbcf0f63..bac785a91 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3d2740769..9ce7fc4be 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 9213a3e32..7aef3730a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 1c5342068..e39fd557d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 0eb0941ec..3584b79ab 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 56dfc6936..d7595d0e5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 bfb0ca039..aac28832f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 bf03ec625..cbf8c4259 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 b2f65585a..598c13d90 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 ec94dac77..d0d7a6a56 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 934a022d8..813d697aa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 67d55ffff..f3811333e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 689fdf6f8..cbcce0b3d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 bf7b3ddc6..3d6c58113 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f5adb8a6e..a9423faa4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 568535ade..249e270b3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f836f4456..0a57040cd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d6530238b..8c3f04885 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7a92b4e24..95f2559aa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 65c1fd058..f0a1d0be8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 1256df558..c52278e9e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e35eeb26d..a4c8ca90b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 00d970824..a171edd98 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8abfafb11..5a6364355 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 271102d64..5a2735d50 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 153a9a4b4..5b0ec5aae 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8d1dfff73..d03f0b6bb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7818d3e8a..f294076e4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 48180682b..241ac7294 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a0c7afbf1..56b39ebdf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 4b94e019d..ef154246d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 eed95b4a6..f00fcebaa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f95c12690..ce4ea5f88 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 45f0c147f..1d0186c6e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 fbf65287a..4a7853b6e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7b95b500d..a1818dc0b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8ff7e58f3..75701d660 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 005d90038..89cdabbe1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 afae1bb6e..015f2d306 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 db214b945..d08115601 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c4481c0fc..e9f2d4acd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 09c862aa0..6dad68092 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e84108973..707cc8f5e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a8d469302..5a55f2792 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3de5484aa..83af1d9f1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a31c49857..c61d895f5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3e5eb4548..ba196a1b0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e9d20eed3..424485adf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 15a11023e..e272eaca9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e099a45fb..22ec9fe8c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 1d041b66a..1a38ea089 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7defceac7..98e1e62dd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 1cf0aea2b..bb5e80b7d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c5a1cc4d8..9b8682a7f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 b91eb2526..61d8b9140 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7507e0897..82aa8660b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c4b867b55..836a14929 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 0c14ffa1b..cebf5e4d6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 dd2d7e7b0..91baead01 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 1a99bfa40..ea5fd19d8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 b8add996a..1afd96cb0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 67eaad7c9..0c0745c4f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f4dbc98d4..d97be2b3a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3e5c4e45c..73ff9cb6e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e66a40dab..299b331a7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 cc4721d79..9c8e563c6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 733932d32..15b0e011e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 01bf17d6b..efbf33dcc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 206249559..aaa518d36 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 ecbaaf670..0d2893567 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 2fe8222f4..c5bf32dd7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8e16c1771..af9953eaf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 0014753f6..84912897b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 46a88588f..9ff3998d3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c5255e42e..b0c9d8fd6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3a67b4328..5676c75bd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d6628a5bc..ab737f25c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 afeafb5e2..3d6682312 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 dbd58b44a..31ad7e0aa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 27d713ead..9b1c40626 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 acb0a78bf..7f1027fce 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8b027214e..50139ddab 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 41b612f0f..cb3263c5b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8a42dffda..25907ebd9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 231156489..52b51c0cd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 4d84fc5e6..4ee17c803 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 0e0ffb509..387171151 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 6f7962d46..9f57779ae 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 1cd886581..6644c2058 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8728bb5de..a6fcb2bed 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d36d3551b..f078d76b0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 4db0927bf..c90669877 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7f8270984..93f39ab1e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7d49fcce9..b2a7e84ce 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e4394f161..ad2108933 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7c19b715b..5dd3c6a35 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f77ac0460..07d5075c8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f1f48e6f4..850b9f19b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 680403252..0b8e984eb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 84ab785fd..5a74f7245 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 79631a244..7b82ae236 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f4fd40f7d..680091662 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d8cbbd6be..72f61b20b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 daa0a3cbe..c54f9c55f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 9eb4b34e9..0e0bfda98 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 @@ -1,28 +1,28 @@ -/* -* Copyright (c) 2012 The Broad Institute -* -* 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 -* restriction, including without limitation the rights to use, -* copy, modify, merge, publish, distribute, sublicense, and/or sell -* 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 -* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR -* THE USE OR OTHER DEALINGS IN THE SOFTWARE. -*/ - +/* +* Copyright 2012-2015 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 +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* 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 +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + package org.broadinstitute.gatk.utils.refdata; import htsjdk.samtools.SAMSequenceDictionary; 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 f21975cce..8b451780e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 bc444b784..ea24c2b5a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d69a37476..a450fce8b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a0473c8a4..42cf87433 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 ef8b27dcc..7863b022d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 86a561ade..34be252a7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 013a6c2ad..743ee95ae 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 73ebf3cc8..4f50460a5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 428055f0b..4f947d119 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 42fa9ffb1..0bee072c2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3c79fc5fd..dc35f7e01 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 025835275..4bba78dc9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 056581351..70a7c6a33 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d672c1ba8..0dbeb3b8e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 97c012a5a..6249f4f21 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 d522dff35..a6e640feb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 359460bd0..f7f5196b3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 018d05500..e40c3f37a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e87e107c0..cf985d5e5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 0166e9847..ee6dfbd96 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 56bfabde5..2fdc5bee2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 bc9229107..25375edf1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3955817ba..682c25800 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 9276de76f..71d90eb31 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7027b9d25..52d2f0688 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7a982dda5..241ebd212 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 37d66f097..bd4298967 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 9ce039ee0..e4a8b571d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7e926d5d3..8aac52dfa 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 db3f458f8..b64bbaccf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7835b2190..04e3ccbe5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 8233252d7..371e0f326 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 