From 2c854e554a8757c3b07090d1e0b556b914a680d8 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Tue, 4 Mar 2014 23:10:36 +0700 Subject: [PATCH] Refactored maven directories and java packages replacing "sting" with "gatk". To reduce merge conflicts, this commit modifies contents of files, while file renamings are in previous commit. See previous commit message for list of changes. --- ant-bridge.sh | 28 +-- pom.xml | 174 +++++++++++------- protected/gatk-package-distribution/pom.xml | 138 ++++++-------- .../src/main/assembly/binary-dist.xml | 6 +- .../gatk-queue-package-distribution/pom.xml | 109 +++++------ .../src/main/assembly/binary-dist.xml | 8 +- protected/gatk-tools-protected/pom.xml | 31 ++-- .../StandardCallerArgumentCollection.java | 14 +- .../org/broadinstitute/gatk/package-info.java | 2 +- .../annotator/BaseQualityRankSumTest.java | 10 +- .../walkers/annotator/ChromosomeCounts.java | 22 +-- .../annotator/ClippingRankSumTest.java | 8 +- .../tools/walkers/annotator/Coverage.java | 18 +- .../annotator/DepthPerAlleleBySample.java | 24 +-- .../walkers/annotator/DepthPerSampleHC.java | 18 +- .../tools/walkers/annotator/FisherStrand.java | 24 +-- .../tools/walkers/annotator/GCContent.java | 24 +-- .../walkers/annotator/GenotypeSummaries.java | 20 +- .../walkers/annotator/HaplotypeScore.java | 38 ++-- .../walkers/annotator/HardyWeinberg.java | 20 +- .../walkers/annotator/HomopolymerRun.java | 18 +- .../walkers/annotator/InbreedingCoeff.java | 22 +-- .../annotator/LikelihoodRankSumTest.java | 6 +- .../walkers/annotator/MVLikelihoodRatio.java | 25 ++- .../annotator/MappingQualityRankSumTest.java | 8 +- .../walkers/annotator/MappingQualityZero.java | 24 +-- .../tools/walkers/annotator/QualByDepth.java | 24 +-- .../walkers/annotator/RMSMappingQuality.java | 26 +-- .../tools/walkers/annotator/RankSumTest.java | 32 ++-- .../walkers/annotator/ReadPosRankSumTest.java | 14 +- .../tools/walkers/annotator/SampleList.java | 14 +- .../walkers/annotator/SpanningDeletions.java | 18 +- .../walkers/annotator/StrandBiasBySample.java | 14 +- .../walkers/annotator/StrandBiasTest.java | 4 +- .../walkers/annotator/StrandOddsRatio.java | 14 +- .../annotator/TandemRepeatAnnotator.java | 20 +- .../TransmissionDisequilibriumTest.java | 24 +-- .../tools/walkers/annotator/VariantType.java | 16 +- .../tools/walkers/bqsr/AnalyzeCovariates.java | 32 ++-- .../gatk/tools/walkers/bqsr/BQSRGatherer.java | 14 +- .../tools/walkers/bqsr/BaseRecalibrator.java | 54 +++--- .../walkers/bqsr/ReadRecalibrationInfo.java | 10 +- .../bqsr/RecalibrationArgumentCollection.java | 14 +- .../walkers/bqsr/RecalibrationEngine.java | 10 +- .../diagnostics/BaseCoverageDistribution.java | 26 +-- .../diagnostics/FindCoveredIntervals.java | 32 ++-- .../AbstractStratification.java | 2 +- .../diagnosetargets/CallableStatus.java | 2 +- .../diagnosetargets/DiagnoseTargets.java | 32 ++-- .../diagnosetargets/IntervalMetric.java | 2 +- .../IntervalStratification.java | 14 +- .../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 | 12 +- .../diagnosetargets/ThresHolder.java | 6 +- .../walkers/diagnostics/missing/Metrics.java | 2 +- .../missing/QualifyMissingIntervals.java | 38 ++-- .../walkers/genotyper/BaseMismatchModel.java | 2 +- .../genotyper/ConsensusAlleleCounter.java | 26 +-- .../DiploidSNPGenotypeLikelihoods.java | 20 +- .../tools/walkers/genotyper/ErrorModel.java | 18 +- .../GeneralPloidyGenotypeLikelihoods.java | 22 +-- ...dyGenotypeLikelihoodsCalculationModel.java | 32 ++-- ...GeneralPloidyIndelGenotypeLikelihoods.java | 24 +-- ...elGenotypeLikelihoodsCalculationModel.java | 18 +- .../GeneralPloidySNPGenotypeLikelihoods.java | 20 +- ...NPGenotypeLikelihoodsCalculationModel.java | 18 +- .../GenotypeLikelihoodsCalculationModel.java | 24 +-- .../walkers/genotyper/GenotypePriors.java | 2 +- .../walkers/genotyper/GenotypingEngine.java | 42 ++--- .../genotyper/GenotypingOutputMode.java | 2 +- ...elGenotypeLikelihoodsCalculationModel.java | 26 +-- .../tools/walkers/genotyper/OutputMode.java | 2 +- .../walkers/genotyper/PoolGenotypePriors.java | 6 +- .../walkers/genotyper/ProbabilityVector.java | 8 +- ...NPGenotypeLikelihoodsCalculationModel.java | 34 ++-- .../genotyper/UnifiedArgumentCollection.java | 8 +- .../walkers/genotyper/UnifiedGenotyper.java | 44 ++--- .../genotyper/UnifiedGenotypingEngine.java | 46 ++--- .../walkers/genotyper/VariantCallContext.java | 2 +- .../walkers/genotyper/afcalc/AFCalc.java | 4 +- .../genotyper/afcalc/AFCalcFactory.java | 14 +- .../afcalc/AFCalcPerformanceTest.java | 16 +- .../genotyper/afcalc/AFCalcResult.java | 6 +- .../genotyper/afcalc/AFCalcTestBuilder.java | 8 +- .../genotyper/afcalc/DiploidExactAFCalc.java | 6 +- .../genotyper/afcalc/ExactACcounts.java | 2 +- .../walkers/genotyper/afcalc/ExactACset.java | 4 +- .../walkers/genotyper/afcalc/ExactAFCalc.java | 12 +- .../genotyper/afcalc/ExactCallLogger.java | 6 +- .../afcalc/GeneralPloidyExactAFCalc.java | 14 +- .../IndependentAllelesDiploidExactAFCalc.java | 4 +- .../afcalc/OriginalDiploidExactAFCalc.java | 6 +- .../afcalc/ReferenceDiploidExactAFCalc.java | 2 +- .../genotyper/afcalc/StateTracker.java | 4 +- .../haplotypecaller/ActiveRegionTrimmer.java | 16 +- .../haplotypecaller/AssemblyResult.java | 6 +- .../haplotypecaller/AssemblyResultSet.java | 16 +- .../walkers/haplotypecaller/EventBlock.java | 10 +- .../haplotypecaller/EventBlockFinder.java | 14 +- ...GraphBasedLikelihoodCalculationEngine.java | 20 +- ...edLikelihoodCalculationEngineInstance.java | 28 +-- .../haplotypecaller/HaplotypeCaller.java | 92 ++++----- .../HaplotypeCallerArgumentCollection.java | 8 +- .../HaplotypeCallerGenotypingEngine.java | 34 ++-- .../haplotypecaller/HaplotypeResolver.java | 36 ++-- .../haplotypecaller/HaplotypeRoute.java | 8 +- .../HeterogeneousKmerSizeResolution.java | 2 +- .../walkers/haplotypecaller/KMerCounter.java | 2 +- .../tools/walkers/haplotypecaller/Kmer.java | 2 +- .../walkers/haplotypecaller/KmerSequence.java | 4 +- .../haplotypecaller/KmerSequenceGraphMap.java | 8 +- .../haplotypecaller/LocalAssemblyEngine.java | 18 +- .../PairHMMLikelihoodCalculationEngine.java | 24 +-- .../RandomLikelihoodCalculationEngine.java | 10 +- .../haplotypecaller/ReadAnchoring.java | 12 +- .../walkers/haplotypecaller/ReadCost.java | 6 +- .../haplotypecaller/ReadErrorCorrector.java | 14 +- .../ReadLikelihoodCalculationEngine.java | 6 +- .../ReadSegmentComparator.java | 2 +- .../haplotypecaller/ReadSegmentCost.java | 12 +- .../haplotypecaller/RefVsAnyResult.java | 2 +- .../ReferenceConfidenceMode.java | 2 +- .../ReferenceConfidenceModel.java | 38 ++-- .../graphs/AggregatedSubHaplotypeFinder.java | 4 +- .../haplotypecaller/graphs/BaseEdge.java | 2 +- .../haplotypecaller/graphs/BaseGraph.java | 2 +- .../graphs/BaseGraphIterator.java | 2 +- .../haplotypecaller/graphs/BaseVertex.java | 4 +- .../graphs/CommonSuffixSplitter.java | 2 +- .../graphs/DeBruijnVertex.java | 2 +- .../DeadEndKBestSubHaplotypeFinder.java | 4 +- .../graphs/EmptyPathHaplotypeFinder.java | 6 +- .../haplotypecaller/graphs/GraphUtils.java | 4 +- .../graphs/KBestHaplotype.java | 4 +- .../graphs/KBestHaplotypeFinder.java | 6 +- .../graphs/KBestSubHaplotypeFinder.java | 4 +- .../graphs/KmerSearchableGraph.java | 4 +- .../graphs/LowWeightChainPruner.java | 2 +- .../graphs/MultiSampleEdge.java | 2 +- .../walkers/haplotypecaller/graphs/Path.java | 4 +- .../graphs/RecursiveSubHaplotypeFinder.java | 6 +- .../walkers/haplotypecaller/graphs/Route.java | 2 +- .../haplotypecaller/graphs/RouteFinder.java | 6 +- .../haplotypecaller/graphs/SeqGraph.java | 4 +- .../haplotypecaller/graphs/SeqVertex.java | 2 +- .../graphs/SharedSequenceMerger.java | 2 +- .../graphs/SharedVertexSequenceSplitter.java | 4 +- .../haplotypecaller/graphs/TestGraph.java | 2 +- .../haplotypecaller/graphs/VertexOrder.java | 2 +- .../DanglingChainMergingGraph.java | 8 +- .../readthreading/HaplotypeGraph.java | 18 +- .../readthreading/MultiDeBruijnVertex.java | 6 +- .../readthreading/ReadThreadingAssembler.java | 14 +- .../readthreading/ReadThreadingGraph.java | 12 +- .../readthreading/SequenceForKmers.java | 2 +- .../indels/ConstrainedMateFixingManager.java | 10 +- .../indels/HaplotypeIndelErrorModel.java | 14 +- .../tools/walkers/indels/IndelRealigner.java | 68 +++---- .../tools/walkers/indels/LeftAlignIndels.java | 24 +-- .../indels/PairHMMIndelErrorModel.java | 30 +-- .../gatk/tools/walkers/indels/ReadBin.java | 12 +- .../indels/RealignerTargetCreator.java | 36 ++-- .../tools/walkers/phasing/AllelePair.java | 6 +- .../gatk/tools/walkers/phasing/BaseArray.java | 4 +- .../walkers/phasing/CardinalityCounter.java | 6 +- .../phasing/CloneableIteratorLinkedList.java | 2 +- .../tools/walkers/phasing/DisjointSet.java | 2 +- .../gatk/tools/walkers/phasing/Haplotype.java | 8 +- ...eSegregatingAlternateAllelesVCFWriter.java | 20 +- .../walkers/phasing/PhaseByTransmission.java | 36 ++-- .../tools/walkers/phasing/PhasingGraph.java | 2 +- .../walkers/phasing/PhasingGraphEdge.java | 2 +- .../tools/walkers/phasing/PhasingRead.java | 10 +- .../tools/walkers/phasing/PhasingUtils.java | 18 +- .../phasing/PreciseNonNegativeDouble.java | 2 +- .../walkers/phasing/ReadBackedPhasing.java | 58 +++--- .../gatk/tools/walkers/phasing/ReadBase.java | 2 +- .../walkers/phasing/ReadBasesAtPosition.java | 4 +- .../tools/walkers/phasing/SNPallelePair.java | 12 +- .../walkers/rnaseq/OverhangFixingManager.java | 12 +- .../walkers/rnaseq/SplitNCigarReads.java | 48 ++--- .../SimulateReadsForVariants.java | 42 +++-- .../validation/GenotypeAndValidate.java | 28 +-- .../FrequencyModeSelector.java | 4 +- .../GLBasedSampleSelector.java | 8 +- .../GTBasedSampleSelector.java | 2 +- .../validationsiteselector/GenomeEvent.java | 10 +- .../KeepAFSpectrumFrequencySelector.java | 8 +- .../NullSampleSelector.java | 2 +- .../SampleSelector.java | 2 +- .../UniformSamplingFrequencySelector.java | 6 +- .../ValidationSiteSelector.java | 26 +-- .../ApplyRecalibration.java | 31 ++-- .../GaussianMixtureModel.java | 6 +- .../MultivariateGaussian.java | 8 +- .../variantrecalibration/TrainingSet.java | 6 +- .../walkers/variantrecalibration/Tranche.java | 12 +- .../variantrecalibration/TrancheManager.java | 4 +- .../VariantDataManager.java | 20 +- .../variantrecalibration/VariantDatum.java | 4 +- .../VariantRecalibrator.java | 40 ++-- ...VariantRecalibratorArgumentCollection.java | 12 +- .../VariantRecalibratorEngine.java | 4 +- .../CalculateGenotypePosteriors.java | 30 +-- .../walkers/variantutils/CombineGVCFs.java | 32 ++-- .../walkers/variantutils/GenotypeGVCFs.java | 42 ++--- .../PosteriorLikelihoodsUtils.java | 10 +- .../variantutils/RegenotypeVariants.java | 30 +-- .../gatk/utils/SequenceComplexity.java | 2 +- .../gatk/utils/collections/CountSet.java | 2 +- .../gga/GenotypingGivenAllelesUtils.java | 12 +- .../gatk/utils/gvcf/GVCFWriter.java | 4 +- .../gatk/utils/gvcf/HomRefBlock.java | 4 +- .../haplotype/HaplotypeLDCalculator.java | 8 +- .../gatk/utils/haplotype/LDMerger.java | 6 +- .../MergeVariantsAcrossHaplotypes.java | 6 +- .../AllHaplotypeBAMWriter.java | 12 +- .../CalledHaplotypeBAMWriter.java | 12 +- .../HaplotypeBAMWriter.java | 22 +-- .../haplotypeBAMWriter/ReadDestination.java | 8 +- .../utils/pairhmm/ArrayLoglessPairHMM.java | 6 +- .../gatk/utils/pairhmm/CnyPairHMM.java | 8 +- .../utils/pairhmm/DebugJNILoglessPairHMM.java | 14 +- .../utils/pairhmm/FastLoglessPairHMM.java | 10 +- .../gatk/utils/pairhmm/FlexibleHMM.java | 4 +- .../gatk/utils/pairhmm/JNILoglessPairHMM.java | 4 +- .../gatk/utils/pairhmm/LoglessPairHMM.java | 6 +- .../utils/pairhmm/VectorLoglessPairHMM.java | 10 +- .../recalibration/BQSRReadTransformer.java | 12 +- .../recalibration/BaseRecalibration.java | 12 +- .../utils/recalibration/QualQuantizer.java | 22 +-- .../utils/recalibration/QuantizationInfo.java | 10 +- .../utils/recalibration/ReadCovariates.java | 4 +- .../gatk/utils/recalibration/RecalDatum.java | 6 +- .../utils/recalibration/RecalDatumNode.java | 10 +- .../gatk/utils/recalibration/RecalUtils.java | 40 ++-- .../recalibration/RecalibrationReport.java | 22 +-- .../recalibration/RecalibrationTables.java | 8 +- .../covariates/ContextCovariate.java | 20 +- .../recalibration/covariates/Covariate.java | 8 +- .../covariates/CycleCovariate.java | 14 +- .../covariates/ExperimentalCovariate.java | 2 +- .../covariates/QualityScoreCovariate.java | 10 +- .../covariates/ReadGroupCovariate.java | 10 +- .../covariates/RepeatCovariate.java | 14 +- .../covariates/RepeatLengthCovariate.java | 2 +- .../RepeatUnitAndLengthCovariate.java | 2 +- .../covariates/RepeatUnitCovariate.java | 2 +- .../covariates/RequiredCovariate.java | 2 +- .../covariates/StandardCovariate.java | 2 +- .../gatk/utils/sam/ClippedGATKSAMRecord.java | 2 +- .../diffengine/DiffEngineUnitTest.java | 8 +- .../walkers/diffengine/DiffNodeUnitTest.java | 7 +- .../DiffObjectsIntegrationTest.java | 4 +- .../diffengine/DiffableReaderUnitTest.java | 8 +- .../diffengine/DifferenceUnitTest.java | 13 +- .../walkers/WalkerTestIntegrationTest.java | 4 +- .../annotator/GenotypeSummariesUnitTest.java | 2 +- .../annotator/QualByDepthUnitTest.java | 4 +- .../walkers/annotator/RankSumUnitTest.java | 6 +- .../walkers/annotator/SnpEffUnitTest.java | 4 +- .../annotator/StrandOddsRatioUnitTest.java | 2 +- .../VariantAnnotatorIntegrationTest.java | 6 +- .../VariantOverlapAnnotatorUnitTest.java | 12 +- .../walkers/beagle/BeagleIntegrationTest.java | 4 +- .../AnalyzeCovariatesIntegrationTest.java | 8 +- .../walkers/bqsr/BQSRGathererUnitTest.java | 10 +- .../walkers/bqsr/BQSRIntegrationTest.java | 6 +- .../bqsr/ReadRecalibrationInfoUnitTest.java | 12 +- ...seCoverageDistributionIntegrationTest.java | 4 +- .../ErrorRatePerCycleIntegrationTest.java | 4 +- .../ReadGroupPropertiesIntegrationTest.java | 4 +- .../DiagnoseTargetsIntegrationTest.java | 6 +- .../LocusStatisticsUnitTest.java | 2 +- .../QualifyMissingIntervalsUnitTest.java | 8 +- ...astaAlternateReferenceIntegrationTest.java | 6 +- .../VariantFiltrationIntegrationTest.java | 6 +- .../ArtificialReadPileupTestProvider.java | 30 +-- ...eralPloidyGenotypeLikelihoodsUnitTest.java | 14 +- .../IndelGenotypeLikelihoodsUnitTest.java | 8 +- ...ndardCallerArgumentCollectionUnitTest.java | 8 +- .../UnifiedGenotyperEngineUnitTest.java | 12 +- ...perGeneralPloidySuite1IntegrationTest.java | 6 +- ...perGeneralPloidySuite2IntegrationTest.java | 8 +- ...iedGenotyperGeneralPloidyTestExecutor.java | 4 +- ...dGenotyperIndelCallingIntegrationTest.java | 4 +- .../UnifiedGenotyperIntegrationTest.java | 10 +- .../UnifiedGenotyperLargeScaleTest.java | 4 +- ...GenotyperNormalCallingIntegrationTest.java | 4 +- .../afcalc/AFCalcPerformanceUnitTest.java | 10 +- .../afcalc/AFCalcResultUnitTest.java | 10 +- .../genotyper/afcalc/AFCalcUnitTest.java | 12 +- ...neralPloidyAFCalculationModelUnitTest.java | 6 +- ...dentAllelesDiploidExactAFCalcUnitTest.java | 8 +- .../ActiveRegionTestDataSetUnitTest.java | 12 +- .../AssemblyResultSetUnitTest.java | 22 +-- .../tools/walkers/haplotypecaller/Civar.java | 2 +- .../haplotypecaller/CivarUnitTest.java | 4 +- ...LikelihoodCalculationEnginesBenchmark.java | 10 +- ...lexAndSymbolicVariantsIntegrationTest.java | 8 +- .../HaplotypeCallerGVCFIntegrationTest.java | 10 +- ...plotypeCallerGenotypingEngineUnitTest.java | 22 +-- .../HaplotypeCallerIntegrationTest.java | 12 +- .../HaplotypeCallerModesIntegrationTest.java | 6 +- ...aplotypeCallerParallelIntegrationTest.java | 4 +- .../KMerCounterCaseFixUnitTest.java | 4 +- .../walkers/haplotypecaller/KmerUnitTest.java | 6 +- .../LocalAssemblyEngineUnitTest.java | 22 +-- ...MMLikelihoodCalculationEngineUnitTest.java | 14 +- .../ReadErrorCorrectorUnitTest.java | 6 +- ...ngLikelihoodCalculationEngineUnitTest.java | 24 +-- .../ReferenceConfidenceModelUnitTest.java | 24 +-- .../graphs/BaseEdgeUnitTest.java | 4 +- .../graphs/BaseGraphUnitTest.java | 4 +- .../graphs/BaseVertexUnitTest.java | 4 +- .../graphs/CommonSuffixMergerUnitTest.java | 4 +- .../graphs/CommonSuffixSplitterUnitTest.java | 4 +- .../graphs/DeBruijnVertexUnitTest.java | 4 +- .../graphs/GraphUtilsUnitTest.java | 6 +- .../graphs/HaplotypeGraphUnitTest.java | 10 +- .../graphs/KBestHaplotypeFinderUnitTest.java | 10 +- .../graphs/LowWeightChainPrunerUnitTest.java | 4 +- .../graphs/MultiSampleEdgeUnitTest.java | 8 +- .../haplotypecaller/graphs/PathUnitTest.java | 4 +- .../haplotypecaller/graphs/RouteUnitTest.java | 4 +- .../graphs/SeqGraphUnitTest.java | 6 +- .../graphs/SeqVertexUnitTest.java | 4 +- .../SharedVertexSequenceSplitterUnitTest.java | 10 +- .../DanglingChainMergingGraphUnitTest.java | 16 +- .../ReadThreadingAssemblerUnitTest.java | 14 +- .../ReadThreadingGraphUnitTest.java | 14 +- .../SequenceForKmersUnitTest.java | 6 +- .../ConstrainedMateFixingManagerUnitTest.java | 10 +- .../indels/IndelRealignerIntegrationTest.java | 6 +- .../indels/IndelRealignerLargeScaleTest.java | 4 +- .../indels/IndelRealignerUnitTest.java | 10 +- .../PairHMMIndelErrorModelUnitTest.java | 14 +- .../tools/walkers/indels/ReadBinUnitTest.java | 12 +- ...RealignerTargetCreatorIntegrationTest.java | 4 +- .../RealignerTargetCreatorLargeScaleTest.java | 4 +- .../PhaseByTransmissionIntegrationTest.java | 4 +- .../ReadBackedPhasingIntegrationTest.java | 4 +- .../rnaseq/OverhangFixingManagerUnitTest.java | 10 +- .../SplitNCigarReadsIntegrationTest.java | 4 +- .../rnaseq/SplitNCigarReadsUnitTest.java | 12 +- ...mulateReadsForVariantsIntegrationTest.java | 4 +- .../ValidationAmpliconsIntegrationTest.java | 4 +- ...ValidationSiteSelectorIntegrationTest.java | 4 +- .../VariantEvalIntegrationTest.java | 6 +- .../VariantEvalWalkerUnitTest.java | 20 +- .../StratificationManagerUnitTest.java | 8 +- .../ApplyRecalibrationUnitTest.java | 4 +- .../VariantDataManagerUnitTest.java | 4 +- .../VariantGaussianMixtureModelUnitTest.java | 12 +- ...ntRecalibrationWalkersIntegrationTest.java | 6 +- ...lateGenotypePosteriorsIntegrationTest.java | 4 +- .../CombineGVCFsIntegrationTest.java | 6 +- .../CombineVariantsIntegrationTest.java | 4 +- .../variantutils/CombineVariantsUnitTest.java | 4 +- .../ConcordanceMetricsUnitTest.java | 14 +- .../GenotypeConcordanceIntegrationTest.java | 4 +- .../GenotypeGVCFsIntegrationTest.java | 4 +- ...ftAlignAndTrimVariantsIntegrationTest.java | 4 +- .../LeftAlignAndTrimVariantsUnitTest.java | 22 +-- .../LiftoverVariantsIntegrationTest.java | 6 +- .../PosteriorLikelihoodsUtilsUnitTest.java | 8 +- .../RegenotypeVariantsIntegrationTest.java | 6 +- .../SelectVariantsIntegrationTest.java | 6 +- ...SelectVariantsParallelIntegrationTest.java | 6 +- .../VCFStreamingIntegrationTest.java | 4 +- .../ValidateVariantsIntegrationTest.java | 6 +- ...ntsToAllelicPrimitivesIntegrationTest.java | 4 +- .../VariantsToBinaryPedIntegrationTest.java | 8 +- .../VariantsToTableIntegrationTest.java | 6 +- .../VariantsToVCFIntegrationTest.java | 4 +- .../gatk/utils/ContigComparatorUnitTest.java | 6 +- .../broadinstitute/gatk/utils/RandomDNA.java | 2 +- .../utils/collections/CountSetUnitTest.java | 4 +- .../genotyper/DiploidGenotypeUnitTest.java | 4 +- .../genotyper/MostLikelyAlleleUnitTest.java | 4 +- .../PerReadAlleleLikelihoodMapUnitTest.java | 24 +-- .../gatk/utils/gvcf/GVCFWriterUnitTest.java | 10 +- .../gatk/utils/gvcf/HomRefBlockUnitTest.java | 4 +- .../HaplotypeBaseComparatorUnitTest.java | 6 +- .../HaplotypeLDCalculatorUnitTest.java | 4 +- .../HaplotypeScoreComparatorUnitTest.java | 6 +- ...aplotypeSizeAndBaseComparatorUnitTest.java | 6 +- .../utils/haplotype/LDMergerUnitTest.java | 8 +- .../HaplotypeBAMWriterUnitTest.java | 16 +- .../NanoSchedulerIntegrationTest.java | 4 +- .../pairhmm/ActiveRegionTestDataSet.java | 22 +-- .../utils/pairhmm/CnyPairHMMUnitTest.java | 4 +- .../pairhmm/FastLoglessPairHMMUnitTest.java | 8 +- .../pairhmm/PairHMMEmpiricalBenchmark.java | 2 +- .../utils/pairhmm/PairHMMModelUnitTest.java | 6 +- .../PairHMMProbabilityBugIntegrationTest.java | 4 +- .../pairhmm/PairHMMSyntheticBenchmark.java | 6 +- .../gatk/utils/pairhmm/PairHMMTestData.java | 6 +- .../gatk/utils/pairhmm/PairHMMUnitTest.java | 14 +- .../ContextCovariateUnitTest.java | 16 +- .../recalibration/CycleCovariateUnitTest.java | 14 +- .../recalibration/QualQuantizerUnitTest.java | 8 +- .../recalibration/ReadCovariatesUnitTest.java | 14 +- .../ReadGroupCovariateUnitTest.java | 12 +- .../recalibration/RecalDatumUnitTest.java | 8 +- .../recalibration/RecalUtilsUnitTest.java | 8 +- .../RecalibrationReportUnitTest.java | 16 +- .../RecalibrationTablesUnitTest.java | 8 +- .../recalibration/RecalibrationTestUtils.java | 6 +- .../RepeatCovariatesUnitTest.java | 16 +- ...EdgeGreedySWPairwiseAlignmentUnitTest.java | 8 +- .../SWPairwiseAlignmentUnitTest.java | 4 +- protected/pom.xml | 32 +++- public/VectorPairHMM/pom.xml | 20 +- .../VectorPairHMM/src/main/c++/Sandbox.java | 2 +- public/c/bwa/Makefile | 5 +- public/c/bwa/README.md | 68 +++++++ public/c/bwa/build_linux.sh | 5 +- public/c/bwa/build_mac.sh | 7 +- ...atk_engine_alignment_bwa_c_BWACAligner.cpp | 30 +-- ..._gatk_engine_alignment_bwa_c_BWACAligner.h | 40 ++-- public/doc/GATK_Coding_Standards.tex | 4 +- public/external-example/pom.xml | 78 ++++---- .../org/mycompany/app/MyExampleWalker.java | 10 +- .../app/MyExampleWalkerIntegrationTest.java | 2 +- .../app/MyExampleWalkerUnitTest.java | 2 +- .../src/main/assembly/example-resources.xml | 4 +- .../gatk/engine/ReadMetrics.java | 6 +- .../gatk/engine/package-info.java | 2 +- .../gatk-queue-extensions-generator/pom.xml | 14 +- .../gatk/ArgumentDefinitionField.java | 18 +- .../queue/extensions/gatk/ArgumentField.java | 4 +- .../gatk/GATKExtensionsGenerator.java | 61 +++--- .../extensions/gatk/ReadFilterField.java | 8 +- .../src/main/assembly/example-resources.xml | 2 +- .../queue/qscripts/CNV/xhmmCNVpipeline.scala | 16 +- .../queue/qscripts/GATKResourcesBundle.scala | 14 +- .../qscripts/examples/ExampleCountLoci.scala | 6 +- .../qscripts/examples/ExampleCountReads.scala | 6 +- .../examples/ExampleCustomWalker.scala | 6 +- .../qscripts/examples/ExamplePrintReads.scala | 6 +- .../qscripts/examples/ExampleReadFilter.scala | 6 +- .../examples/ExampleRetryMemoryLimit.scala | 8 +- .../examples/ExampleUnifiedGenotyper.scala | 6 +- .../queue/qscripts/examples/HelloWorld.scala | 4 +- .../gatk/queue/qscripts/lib/ChunkVCF.scala | 10 +- .../gatk/queue/qscripts/lib/Vcf2Table.scala | 27 ++- .../gatk/queue/qscripts/lib/VcfToPed.scala | 12 +- .../gatk/queue/extensions/cancer/MuTect.scala | 32 ++-- .../extensions/gatk/BamGatherFunction.scala | 12 +- .../extensions/gatk/CatVariantsGatherer.scala | 8 +- .../gatk/ContigScatterFunction.scala | 6 +- .../gatk/DistributedScatterFunction.scala | 8 +- .../queue/extensions/gatk/DoC/package.scala | 18 +- .../queue/extensions/gatk/GATKIntervals.scala | 10 +- .../extensions/gatk/GATKScatterFunction.scala | 10 +- .../gatk/IntervalScatterFunction.scala | 6 +- .../gatk/LocusScatterFunction.scala | 6 +- .../extensions/gatk/ReadScatterFunction.scala | 2 +- .../queue/extensions/gatk/TaggedFile.scala | 6 +- .../extensions/gatk/VcfGatherFunction.scala | 10 +- .../gatk/WriteFlankingIntervalsFunction.scala | 8 +- .../picard/AddOrReplaceReadGroups.scala | 6 +- .../picard/CalculateHsMetrics.scala | 6 +- .../picard/CollectGcBiasMetrics.scala | 6 +- .../picard/CollectMultipleMetrics.scala | 6 +- .../queue/extensions/picard/FastqToSam.scala | 6 +- .../extensions/picard/MarkDuplicates.scala | 6 +- .../extensions/picard/MergeSamFiles.scala | 6 +- .../extensions/picard/PicardBamFunction.scala | 4 +- .../picard/PicardMetricsFunction.scala | 4 +- .../queue/extensions/picard/ReorderSam.scala | 6 +- .../queue/extensions/picard/RevertSam.scala | 6 +- .../queue/extensions/picard/SamToFastq.scala | 6 +- .../queue/extensions/picard/SortSam.scala | 6 +- .../extensions/picard/ValidateSamFile.scala | 6 +- .../SamtoolsCommandLineFunction.scala | 6 +- .../samtools/SamtoolsIndexFunction.scala | 4 +- .../samtools/SamtoolsMergeFunction.scala | 4 +- .../gatk/queue/extensions/snpeff/SnpEff.scala | 6 +- .../gatk/GATKIntervalsUnitTest.scala | 14 +- .../examples/ExampleCountLociQueueTest.scala | 8 +- .../examples/ExampleCountReadsQueueTest.scala | 8 +- .../examples/ExamplePrintReadsQueueTest.scala | 10 +- .../examples/ExampleReadFilterQueueTest.scala | 8 +- .../ExampleRetryMemoryLimitQueueTest.scala | 8 +- .../ExampleUnifiedGenotyperQueueTest.scala | 16 +- .../examples/HelloWorldQueueTest.scala | 28 +-- public/gatk-queue/pom.xml | 131 +------------ .../gatk/queue/QueueVersion.java | 4 +- .../gatk/queue/package-info.java | 2 +- .../gatk/queue/QCommandLine.scala | 26 +-- .../gatk/queue/QCommandPlugin.scala | 2 +- .../gatk/queue/QException.scala | 6 +- .../broadinstitute/gatk/queue/QScript.scala | 24 +-- .../gatk/queue/QScriptManager.scala | 10 +- .../broadinstitute/gatk/queue/QSettings.scala | 4 +- .../queue/engine/CommandLineJobManager.scala | 4 +- .../queue/engine/CommandLineJobRunner.scala | 8 +- .../engine/CommandLinePluginManager.scala | 4 +- .../gatk/queue/engine/FunctionEdge.scala | 8 +- .../queue/engine/InProcessJobManager.scala | 4 +- .../gatk/queue/engine/InProcessRunner.scala | 6 +- .../gatk/queue/engine/JobManager.scala | 4 +- .../gatk/queue/engine/JobRunInfo.scala | 2 +- .../gatk/queue/engine/JobRunner.scala | 4 +- .../gatk/queue/engine/MappingEdge.scala | 2 +- .../gatk/queue/engine/QEdge.scala | 2 +- .../gatk/queue/engine/QGraph.scala | 18 +- .../gatk/queue/engine/QGraphSettings.scala | 8 +- .../gatk/queue/engine/QNode.scala | 2 +- .../gatk/queue/engine/QStatusMessenger.scala | 4 +- .../gatk/queue/engine/RunnerStatus.scala | 2 +- .../queue/engine/drmaa/DrmaaJobManager.scala | 8 +- .../queue/engine/drmaa/DrmaaJobRunner.scala | 10 +- .../gridengine/GridEngineJobManager.scala | 6 +- .../gridengine/GridEngineJobRunner.scala | 8 +- .../queue/engine/lsf/Lsf706JobManager.scala | 6 +- .../queue/engine/lsf/Lsf706JobRunner.scala | 18 +- .../pbsengine/PbsEngineJobManager.scala | 6 +- .../engine/pbsengine/PbsEngineJobRunner.scala | 8 +- .../queue/engine/shell/ShellJobManager.scala | 6 +- .../queue/engine/shell/ShellJobRunner.scala | 10 +- .../queue/function/CommandLineFunction.scala | 6 +- .../queue/function/InProcessFunction.scala | 2 +- .../function/JavaCommandLineFunction.scala | 6 +- .../queue/function/ListWriterFunction.scala | 4 +- .../gatk/queue/function/QFunction.scala | 10 +- .../queue/function/RetryMemoryLimit.scala | 4 +- .../scattergather/CloneFunction.scala | 8 +- .../ConcatenateLogsFunction.scala | 10 +- .../scattergather/GatherFunction.scala | 10 +- .../scattergather/GathererFunction.scala | 6 +- .../scattergather/ScatterFunction.scala | 6 +- .../ScatterGatherableFunction.scala | 12 +- .../SimpleTextGatherFunction.scala | 6 +- .../library/clf/vcf/VCFExtractIntervals.scala | 6 +- .../library/clf/vcf/VCFExtractSamples.scala | 8 +- .../gatk/queue/library/ipf/SortByRef.scala | 8 +- .../library/ipf/vcf/VCFExtractIntervals.scala | 8 +- .../library/ipf/vcf/VCFExtractSamples.scala | 8 +- .../library/ipf/vcf/VCFExtractSites.scala | 8 +- .../library/ipf/vcf/VCFSimpleMerge.scala | 10 +- .../gatk/queue/util/ClassFieldCache.scala | 6 +- .../gatk/queue/util/CollectionUtils.scala | 2 +- .../gatk/queue/util/EmailMessage.scala | 2 +- .../gatk/queue/util/EmailSettings.scala | 4 +- .../gatk/queue/util/Logging.scala | 2 +- .../util/PrimitiveOptionConversions.scala | 2 +- .../gatk/queue/util/QJobReport.scala | 8 +- .../gatk/queue/util/QJobsReporter.scala | 14 +- .../gatk/queue/util/QScriptUtils.scala | 2 +- .../gatk/queue/util/ReflectionUtils.scala | 12 +- .../gatk/queue/util/RemoteFile.scala | 4 +- .../gatk/queue/util/RemoteFileConverter.scala | 2 +- .../gatk/queue/util/Retry.scala | 4 +- .../gatk/queue/util/RetryException.scala | 4 +- .../ScalaCompoundArgumentTypeDescriptor.scala | 8 +- .../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 | 16 +- .../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 +- public/gatk-root/pom.xml | 96 +++++++--- public/gatk-tools-public/pom.xml | 33 +--- .../java/htsjdk/samtools/GATKBAMFileSpan.java | 4 +- .../main/java/htsjdk/samtools/GATKChunk.java | 2 +- .../gatk/engine/CommandLineExecutable.java | 32 ++-- .../gatk/engine/CommandLineGATK.java | 30 +-- .../gatk/engine/GenomeAnalysisEngine.java | 78 ++++---- .../gatk/engine/ReadProperties.java | 12 +- .../gatk/engine/WalkerManager.java | 32 ++-- .../gatk/engine/alignment/Aligner.java | 2 +- .../gatk/engine/alignment/Alignment.java | 10 +- .../gatk/engine/alignment/CheckAlignment.java | 30 +-- .../gatk/engine/alignment/bwa/BWAAligner.java | 4 +- .../alignment/bwa/BWAConfiguration.java | 2 +- .../gatk/engine/alignment/bwa/BWTFiles.java | 20 +- .../engine/alignment/bwa/c/BWACAligner.java | 38 ++-- .../gatk/engine/alignment/bwa/c/BWAPath.java | 2 +- .../bwa/java/AlignerTestHarness.java | 16 +- .../bwa/java/AlignmentMatchSequence.java | 10 +- .../alignment/bwa/java/AlignmentState.java | 2 +- .../alignment/bwa/java/BWAAlignment.java | 8 +- .../alignment/bwa/java/BWAJavaAligner.java | 14 +- .../engine/alignment/bwa/java/LowerBound.java | 4 +- .../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 | 8 +- .../alignment/reference/bwt/BWTReader.java | 16 +- .../bwt/BWTSupplementaryFileGenerator.java | 2 +- .../alignment/reference/bwt/BWTWriter.java | 14 +- .../engine/alignment/reference/bwt/Bases.java | 6 +- .../alignment/reference/bwt/Counts.java | 6 +- .../reference/bwt/CreateBWTFromReference.java | 10 +- .../reference/bwt/SequenceBlock.java | 2 +- .../alignment/reference/bwt/SuffixArray.java | 8 +- .../reference/bwt/SuffixArrayReader.java | 14 +- .../reference/bwt/SuffixArrayWriter.java | 12 +- .../packing/BasePackedInputStream.java | 6 +- .../packing/BasePackedOutputStream.java | 6 +- .../packing/CreatePACFromReference.java | 2 +- .../reference/packing/PackUtils.java | 14 +- .../packing/UnsignedIntPackedInputStream.java | 2 +- .../UnsignedIntPackedOutputStream.java | 2 +- .../arguments/DbsnpArgumentCollection.java | 6 +- .../arguments/GATKArgumentCollection.java | 22 +-- ...VariantContextInputArgumentCollection.java | 6 +- .../engine/arguments/ValidationExclusion.java | 4 +- .../engine/contexts/AlignmentContext.java | 18 +- .../contexts/AlignmentContextUtils.java | 14 +- .../engine/contexts/ReferenceContext.java | 8 +- .../gatk/engine/datasources/package-info.java | 2 +- .../datasources/providers/AllLocusView.java | 12 +- .../providers/CoveredLocusView.java | 4 +- .../IntervalOverlappingRODsFromStream.java | 10 +- .../IntervalReferenceOrderedView.java | 18 +- .../providers/InvalidPositionException.java | 2 +- .../providers/LocusReferenceView.java | 18 +- .../providers/LocusShardDataProvider.java | 14 +- .../datasources/providers/LocusView.java | 16 +- .../ManagingReferenceOrderedView.java | 14 +- .../providers/RODMetaDataContainer.java | 6 +- .../ReadBasedReferenceOrderedView.java | 16 +- .../providers/ReadReferenceView.java | 6 +- .../providers/ReadShardDataProvider.java | 16 +- .../datasources/providers/ReadView.java | 8 +- .../providers/ReferenceOrderedView.java | 6 +- .../datasources/providers/ReferenceView.java | 10 +- .../datasources/providers/RodLocusView.java | 20 +- .../providers/ShardDataProvider.java | 14 +- .../engine/datasources/providers/View.java | 2 +- .../datasources/providers/package-info.java | 2 +- .../reads/ActiveRegionShardBalancer.java | 2 +- .../datasources/reads/BAMAccessPlan.java | 3 +- .../engine/datasources/reads/BAMSchedule.java | 20 +- .../datasources/reads/BAMScheduler.java | 18 +- .../reads/BGZFBlockLoadingDispatcher.java | 6 +- .../datasources/reads/BlockInputStream.java | 22 +-- .../engine/datasources/reads/BlockLoader.java | 10 +- .../datasources/reads/FileHandleCache.java | 12 +- .../engine/datasources/reads/FilePointer.java | 26 +-- .../datasources/reads/GATKBAMIndex.java | 28 +-- .../datasources/reads/GATKBAMIndexData.java | 2 +- .../IntervalOverlapFilteringIterator.java | 10 +- .../datasources/reads/IntervalSharder.java | 8 +- .../engine/datasources/reads/LocusShard.java | 8 +- .../datasources/reads/LocusShardBalancer.java | 2 +- .../engine/datasources/reads/ReadShard.java | 20 +- .../datasources/reads/ReadShardBalancer.java | 8 +- .../datasources/reads/SAMDataSource.java | 80 ++++---- .../engine/datasources/reads/SAMReaderID.java | 4 +- .../gatk/engine/datasources/reads/Shard.java | 16 +- .../datasources/reads/ShardBalancer.java | 4 +- .../datasources/reads/package-info.java | 2 +- .../reads/utilities/BAMFileStat.java | 14 +- .../reads/utilities/BAMTagRenamer.java | 6 +- .../reads/utilities/FindLargeShards.java | 30 +-- .../reads/utilities/PrintBAMRegion.java | 8 +- .../reads/utilities/PrintBGZFBounds.java | 6 +- .../reads/utilities/UnzipSingleBlock.java | 6 +- .../reads/utilities/package-info.java | 2 +- .../reference/ReferenceDataSource.java | 18 +- .../datasources/reference/package-info.java | 2 +- .../datasources/rmd/DataStreamSegment.java | 2 +- .../engine/datasources/rmd/EntireStream.java | 2 +- .../datasources/rmd/MappedStreamSegment.java | 6 +- .../rmd/ReferenceOrderedDataPool.java | 24 +-- .../rmd/ReferenceOrderedDataSource.java | 24 +-- .../engine/datasources/rmd/ResourcePool.java | 10 +- .../engine/datasources/rmd/package-info.java | 2 +- .../AlleleBiasedDownsamplingUtils.java | 22 +-- .../engine/downsampling/DownsampleType.java | 2 +- .../gatk/engine/downsampling/Downsampler.java | 2 +- .../downsampling/DownsamplingMethod.java | 10 +- .../DownsamplingReadsIterator.java | 12 +- .../downsampling/DownsamplingUtils.java | 6 +- .../downsampling/FractionalDownsampler.java | 8 +- .../FractionalDownsamplerFactory.java | 2 +- .../downsampling/LevelingDownsampler.java | 4 +- .../downsampling/PassThroughDownsampler.java | 2 +- .../PerSampleDownsamplingReadsIterator.java | 12 +- .../engine/downsampling/ReadsDownsampler.java | 2 +- .../downsampling/ReadsDownsamplerFactory.java | 2 +- .../downsampling/ReservoirDownsampler.java | 8 +- .../ReservoirDownsamplerFactory.java | 2 +- .../SimplePositionalDownsampler.java | 2 +- .../SimplePositionalDownsamplerFactory.java | 2 +- .../gatk/engine/executive/Accumulator.java | 20 +- .../executive/HierarchicalMicroScheduler.java | 34 ++-- .../HierarchicalMicroSchedulerMBean.java | 2 +- .../executive/LinearMicroScheduler.java | 30 +-- .../gatk/engine/executive/MicroScheduler.java | 44 ++--- .../engine/executive/MicroSchedulerMBean.java | 2 +- .../engine/executive/OutputMergeTask.java | 4 +- .../gatk/engine/executive/ReduceTree.java | 2 +- .../gatk/engine/executive/ShardTraverser.java | 20 +- .../gatk/engine/executive/TreeReducer.java | 10 +- .../gatk/engine/executive/WindowMaker.java | 34 ++-- .../gatk/engine/executive/package-info.java | 2 +- .../gatk/engine/filters/BadCigarFilter.java | 2 +- .../gatk/engine/filters/BadMateFilter.java | 2 +- .../filters/CountingFilteringIterator.java | 6 +- .../engine/filters/DuplicateReadFilter.java | 2 +- .../FailsVendorQualityCheckFilter.java | 2 +- .../gatk/engine/filters/FilterManager.java | 8 +- .../engine/filters/LibraryReadFilter.java | 6 +- .../engine/filters/MalformedReadFilter.java | 14 +- .../engine/filters/MappingQualityFilter.java | 4 +- .../MappingQualityUnavailableFilter.java | 4 +- .../filters/MappingQualityZeroFilter.java | 2 +- .../engine/filters/MateSameStrandFilter.java | 2 +- .../engine/filters/MaxInsertSizeFilter.java | 4 +- .../filters/MissingReadGroupFilter.java | 2 +- .../filters/NDNCigarReadTransformer.java | 14 +- .../NoOriginalQualityScoresFilter.java | 2 +- .../filters/NotPrimaryAlignmentFilter.java | 2 +- .../engine/filters/Platform454Filter.java | 6 +- .../gatk/engine/filters/PlatformFilter.java | 8 +- .../engine/filters/PlatformUnitFilter.java | 4 +- .../filters/PlatformUnitFilterHelper.java | 6 +- .../gatk/engine/filters/ReadFilter.java | 8 +- .../filters/ReadGroupBlackListFilter.java | 6 +- .../gatk/engine/filters/ReadLengthFilter.java | 4 +- .../gatk/engine/filters/ReadNameFilter.java | 4 +- .../gatk/engine/filters/ReadStrandFilter.java | 4 +- .../filters/ReassignMappingQualityFilter.java | 4 +- .../ReassignOneMappingQualityFilter.java | 4 +- .../gatk/engine/filters/SampleFilter.java | 4 +- .../engine/filters/SingleReadGroupFilter.java | 4 +- .../engine/filters/UnmappedReadFilter.java | 2 +- .../gatk/engine/filters/package-info.java | 2 +- .../gatk/engine/io/DirectOutputTracker.java | 8 +- .../gatk/engine/io/FastqFileWriter.java | 10 +- .../gatk/engine/io/GATKSAMFileWriter.java | 4 +- .../gatk/engine/io/OutputTracker.java | 22 +-- .../engine/io/ThreadGroupOutputTracker.java | 18 +- .../io/storage/OutputStreamStorage.java | 10 +- .../io/storage/SAMFileWriterStorage.java | 8 +- .../gatk/engine/io/storage/Storage.java | 2 +- .../engine/io/storage/StorageFactory.java | 14 +- .../storage/VariantContextWriterStorage.java | 16 +- .../OutputStreamArgumentTypeDescriptor.java | 12 +- .../engine/io/stubs/OutputStreamStub.java | 4 +- .../SAMFileReaderArgumentTypeDescriptor.java | 10 +- .../SAMFileWriterArgumentTypeDescriptor.java | 16 +- .../engine/io/stubs/SAMFileWriterStub.java | 28 +-- .../gatk/engine/io/stubs/Stub.java | 4 +- .../VCFWriterArgumentTypeDescriptor.java | 10 +- .../io/stubs/VariantContextWriterStub.java | 8 +- .../engine/iterators/BoundedReadIterator.java | 8 +- .../engine/iterators/GATKSAMIterator.java | 8 +- .../iterators/GATKSAMIteratorAdapter.java | 24 +-- .../iterators/GATKSAMRecordIterator.java | 10 +- .../engine/iterators/GenomeLocusIterator.java | 6 +- .../engine/iterators/IterableIterator.java | 2 +- .../MalformedBAMErrorReformatingIterator.java | 4 +- .../engine/iterators/NullSAMIterator.java | 6 +- .../engine/iterators/PeekingIterator.java | 2 +- .../iterators/PositionTrackingIterator.java | 8 +- .../engine/iterators/PushbackIterator.java | 2 +- .../engine/iterators/RNAReadTransformer.java | 2 +- .../iterators/ReadFormattingIterator.java | 12 +- .../engine/iterators/ReadTransformer.java | 8 +- .../iterators/ReadTransformersMode.java | 2 +- .../iterators/VerifyingSamIterator.java | 12 +- .../gatk/engine/iterators/package-info.java | 2 +- .../gatk/engine/phonehome/GATKRunReport.java | 32 ++-- .../phonehome/GATKRunReportException.java | 4 +- .../engine/refdata/RODRecordListImpl.java | 18 +- .../engine/refdata/RefMetaDataTracker.java | 12 +- .../ReferenceDependentFeatureCodec.java | 4 +- .../engine/refdata/ReferenceOrderedDatum.java | 6 +- .../engine/refdata/SeekableRODIterator.java | 28 +-- .../refdata/VariantContextAdaptors.java | 12 +- .../gatk/engine/refdata/package-info.java | 2 +- .../engine/refdata/tracks/FeatureManager.java | 16 +- .../refdata/tracks/IndexDictionaryUtils.java | 6 +- .../gatk/engine/refdata/tracks/RMDTrack.java | 12 +- .../refdata/tracks/RMDTrackBuilder.java | 34 ++-- .../utils/FeatureToGATKFeatureIterator.java | 4 +- .../refdata/utils/FlashBackIterator.java | 6 +- .../engine/refdata/utils/GATKFeature.java | 10 +- .../LocationAwareSeekableRODIterator.java | 4 +- .../gatk/engine/refdata/utils/RMDTriplet.java | 4 +- .../engine/refdata/utils/RODRecordList.java | 6 +- .../gatk/engine/report/GATKReport.java | 18 +- .../gatk/engine/report/GATKReportColumn.java | 2 +- .../engine/report/GATKReportColumnFormat.java | 2 +- .../engine/report/GATKReportDataType.java | 2 +- .../engine/report/GATKReportGatherer.java | 6 +- .../gatk/engine/report/GATKReportTable.java | 32 ++-- .../gatk/engine/report/GATKReportVersion.java | 6 +- .../resourcemanagement/ThreadAllocation.java | 10 +- .../gatk/engine/samples/Affection.java | 2 +- .../gatk/engine/samples/Gender.java | 2 +- .../gatk/engine/samples/PedReader.java | 12 +- .../samples/PedigreeValidationType.java | 2 +- .../gatk/engine/samples/Sample.java | 4 +- .../gatk/engine/samples/SampleDB.java | 6 +- .../gatk/engine/samples/SampleDBBuilder.java | 8 +- .../gatk/engine/samples/Trio.java | 2 +- .../traversals/TAROrderedReadCache.java | 10 +- .../engine/traversals/TraversalEngine.java | 19 +- .../traversals/TraverseActiveRegions.java | 44 ++--- .../engine/traversals/TraverseDuplicates.java | 18 +- .../engine/traversals/TraverseLociNano.java | 30 +-- .../engine/traversals/TraverseReadPairs.java | 14 +- .../engine/traversals/TraverseReadsNano.java | 26 +-- .../gatk/engine/traversals/package-info.java | 2 +- .../ActiveRegionTraversalParameters.java | 4 +- .../engine/walkers/ActiveRegionWalker.java | 32 ++-- .../gatk/engine/walkers/Allows.java | 2 +- .../gatk/engine/walkers/Attribution.java | 2 +- .../gatk/engine/walkers/BAQMode.java | 6 +- .../gatk/engine/walkers/By.java | 2 +- .../gatk/engine/walkers/DataSource.java | 2 +- .../gatk/engine/walkers/Downsample.java | 4 +- .../gatk/engine/walkers/DuplicateWalker.java | 12 +- .../gatk/engine/walkers/LocusWalker.java | 20 +- .../gatk/engine/walkers/Multiplex.java | 2 +- .../gatk/engine/walkers/Multiplexer.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 | 4 +- .../gatk/engine/walkers/ReadPairWalker.java | 2 +- .../gatk/engine/walkers/ReadWalker.java | 10 +- .../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 | 26 +-- .../gatk/engine/walkers/WalkerName.java | 2 +- .../gatk/engine/walkers/Window.java | 2 +- .../walkers/diffengine/BAMDiffableReader.java | 2 +- .../walkers/diffengine/DiffElement.java | 8 +- .../engine/walkers/diffengine/DiffEngine.java | 20 +- .../engine/walkers/diffengine/DiffNode.java | 12 +- .../walkers/diffengine/DiffObjects.java | 22 +-- .../engine/walkers/diffengine/DiffValue.java | 2 +- .../walkers/diffengine/DiffableReader.java | 2 +- .../engine/walkers/diffengine/Difference.java | 2 +- .../diffengine/GATKReportDiffableReader.java | 8 +- .../walkers/diffengine/VCFDiffableReader.java | 4 +- .../gatk/tools/CatVariants.java | 26 +-- .../gatk/tools/ListAnnotations.java | 16 +- .../walkers/annotator/AlleleBalance.java | 18 +- .../annotator/AlleleBalanceBySample.java | 18 +- .../tools/walkers/annotator/BaseCounts.java | 16 +- .../annotator/ChromosomeCountConstants.java | 2 +- .../gatk/tools/walkers/annotator/LowMQ.java | 16 +- .../annotator/MappingQualityZeroBySample.java | 18 +- .../tools/walkers/annotator/NBaseCount.java | 18 +- .../gatk/tools/walkers/annotator/SnpEff.java | 26 +-- .../tools/walkers/annotator/SnpEffUtil.java | 4 +- .../walkers/annotator/VariantAnnotator.java | 36 ++-- .../annotator/VariantAnnotatorEngine.java | 20 +- .../annotator/VariantOverlapAnnotator.java | 12 +- .../ActiveRegionBasedAnnotation.java | 4 +- .../AnnotationInterfaceManager.java | 8 +- .../annotator/interfaces/AnnotationType.java | 2 +- .../interfaces/AnnotatorCompatible.java | 4 +- .../interfaces/ExperimentalAnnotation.java | 2 +- .../interfaces/GenotypeAnnotation.java | 10 +- .../interfaces/InfoFieldAnnotation.java | 10 +- .../interfaces/RodRequiringAnnotation.java | 2 +- .../interfaces/StandardAnnotation.java | 2 +- .../VariantAnnotatorAnnotation.java | 8 +- .../interfaces/WorkInProgressAnnotation.java | 2 +- .../walkers/beagle/BeagleOutputToVCF.java | 28 +-- .../walkers/beagle/ProduceBeagleInput.java | 40 ++-- .../beagle/VariantsToBeagleUnphased.java | 34 ++-- .../tools/walkers/coverage/CallableLoci.java | 32 ++-- .../walkers/coverage/CompareCallableLoci.java | 28 +-- .../tools/walkers/coverage/CoverageUtils.java | 18 +- .../walkers/coverage/DepthOfCoverage.java | 58 +++--- .../coverage/DepthOfCoverageStats.java | 6 +- .../tools/walkers/coverage/DoCOutputType.java | 2 +- .../walkers/coverage/GCContentByInterval.java | 24 +-- .../diagnostics/CoveredByNSamplesSites.java | 29 +-- .../diagnostics/ErrorRatePerCycle.java | 32 ++-- .../diagnostics/ReadGroupProperties.java | 26 +-- .../diagnostics/ReadLengthDistribution.java | 22 +-- .../walkers/examples/GATKDocsExample.java | 16 +- .../walkers/examples/GATKPaperGenotyper.java | 28 +-- .../fasta/FastaAlternateReferenceMaker.java | 36 ++-- .../walkers/fasta/FastaReferenceMaker.java | 24 +-- .../tools/walkers/fasta/FastaSequence.java | 6 +- .../gatk/tools/walkers/fasta/FastaStats.java | 20 +- .../tools/walkers/filters/ClusteredSnps.java | 10 +- .../walkers/filters/FiltrationContext.java | 4 +- .../filters/FiltrationContextWindow.java | 8 +- .../walkers/filters/VariantFiltration.java | 32 ++-- .../HCMappingQualityFilter.java | 8 +- .../gatk/tools/walkers/package-info.java | 2 +- .../gatk/tools/walkers/qc/CheckPileup.java | 42 ++--- .../gatk/tools/walkers/qc/CountBases.java | 20 +- .../gatk/tools/walkers/qc/CountIntervals.java | 28 +-- .../gatk/tools/walkers/qc/CountLoci.java | 22 +-- .../gatk/tools/walkers/qc/CountMales.java | 26 +-- .../gatk/tools/walkers/qc/CountRODs.java | 38 ++-- .../gatk/tools/walkers/qc/CountRODsByRef.java | 26 +-- .../tools/walkers/qc/CountReadEvents.java | 26 +-- .../gatk/tools/walkers/qc/CountReads.java | 22 +-- .../tools/walkers/qc/CountTerminusEvent.java | 26 +-- .../tools/walkers/qc/DocumentationTest.java | 16 +- .../gatk/tools/walkers/qc/ErrorThrowing.java | 33 ++-- .../gatk/tools/walkers/qc/FlagStat.java | 24 +-- .../gatk/tools/walkers/qc/Pileup.java | 28 +-- .../gatk/tools/walkers/qc/PrintRODs.java | 22 +-- .../gatk/tools/walkers/qc/QCRef.java | 24 +-- .../tools/walkers/qc/ReadClippingStats.java | 34 ++-- .../tools/walkers/qc/RodSystemValidation.java | 24 +-- .../tools/walkers/readutils/ClipReads.java | 44 ++--- .../tools/walkers/readutils/PrintReads.java | 38 ++-- .../walkers/readutils/ReadAdaptorTrimmer.java | 31 ++-- .../tools/walkers/readutils/SplitSamFile.java | 26 +-- .../validation/ValidationAmplicons.java | 38 ++-- .../walkers/varianteval/VariantEval.java | 50 ++--- .../varianteval/VariantEvalReportWriter.java | 38 ++-- .../varianteval/evaluators/CompOverlap.java | 12 +- .../varianteval/evaluators/CountVariants.java | 18 +- .../evaluators/IndelLengthHistogram.java | 16 +- .../varianteval/evaluators/IndelSummary.java | 20 +- .../MendelianViolationEvaluator.java | 18 +- .../evaluators/MultiallelicSummary.java | 16 +- .../evaluators/PrintMissingComp.java | 12 +- .../varianteval/evaluators/StandardEval.java | 2 +- .../evaluators/ThetaVariantEvaluator.java | 12 +- .../evaluators/TiTvVariantEvaluator.java | 16 +- .../evaluators/ValidationReport.java | 16 +- .../evaluators/VariantEvaluator.java | 14 +- .../evaluators/VariantSummary.java | 22 +-- .../stratifications/AlleleCount.java | 12 +- .../stratifications/AlleleFrequency.java | 8 +- .../varianteval/stratifications/CompRod.java | 8 +- .../varianteval/stratifications/Contig.java | 6 +- .../varianteval/stratifications/CpG.java | 6 +- .../stratifications/Degeneracy.java | 6 +- .../DynamicStratification.java | 2 +- .../varianteval/stratifications/EvalRod.java | 8 +- .../varianteval/stratifications/Filter.java | 6 +- .../stratifications/FunctionalClass.java | 8 +- .../stratifications/IndelSize.java | 6 +- .../IntervalStratification.java | 12 +- .../stratifications/JexlExpression.java | 8 +- .../varianteval/stratifications/Novelty.java | 8 +- .../stratifications/OneBPIndel.java | 6 +- .../RequiredStratification.java | 2 +- .../varianteval/stratifications/Sample.java | 10 +- .../SnpEffPositionModifier.java | 14 +- .../StandardStratification.java | 2 +- .../stratifications/TandemRepeat.java | 8 +- .../stratifications/VariantStratifier.java | 12 +- .../stratifications/VariantType.java | 6 +- .../stratifications/manager/StratNode.java | 10 +- .../manager/StratNodeIterator.java | 6 +- .../manager/StratificationManager.java | 38 ++-- .../stratifications/manager/Stratifier.java | 2 +- .../walkers/varianteval/util/Analysis.java | 2 +- .../util/AnalysisModuleScanner.java | 10 +- .../walkers/varianteval/util/DataPoint.java | 2 +- .../varianteval/util/EvaluationContext.java | 22 +-- .../walkers/varianteval/util/Molten.java | 2 +- .../util/SortableJexlVCMatchExp.java | 2 +- .../varianteval/util/VariantEvalUtils.java | 30 +-- .../VQSRCalibrationCurve.java | 10 +- .../walkers/variantutils/CombineVariants.java | 36 ++-- .../variantutils/ConcordanceMetrics.java | 10 +- .../variantutils/FilterLiftedVariants.java | 28 +-- .../variantutils/GenotypeConcordance.java | 26 +-- .../LeftAlignAndTrimVariants.java | 39 ++-- .../variantutils/LiftoverVariants.java | 32 ++-- .../variantutils/RandomlySplitVariants.java | 32 ++-- .../walkers/variantutils/SelectHeaders.java | 34 ++-- .../walkers/variantutils/SelectVariants.java | 40 ++-- .../variantutils/ValidateVariants.java | 30 +-- .../VariantValidationAssessor.java | 32 ++-- .../VariantsToAllelicPrimitives.java | 28 +-- .../variantutils/VariantsToBinaryPed.java | 53 +++--- .../walkers/variantutils/VariantsToTable.java | 28 +-- .../walkers/variantutils/VariantsToVCF.java | 46 ++--- .../gatk/utils/AutoFormattingTime.java | 2 +- .../broadinstitute/gatk/utils/BaseUtils.java | 10 +- .../gatk/utils/BitSetUtils.java | 2 +- .../gatk/utils/ContigComparator.java | 2 +- .../gatk/utils/DeprecatedToolChecks.java | 2 +- .../gatk/utils/GenomeLocParser.java | 8 +- .../gatk/utils/GenomeLocSortedSet.java | 10 +- .../gatk/utils/HeapSizeMonitor.java | 8 +- .../broadinstitute/gatk/utils/IndelUtils.java | 8 +- .../broadinstitute/gatk/utils/LRUCache.java | 2 +- .../MRUCachingSAMSequenceDictionary.java | 14 +- .../gatk/utils/MannWhitneyU.java | 12 +- .../broadinstitute/gatk/utils/MathUtils.java | 16 +- .../org/broadinstitute/gatk/utils/Median.java | 2 +- .../gatk/utils/MendelianViolation.java | 4 +- .../gatk/utils/MultiThreadedErrorTracker.java | 10 +- .../gatk/utils/NGSPlatform.java | 6 +- .../broadinstitute/gatk/utils/PathUtils.java | 6 +- .../gatk/utils/QualityUtils.java | 2 +- .../gatk/utils/R/RScriptExecutor.java | 20 +- .../utils/R/RScriptExecutorException.java | 6 +- .../gatk/utils/R/RScriptLibrary.java | 6 +- .../broadinstitute/gatk/utils/R/RUtils.java | 2 +- .../gatk/utils/SampleUtils.java | 16 +- .../gatk/utils/SequenceDictionaryUtils.java | 10 +- .../gatk/utils/UnvalidatingGenomeLoc.java | 2 +- .../org/broadinstitute/gatk/utils/Utils.java | 14 +- .../gatk/utils/activeregion/ActiveRegion.java | 16 +- .../activeregion/ActiveRegionReadState.java | 2 +- .../utils/activeregion/ActivityProfile.java | 8 +- .../activeregion/ActivityProfileState.java | 4 +- .../activeregion/BandPassActivityProfile.java | 14 +- .../gatk/utils/analysis/AminoAcid.java | 2 +- .../gatk/utils/analysis/AminoAcidTable.java | 2 +- .../gatk/utils/analysis/AminoAcidUtils.java | 2 +- .../broadinstitute/gatk/utils/baq/BAQ.java | 40 ++-- .../gatk/utils/baq/BAQReadTransformer.java | 20 +- .../utils/baq/ReadTransformingIterator.java | 14 +- .../gatk/utils/classloader/JVMUtils.java | 22 +-- .../gatk/utils/classloader/PluginManager.java | 14 +- .../classloader/ProtectedPackageSource.java | 2 +- .../classloader/PublicPackageSource.java | 2 +- .../gatk/utils/clipping/ClippingOp.java | 18 +- .../clipping/ClippingRepresentation.java | 2 +- .../gatk/utils/clipping/ReadClipper.java | 22 +-- .../gatk/utils/codecs/beagle/BeagleCodec.java | 8 +- .../utils/codecs/beagle/BeagleFeature.java | 2 +- .../utils/codecs/hapmap/RawHapMapCodec.java | 2 +- .../utils/codecs/hapmap/RawHapMapFeature.java | 2 +- .../gatk/utils/codecs/refseq/RefSeqCodec.java | 12 +- .../utils/codecs/refseq/RefSeqFeature.java | 12 +- .../gatk/utils/codecs/refseq/Transcript.java | 6 +- .../codecs/sampileup/SAMPileupCodec.java | 4 +- .../codecs/sampileup/SAMPileupFeature.java | 2 +- .../utils/codecs/samread/SAMReadCodec.java | 2 +- .../utils/codecs/samread/SAMReadFeature.java | 2 +- .../utils/codecs/table/BedTableCodec.java | 4 +- .../gatk/utils/codecs/table/TableCodec.java | 8 +- .../gatk/utils/codecs/table/TableFeature.java | 6 +- .../utils/collections/DefaultHashMap.java | 2 +- .../utils/collections/ExpandingArrayList.java | 2 +- .../LoggingNestedIntegerArray.java | 6 +- .../utils/collections/NestedIntegerArray.java | 10 +- .../gatk/utils/collections/Pair.java | 2 +- .../gatk/utils/collections/PrimitivePair.java | 2 +- .../utils/collections/RODMergingIterator.java | 14 +- .../gatk/utils/commandline/Advanced.java | 2 +- .../gatk/utils/commandline/Argument.java | 2 +- .../utils/commandline/ArgumentCollection.java | 2 +- .../utils/commandline/ArgumentDefinition.java | 8 +- .../commandline/ArgumentDefinitionGroup.java | 6 +- .../commandline/ArgumentDefinitions.java | 8 +- .../utils/commandline/ArgumentException.java | 4 +- .../utils/commandline/ArgumentIOType.java | 6 +- .../gatk/utils/commandline/ArgumentMatch.java | 4 +- .../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 | 4 +- .../utils/commandline/ArgumentSource.java | 6 +- .../commandline/ArgumentTypeDescriptor.java | 50 ++--- .../gatk/utils/commandline/ClassType.java | 2 +- .../utils/commandline/CommandLineProgram.java | 18 +- .../utils/commandline/CommandLineUtils.java | 14 +- .../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 | 6 +- .../utils/commandline/IntervalBinding.java | 16 +- .../MissingArgumentValueException.java | 4 +- .../gatk/utils/commandline/Output.java | 2 +- .../gatk/utils/commandline/ParsedArgs.java | 2 +- .../utils/commandline/ParsedListArgs.java | 2 +- .../gatk/utils/commandline/ParsingEngine.java | 26 +-- .../ParsingEngineArgumentFiles.java | 2 +- .../ParsingEngineArgumentProvider.java | 2 +- .../gatk/utils/commandline/ParsingMethod.java | 4 +- .../gatk/utils/commandline/RodBinding.java | 2 +- .../commandline/RodBindingCollection.java | 4 +- .../gatk/utils/commandline/Tags.java | 2 +- .../gatk/utils/commandline/package-info.java | 2 +- .../gatk/utils/crypt/CryptUtils.java | 28 +-- .../gatk/utils/crypt/GATKKey.java | 24 +-- .../gatk/utils/duplicates/DupUtils.java | 24 +-- .../gatk/utils/duplicates/DuplicateComp.java | 2 +- .../DynamicClassResolutionException.java | 2 +- .../gatk/utils/exceptions/UserException.java | 16 +- .../utils/fasta/ArtificialFastaUtils.java | 10 +- .../CachingIndexedFastaSequenceFile.java | 8 +- .../gatk/utils/fasta/package-info.java | 2 +- .../gatk/utils/file/FSLockWithShared.java | 4 +- .../utils/fragments/FragmentCollection.java | 2 +- .../gatk/utils/fragments/FragmentUtils.java | 22 +-- .../gatk/utils/genotyper/DiploidGenotype.java | 4 +- .../utils/genotyper/MostLikelyAllele.java | 4 +- .../genotyper/PerReadAlleleLikelihoodMap.java | 14 +- .../gatk/utils/haplotype/EventMap.java | 12 +- .../gatk/utils/haplotype/Haplotype.java | 14 +- .../haplotype/HaplotypeBaseComparator.java | 2 +- .../haplotype/HaplotypeScoreComparator.java | 2 +- .../HaplotypeSizeAndBaseComparator.java | 2 +- .../gatk/utils/help/ApplicationDetails.java | 10 +- .../gatk/utils/help/DocletUtils.java | 4 +- .../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 | 18 +- .../help/GenericDocumentationHandler.java | 32 ++-- .../gatk/utils/help/HelpConstants.java | 2 +- .../gatk/utils/help/HelpFormatter.java | 12 +- .../gatk/utils/help/HelpUtils.java | 12 +- .../help/ResourceBundleExtractorDoclet.java | 8 +- .../gatk/utils/instrumentation/Sizeof.java | 10 +- .../utils/interval/IntervalMergingRule.java | 2 +- .../gatk/utils/interval/IntervalSetRule.java | 2 +- .../gatk/utils/interval/IntervalUtils.java | 28 +-- .../gatk/utils/io/FileExtension.java | 2 +- .../io/HardThresholdingOutputStream.java | 2 +- .../broadinstitute/gatk/utils/io/IOUtils.java | 24 +-- .../gatk/utils/io/Resource.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 | 8 +- .../gatk/utils/jna/lsf/v7_0_6/LibLsf.java | 8 +- .../locusiterator/AlignmentStateMachine.java | 12 +- .../locusiterator/LIBSDownsamplingInfo.java | 2 +- .../utils/locusiterator/LIBSPerformance.java | 30 +-- .../utils/locusiterator/LocusIterator.java | 4 +- .../locusiterator/LocusIteratorByState.java | 26 +-- .../PerSampleReadStateManager.java | 6 +- .../utils/locusiterator/ReadStateManager.java | 4 +- .../locusiterator/SamplePartitioner.java | 8 +- .../utils/nanoScheduler/EOFMarkedValue.java | 2 +- .../utils/nanoScheduler/InputProducer.java | 2 +- .../gatk/utils/nanoScheduler/MapResult.java | 2 +- .../utils/nanoScheduler/MapResultsQueue.java | 4 +- .../utils/nanoScheduler/NSMapFunction.java | 2 +- .../nanoScheduler/NSProgressFunction.java | 2 +- .../utils/nanoScheduler/NSReduceFunction.java | 2 +- .../utils/nanoScheduler/NanoScheduler.java | 6 +- .../gatk/utils/nanoScheduler/Reducer.java | 4 +- .../gatk/utils/pairhmm/BatchPairHMM.java | 4 +- .../gatk/utils/pairhmm/Log10PairHMM.java | 8 +- .../gatk/utils/pairhmm/N2MemoryPairHMM.java | 2 +- .../gatk/utils/pairhmm/PairHMM.java | 10 +- .../gatk/utils/pairhmm/PairHMMModel.java | 6 +- .../utils/pairhmm/PairHMMReadyHaplotypes.java | 2 +- .../pileup/MergingPileupElementIterator.java | 2 +- .../gatk/utils/pileup/PileupElement.java | 6 +- .../utils/pileup/PileupElementFilter.java | 2 +- .../utils/pileup/PileupElementTracker.java | 2 +- .../gatk/utils/pileup/ReadBackedPileup.java | 10 +- .../utils/pileup/ReadBackedPileupImpl.java | 32 ++-- .../utils/progressmeter/ProgressMeter.java | 6 +- .../progressmeter/ProgressMeterDaemon.java | 2 +- .../progressmeter/ProgressMeterData.java | 2 +- .../utils/recalibration/BQSRArgumentSet.java | 4 +- .../gatk/utils/recalibration/BQSRMode.java | 4 +- .../gatk/utils/recalibration/EventType.java | 2 +- .../utils/runtime/CapturedStreamOutput.java | 10 +- .../utils/runtime/InputStreamSettings.java | 2 +- .../utils/runtime/OutputStreamSettings.java | 2 +- .../gatk/utils/runtime/ProcessController.java | 18 +- .../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 | 18 +- .../gatk/utils/sam/ArtificialBAMBuilder.java | 6 +- .../sam/ArtificialGATKSAMFileWriter.java | 8 +- .../sam/ArtificialMultiSampleReadStream.java | 14 +- .../sam/ArtificialPatternedSAMIterator.java | 2 +- .../utils/sam/ArtificialReadsTraversal.java | 12 +- .../utils/sam/ArtificialSAMFileReader.java | 10 +- .../gatk/utils/sam/ArtificialSAMIterator.java | 8 +- .../utils/sam/ArtificialSAMQueryIterator.java | 10 +- .../gatk/utils/sam/ArtificialSAMUtils.java | 44 ++--- .../sam/ArtificialSingleSampleReadStream.java | 28 +-- ...ificialSingleSampleReadStreamAnalyzer.java | 38 ++-- .../gatk/utils/sam/BySampleSAMFileWriter.java | 10 +- .../gatk/utils/sam/CigarUtils.java | 12 +- .../utils/sam/GATKSAMReadGroupRecord.java | 4 +- .../gatk/utils/sam/GATKSAMRecord.java | 12 +- .../gatk/utils/sam/GATKSamRecordFactory.java | 4 +- .../MisencodedBaseQualityReadTransformer.java | 12 +- .../gatk/utils/sam/NWaySAMFileWriter.java | 18 +- ...eadUnclippedStartWithNoTiesComparator.java | 2 +- .../gatk/utils/sam/ReadUtils.java | 26 +-- .../gatk/utils/sam/SAMFileReaderBuilder.java | 8 +- .../utils/sam/SimplifyingSAMFileWriter.java | 2 +- .../gatk/utils/sam/package-info.java | 2 +- .../GlobalEdgeGreedySWPairwiseAlignment.java | 6 +- .../gatk/utils/smithwaterman/Parameters.java | 2 +- .../smithwaterman/SWPairwiseAlignment.java | 8 +- .../SWPairwiseAlignmentMain.java | 6 +- .../utils/smithwaterman/SWParameterSet.java | 2 +- .../utils/smithwaterman/SmithWaterman.java | 2 +- .../gatk/utils/text/ListFileUtils.java | 16 +- .../gatk/utils/text/TextFormattingUtils.java | 14 +- .../gatk/utils/text/XReadLines.java | 2 +- .../EfficiencyMonitoringThreadFactory.java | 4 +- .../utils/threading/NamedThreadFactory.java | 2 +- .../threading/ThreadEfficiencyMonitor.java | 4 +- .../utils/threading/ThreadLocalArray.java | 2 +- .../utils/threading/ThreadPoolMonitor.java | 2 +- .../gatk/utils/threading/package-info.java | 2 +- .../gatk/utils/variant/GATKVCFIndexType.java | 4 +- .../gatk/utils/variant/GATKVCFUtils.java | 14 +- .../variant/GATKVariantContextUtils.java | 8 +- .../utils/variant/HomoSapiensConstants.java | 2 +- .../gatk/utils/wiggle/WiggleHeader.java | 2 +- .../gatk/utils/wiggle/WiggleWriter.java | 10 +- .../gatk/engine/CommandLineGATKUnitTest.java | 4 +- .../engine/EngineFeaturesIntegrationTest.java | 48 ++--- .../engine/GenomeAnalysisEngineUnitTest.java | 28 +-- .../engine/MaxRuntimeIntegrationTest.java | 18 +- .../gatk/engine/ReadMetricsUnitTest.java | 52 +++--- .../gatk/engine/WalkerManagerUnitTest.java | 12 +- .../providers/AllLocusViewUnitTest.java | 8 +- .../providers/CoveredLocusViewUnitTest.java | 10 +- .../IntervalReferenceOrderedViewUnitTest.java | 22 +-- .../providers/LocusReferenceViewUnitTest.java | 12 +- .../providers/LocusViewTemplate.java | 28 +-- .../providers/ReadReferenceViewUnitTest.java | 4 +- .../ReferenceOrderedViewUnitTest.java | 28 +-- .../providers/ReferenceViewTemplate.java | 10 +- .../providers/ShardDataProviderUnitTest.java | 10 +- .../ActiveRegionShardBalancerUnitTest.java | 12 +- .../reads/DownsamplerBenchmark.java | 9 +- .../reads/FilePointerUnitTest.java | 12 +- .../reads/GATKBAMIndexUnitTest.java | 6 +- .../reads/GATKWalkerBenchmark.java | 30 +-- ...ervalOverlapFilteringIteratorUnitTest.java | 12 +- .../datasources/reads/MockLocusShard.java | 14 +- .../reads/PicardBaselineBenchmark.java | 2 +- .../reads/ReadProcessingBenchmark.java | 6 +- .../reads/ReadShardBalancerUnitTest.java | 26 +-- .../reads/SAMDataSourceUnitTest.java | 28 +-- .../reads/SAMReaderIDUnitTest.java | 6 +- .../reads/SeekableBufferedStreamUnitTest.java | 6 +- .../reads/TheoreticalMinimaBenchmark.java | 2 +- .../ReferenceDataSourceIntegrationTest.java | 6 +- .../rmd/ReferenceOrderedDataPoolUnitTest.java | 22 +-- ...ReferenceOrderedQueryDataPoolUnitTest.java | 14 +- ...AlleleBiasedDownsamplingUtilsUnitTest.java | 12 +- .../DownsamplingIntegrationTest.java | 6 +- .../DownsamplingReadsIteratorUnitTest.java | 14 +- .../FractionalDownsamplerUnitTest.java | 8 +- .../LevelingDownsamplerUnitTest.java | 6 +- ...mpleDownsamplingReadsIteratorUnitTest.java | 26 +-- ...ificialSingleSampleReadStreamAnalyzer.java | 40 ++-- .../ReservoirDownsamplerUnitTest.java | 8 +- .../SimplePositionalDownsamplerUnitTest.java | 10 +- .../engine/executive/ReduceTreeUnitTest.java | 4 +- ...llowNCigarMalformedReadFilterUnitTest.java | 4 +- .../filters/BadCigarFilterUnitTest.java | 6 +- .../filters/BadReadGroupsIntegrationTest.java | 6 +- .../filters/MalformedReadFilterUnitTest.java | 16 +- .../NDNCigarReadTransformerUnitTest.java | 4 +- .../gatk/engine/filters/ReadFilterTest.java | 18 +- .../ReadGroupBlackListFilterUnitTest.java | 12 +- .../UnsafeMalformedReadFilterUnitTest.java | 4 +- .../BoundedReadIteratorUnitTest.java | 10 +- .../GATKSAMIteratorAdapterUnitTest.java | 16 +- .../ReadFormattingIteratorUnitTest.java | 8 +- .../VerifyingSamIteratorUnitTest.java | 14 +- .../phonehome/GATKRunReportUnitTest.java | 36 ++-- .../refdata/RefMetaDataTrackerUnitTest.java | 22 +-- .../tracks/FeatureManagerUnitTest.java | 14 +- .../tracks/RMDTrackBuilderUnitTest.java | 10 +- .../CheckableCloseableTribbleIterator.java | 2 +- .../FeatureToGATKFeatureIteratorUnitTest.java | 10 +- .../utils/FlashBackIteratorUnitTest.java | 12 +- .../refdata/utils/TestFeatureReader.java | 2 +- .../refdata/utils/TestRMDTrackBuilder.java | 12 +- .../engine/report/GATKReportUnitTest.java | 4 +- .../engine/samples/PedReaderUnitTest.java | 8 +- .../gatk/engine/samples/SampleDBUnitTest.java | 8 +- .../gatk/engine/samples/SampleUnitTest.java | 4 +- .../traversals/DummyActiveRegionWalker.java | 20 +- .../TAROrderedReadCacheUnitTest.java | 10 +- .../TraverseActiveRegionsUnitTest.java | 47 +++-- .../TraverseDuplicatesUnitTest.java | 10 +- .../traversals/TraverseReadsUnitTest.java | 26 +-- .../gatk/engine/walkers/WalkerTest.java | 27 +-- .../tools/CatVariantsIntegrationTest.java | 14 +- .../tools/walkers/BAQIntegrationTest.java | 4 +- .../CNV/SymbolicAllelesIntegrationTest.java | 4 +- .../walkers/annotator/SnpEffUtilUnitTest.java | 4 +- .../coverage/CallableLociIntegrationTest.java | 4 +- ...pareCallableLociWalkerIntegrationTest.java | 4 +- .../DepthOfCoverageB36IntegrationTest.java | 4 +- .../DepthOfCoverageIntegrationTest.java | 4 +- .../qc/CheckPileupIntegrationTest.java | 4 +- .../tools/walkers/qc/CountReadsUnitTest.java | 4 +- .../DictionaryConsistencyIntegrationTest.java | 8 +- .../walkers/qc/FlagStatIntegrationTest.java | 4 +- .../qc/PileupWalkerIntegrationTest.java | 4 +- .../ClipReadsWalkersIntegrationTest.java | 4 +- .../readutils/PrintReadsIntegrationTest.java | 4 +- .../readutils/PrintReadsLargeScaleTest.java | 4 +- .../walkers/readutils/PrintReadsUnitTest.java | 22 +-- .../ReadAdaptorTrimmerIntegrationTest.java | 4 +- .../FilterLiftedVariantsUnitTest.java | 4 +- .../variantutils/SelectVariantsUnitTest.java | 6 +- .../utils/AutoFormattingTimeUnitTest.java | 6 +- .../broadinstitute/gatk/utils/BaseTest.java | 18 +- .../gatk/utils/BaseUtilsUnitTest.java | 6 +- .../gatk/utils/BitSetUtilsUnitTest.java | 4 +- .../gatk/utils/ExampleToCopyUnitTest.java | 24 +-- .../gatk/utils/GATKTextReporter.java | 8 +- .../gatk/utils/GenomeLocParserBenchmark.java | 4 +- .../gatk/utils/GenomeLocParserUnitTest.java | 22 +-- .../utils/GenomeLocSortedSetUnitTest.java | 10 +- .../gatk/utils/GenomeLocUnitTest.java | 16 +- .../org/broadinstitute/gatk/utils/MD5DB.java | 11 +- .../gatk/utils/MD5Mismatch.java | 2 +- ...achingSAMSequencingDictionaryUnitTest.java | 16 +- .../broadinstitute/gatk/utils/MWUnitTest.java | 6 +- .../gatk/utils/MathUtilsUnitTest.java | 4 +- .../gatk/utils/MedianUnitTest.java | 4 +- .../gatk/utils/NGSPlatformUnitTest.java | 10 +- .../gatk/utils/PathUtilsUnitTest.java | 8 +- .../gatk/utils/QualityUtilsUnitTest.java | 4 +- .../gatk/utils/R/RScriptExecutorUnitTest.java | 6 +- .../gatk/utils/R/RScriptLibraryUnitTest.java | 2 +- .../gatk/utils/R/RUtilsUnitTest.java | 2 +- .../gatk/utils/SampleUtilsUnitTest.java | 8 +- .../SequenceDictionaryUtilsUnitTest.java | 12 +- .../gatk/utils/SimpleTimerUnitTest.java | 4 +- .../gatk/utils/TestNGTestTransformer.java | 2 +- .../gatk/utils/UtilsUnitTest.java | 6 +- .../activeregion/ActiveRegionUnitTest.java | 16 +- .../ActivityProfileStateUnitTest.java | 8 +- .../activeregion/ActivityProfileUnitTest.java | 14 +- .../BandPassActivityProfileUnitTest.java | 16 +- .../gatk/utils/baq/BAQUnitTest.java | 10 +- .../utils/classloader/JVMUtilsUnitTest.java | 2 +- .../utils/clipping/ReadClipperTestUtils.java | 10 +- .../utils/clipping/ReadClipperUnitTest.java | 10 +- .../utils/codecs/hapmap/HapMapUnitTest.java | 4 +- .../collections/DefaultHashMapUnitTest.java | 4 +- .../ExpandingArrayListUnitTest.java | 4 +- .../ArgumentMatchSiteUnitTest.java | 2 +- .../ArgumentMatchSourceUnitTest.java | 4 +- .../ArgumentTypeDescriptorUnitTest.java | 20 +- .../InvalidArgumentIntegrationTest.java | 8 +- .../commandline/LoggingIntegrationTest.java | 12 +- .../commandline/ParsingEngineUnitTest.java | 14 +- .../RodBindingCollectionUnitTest.java | 6 +- .../utils/commandline/RodBindingUnitTest.java | 4 +- .../gatk/utils/crypt/CryptUtilsUnitTest.java | 10 +- .../utils/crypt/GATKKeyIntegrationTest.java | 8 +- .../gatk/utils/crypt/GATKKeyUnitTest.java | 12 +- ...chingIndexedFastaSequenceFileUnitTest.java | 6 +- .../utils/file/FSLockWithSharedUnitTest.java | 6 +- .../fragments/FragmentUtilsBenchmark.java | 10 +- .../fragments/FragmentUtilsUnitTest.java | 20 +- .../utils/haplotype/EventMapUnitTest.java | 12 +- .../utils/haplotype/HaplotypeUnitTest.java | 10 +- .../interval/IntervalIntegrationTest.java | 4 +- .../utils/interval/IntervalUtilsUnitTest.java | 22 +-- .../gatk/utils/io/IOUtilsUnitTest.java | 22 +-- .../gatk/utils/jna/clibrary/LibCUnitTest.java | 4 +- .../jna/drmaa/v1_0/JnaSessionQueueTest.java | 4 +- .../jna/drmaa/v1_0/LibDrmaaQueueTest.java | 4 +- .../utils/jna/lsf/v7_0_6/LibBatQueueTest.java | 8 +- .../AlignmentStateMachineUnitTest.java | 4 +- .../utils/locusiterator/LIBS_position.java | 2 +- .../locusiterator/LocusIteratorBenchmark.java | 26 +-- .../LocusIteratorByStateBaseTest.java | 26 +-- .../LocusIteratorByStateUnitTest.java | 28 +-- .../PerSampleReadStateManagerUnitTest.java | 8 +- .../nanoScheduler/InputProducerUnitTest.java | 4 +- .../nanoScheduler/MapResultUnitTest.java | 4 +- .../nanoScheduler/NanoSchedulerUnitTest.java | 14 +- .../utils/nanoScheduler/ReducerUnitTest.java | 8 +- .../utils/pileup/PileupElementUnitTest.java | 14 +- .../pileup/ReadBackedPileupUnitTest.java | 12 +- .../ProgressMeterDaemonUnitTest.java | 10 +- .../ProgressMeterDataUnitTest.java | 6 +- .../recalibration/EventTypeUnitTest.java | 4 +- .../report/ReportMarshallerUnitTest.java | 4 +- .../runtime/ProcessControllerUnitTest.java | 14 +- .../utils/runtime/RuntimeUtilsUnitTest.java | 4 +- .../utils/sam/AlignmentUtilsUnitTest.java | 6 +- .../sam/ArtificialBAMBuilderUnitTest.java | 4 +- ...rtificialPatternedSAMIteratorUnitTest.java | 4 +- .../sam/ArtificialSAMFileWriterUnitTest.java | 12 +- .../ArtificialSAMQueryIteratorUnitTest.java | 4 +- .../utils/sam/ArtificialSAMUtilsUnitTest.java | 14 +- ...ificialSingleSampleReadStreamUnitTest.java | 10 +- .../gatk/utils/sam/GATKSAMRecordUnitTest.java | 4 +- .../sam/MisencodedBaseQualityUnitTest.java | 6 +- .../gatk/utils/sam/ReadUtilsUnitTest.java | 12 +- .../smithwaterman/SmithWatermanBenchmark.java | 4 +- .../utils/text/ListFileUtilsUnitTest.java | 12 +- .../text/TextFormattingUtilsUnitTest.java | 14 +- ...ciencyMonitoringThreadFactoryUnitTest.java | 12 +- .../threading/ThreadPoolMonitorUnitTest.java | 4 +- .../utils/variant/GATKVCFUtilsUnitTest.java | 16 +- .../GATKVariantContextUtilsUnitTest.java | 14 +- .../utils/variant/VCFIntegrationTest.java | 6 +- .../variant/VariantContextBenchmark.java | 2 +- public/gatk-utils/pom.xml | 91 +++++++-- .../broadinstitute/gatk/utils/GenomeLoc.java | 36 ++-- .../gatk/utils/HasGenomeLocation.java | 2 +- .../gatk/utils/SimpleTimer.java | 2 +- .../gatk/utils/exceptions/GATKException.java | 10 +- .../exceptions/ReviewedGATKException.java | 12 +- .../gatk/utils/package-info.java | 2 +- public/gsalib/pom.xml | 12 +- public/java/config/log4j.properties | 2 +- public/package-tests/pom.xml | 83 ++++----- public/pom.xml | 28 +-- .../htsjdk/1.112.1452/htsjdk-1.112.1452.pom | 2 +- 1457 files changed, 8211 insertions(+), 8123 deletions(-) mode change 100755 => 100644 protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java create mode 100644 public/c/bwa/README.md mode change 100644 => 100755 public/c/bwa/build_mac.sh mode change 100755 => 100644 public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java mode change 100755 => 100644 public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java diff --git a/ant-bridge.sh b/ant-bridge.sh index fe0549fa1..a2f686586 100755 --- a/ant-bridge.sh +++ b/ant-bridge.sh @@ -100,44 +100,44 @@ for arg in "${@}" ; do local_repo="sitetemprepo" mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify" mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}" - mvn_args="${mvn_args} -Dsting.packagetests.enabled=true" - mvn_args="${mvn_args} -Dsting.packagecommittests.skipped=false" + mvn_args="${mvn_args} -Dgatk.packagetests.enabled=true" + mvn_args="${mvn_args} -Dgatk.packagecommittests.skipped=false" # TODO: This runs only the queue tests (full, non-dry run), but not the commit tests for Queue. elif [[ "${arg}" == "queuefull.binary.release.tests" ]] ; then local_repo="sitetemprepo" mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify" mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}" - mvn_args="${mvn_args} -Dsting.packagetests.enabled=true" - mvn_args="${mvn_args} -Dsting.packagequeuetests.skipped=false" - mvn_args="${mvn_args} -Dsting.queuetests.run=true" + mvn_args="${mvn_args} -Dgatk.packagetests.enabled=true" + mvn_args="${mvn_args} -Dgatk.packagequeuetests.skipped=false" + mvn_args="${mvn_args} -Dgatk.queuetests.run=true" elif [[ "${arg}" == "committests" ]] ; then - mvn_args="verify -Dsting.committests.skipped=false" + mvn_args="verify -Dgatk.committests.skipped=false" elif [[ "${arg}" == "test" ]] ; then - mvn_args="test -Dsting.unittests.skipped=false" + mvn_args="test -Dgatk.unittests.skipped=false" elif [[ "${arg}" == "unittest" ]] ; then - mvn_args="test -Dsting.unittests.skipped=false" + mvn_args="test -Dgatk.unittests.skipped=false" elif [[ "${arg}" == "integrationtest" ]] ; then - mvn_args="verify -Dsting.integrationtests.skipped=false" + mvn_args="verify -Dgatk.integrationtests.skipped=false" elif [[ "${arg}" == "largescaletest" ]] ; then - mvn_args="verify -Dsting.largescaletests.skipped=false" + mvn_args="verify -Dgatk.largescaletests.skipped=false" elif [[ "${arg}" == "knowledgebasetest" ]] ; then - mvn_args="verify -Dsting.knowledgebasetests.skipped=false" + mvn_args="verify -Dgatk.knowledgebasetests.skipped=false" elif [[ "${arg}" == "queuetest" ]] ; then - mvn_args="verify -Dsting.queuetests.skipped=false" + mvn_args="verify -Dgatk.queuetests.skipped=false" elif [[ "${arg}" == "queuetestrun" ]] ; then - mvn_args="verify -Dsting.queuetests.skipped=false -Dsting.queuetests.run=true" + mvn_args="verify -Dgatk.queuetests.skipped=false -Dgatk.queuetests.run=true" elif [[ "${arg}" == "fasttest" ]] ; then - mvn_args="verify -Dsting.committests.skipped=false -pl private/gatk-private -am -Dresource.bundle.skip=true" + mvn_args="verify -Dgatk.committests.skipped=false -pl private/gatk-tools-private -am -Dresource.bundle.skip=true" else unknown_args="${unknown_args} \"${arg}\"" diff --git a/pom.xml b/pom.xml index 209da06c8..bcf50842d 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 - org.broadinstitute.sting - sting-root + org.broadinstitute.gatk + gatk-root 3.2-SNAPSHOT - public/sting-root + public/gatk-root - sting-aggregator + gatk-aggregator pom - Sting Aggregator + GATK Aggregator public @@ -27,8 +27,8 @@ - ${project.basedir} - StingText.properties + ${project.basedir} + GATKText.properties false -build-timestamp "${maven.build.timestamp}" @@ -36,21 +36,21 @@ - package - generate-resources - process-resources - process-test-resources + package + generate-resources + process-resources + process-test-resources - true - ${sting.packagecommittests.skipped} - ${sting.packagecommittests.skipped} - ${sting.packagecommittests.skipped} - true - true + true + ${gatk.packagecommittests.skipped} + ${gatk.packagecommittests.skipped} + ${gatk.packagecommittests.skipped} + true + true - true - ${sting.serialcommittests.skipped} - ${sting.serialcommittests.skipped} - ${sting.serialcommittests.skipped} - true - true + true + ${gatk.serialcommittests.skipped} + ${gatk.serialcommittests.skipped} + ${gatk.serialcommittests.skipped} + true + true @@ -121,11 +121,21 @@ unpack-dependencies none + true ${project.build.outputDirectory} jar - system + runtime + + ${resource.bundle.path} @@ -140,14 +150,14 @@ resources - ${sting.process-resources.phase} + ${gatk.process-resources.phase} default-testResources testResources - ${sting.process-test-resources.phase} + ${gatk.process-test-resources.phase} copy-resource-bundle-log4j @@ -156,10 +166,14 @@ none + ${project.reporting.outputDirectory}/apidocs - ${sting.basedir}/sting-utils/src/main/config/org/broadinstitute/sting/utils/help + ${gatk.basedir}/gatk-utils/src/main/config/org/broadinstitute/gatk/utils/help @@ -179,13 +193,13 @@ ${resource.bundle.skip} - org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet + org.broadinstitute.gatk.utils.help.ResourceBundleExtractorDoclet ${project.build.outputDirectory} ${project.groupId} - - gatk-framework + + gatk-tools-public ${project.version} 2g @@ -307,14 +321,14 @@ default-jar - ${sting.jar.phase} + ${gatk.jar.phase} test-jar test-jar - ${sting.jar.phase} + ${gatk.jar.phase} true @@ -327,7 +341,7 @@ maven-shade-plugin - sting-executable + gatk-executable shade @@ -336,8 +350,8 @@ true - org.broadinstitute.sting:gsalib:tar.gz:* - org.broadinstitute.sting:*:tar.bz2:example-resources + org.broadinstitute.gatk:gsalib:tar.gz:* + org.broadinstitute.gatk:*:tar.bz2:example-resources @@ -413,7 +427,7 @@ ${basedir}/public/testdata - ${sting.basedir}/public/gatk-framework/src/test/resources + ${gatk.basedir}/public/gatk-engine/src/test/resources @@ -428,7 +442,7 @@ ${basedir}/public/testdata - ${sting.basedir}/public/gatk-framework/src/test/resources + ${gatk.basedir}/public/gatk-engine/src/test/resources @@ -443,7 +457,7 @@ ${basedir}/private/testdata - ${sting.basedir}/private/gatk-private/src/test/resources + ${gatk.basedir}/private/gatk-tools-private/src/test/resources @@ -458,7 +472,7 @@ ${basedir}/private/testdata - ${sting.basedir}/private/gatk-private/src/test/resources + ${gatk.basedir}/private/gatk-tools-private/src/test/resources @@ -473,7 +487,7 @@ ${basedir}/public/scala/qscript - ${sting.basedir}/public/queue-framework/src/main/qscripts + ${gatk.basedir}/public/gatk-queue-extensions-public/src/main/qscripts @@ -488,7 +502,7 @@ ${basedir}/public/scala/qscript - ${sting.basedir}/public/queue-framework/