99fd76213..d430ab7c4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 010759ecf..3d7c3c784 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e82355da9..99b317446 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c0390a3a9..3d0a691ac 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 e4bdfbc23..aa035233c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 fe7f7b0e7..e4f8b799a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 bad7ef643..2d192d32d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 93d27f7d5..d3eb73dca 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 196fa7182..3c7b2aff8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 06e0653f5..3017b56f2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7949dd49e..e04787f22 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 6af90597d..6d85d7d0b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 968ae0b89..8a9f0448c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 314facdd5..1560dce92 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 9d2a3912e..d57238ef6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 ce56a329f..b3d945ec0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 19d2315f4..6b72d0c08 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 4b93c3b7e..1338f7cda 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 421461996..c431528b1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 ee2bcec57..c41b5bfeb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 666ca8bab..66b897054 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 46cb8bee1..f423a1ad1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 aa38c064d..b750b35ca 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3d2ddd1aa..40e45d93c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 7226a98f5..a5152735e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 c4184e16e..a913c5abe 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a2d796f52..91db56bf3 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 b4409a919..044a65783 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f41015612..267ab5f0c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 72820832d..97d280a64 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 6c840869a..ceb238052 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 cee91a435..8d9bddd17 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 b8dea067b..61d4c0d4d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 92618709e..9af1b366b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 83093ba98..6865d11ac 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 72ed4e4f6..8b1aa1d44 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 a7e9bf0de..f8714d0ca 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 fff7ea5f1..f5aa6bddf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 f142da261..0ca4a341f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 1b0c0a47a..31c8404eb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 0b1543bf9..a8695fe84 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 3263d9bf6..85f2ba3ec 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 85681c40f..4368ffd70 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to 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 af9268bb6..c7071f1dd 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 aaa20c0e5..f0a1c9c17 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2b08fc4d4..234bbcf7e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 22e9517c8..fb95d6777 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 1669406c8..616c85b3a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 83dfc8cd2..92a412f93 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 5a0bc0bbf..0124a0862 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2ec1eb8d2..6f8a6789d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 957ccd2f9..69e66fbda 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7f1987981..402e3edaf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c3f5bbd88..2f49bbd60 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 655312056..cc6315df5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ae86ca5a5..c60356942 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b753bc2fa..2f88c4e04 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 11064d109..a85debde1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 978a9a74d..ef6ef7738 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c148dc92b..fb0057898 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4e2fd31d4..283558256 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 21f3d898b..74dfdb909 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b247f590d..998ef1d6f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 00cc0dc20..45bef5866 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 86b436bd9..993878bf1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7a56b99de..98f973690 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b89686cbe..ac3118ecb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 51ab6f79c..8e96d62f9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c53c01bd5..bbbcb94e7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 85aec815e..05203ad11 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e804e70d9..e4772b3af 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 dc3909e65..22e534844 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 41f7a76dc..8fc6420a4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 75e9d9a37..dfc30ae03 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b3442b331..7ee1040e7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f0666aca2..fa75e7163 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 be9621e76..1e9fd88b1 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c232e1c12..96ec5f6b2 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7c1fb32f6..06b70b744 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0c8dd761f..69abeb2b5 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0ff50d726..ea2fda76a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a87aebacc..78865bee0 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7f9d80861..78b19d6ff 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b1ba78416..32cec45b9 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8837f4b5d..418bfe151 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d3c85b6bc..6b80ebd4b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a846384dc..7fdd7b835 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 bffb1d2cf..efed9c195 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 61d346d5a..b5bea3247 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 3e877b900..17cdb0938 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 63d98a277..7dbf3472c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f388d14ef..decb8284a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4984d0a71..1700baf12 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 c4ff9b587..2188dbce8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e71413d12..42801a39c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 48c6cb480..0fbb0b2a8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 46b2e949f..66f619007 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 f695d899b..7d622868f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e683f4be8..e2dc57b9c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 accc0febb..ecc0f9a8e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e9df412e7..29b7ad015 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b8d9c3149..df20a7e27 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 92680a7ea..60bbe6a87 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0d06c61c6..ea7165b2f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 8f5d8f7b2..e39045782 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 cbbdf3609..78185d817 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4a760b5d6..2522b8c35 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d99a07966..ff4280e36 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 93105cdfb..2b6243745 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 72636f01b..f45daa270 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 987d13f2a..03c92a02d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 90d235f99..5c4987401 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 9b3b3b8c3..70377e1c7 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 9d549ea21..57ce9d956 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0c97377c3..2f11f2543 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7749fb2c3..e514b670f 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 62a704217..3dbfbfcd6 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b0805e161..0194d4941 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 5019e78e7..7b25724ce 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 cee60aace..191c68993 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 768bf50df..789ef1886 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ee5f17ef9..5ca887edf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 190ec846b..7b9a0feeb 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 2750e271e..436c4f422 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fa34fb71b..d67851771 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ebeb1581d..5d9478ab8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4fa7ef5de..eeaac020a 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 95737748d..8f60ff0a8 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d0d6eb442..6dca140ba 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 b7042a6aa..d3a7c5c0b 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 fe5fba7ee..b556c0eaf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 d52762402..0df8bbf6d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 32409c60b..19ef63f6e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a4e6be203..70d25a585 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 4117f7487..5f6b36c1c 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 e703c52fb..470671d09 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 14b56718e..c6233f17d 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 44ba64c82..f6aff7ba4 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 ac301ce37..aeb1101cf 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 54573103a..b8bf04b56 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 0c988131e..bbd594d27 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 a73cb26f9..ecc611f7e 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 410bd848f..d8f76e9fc 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is 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 7c1b2028f..79ee95611 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 (c) 2012 The Broad Institute +* Copyright 2012-2015 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation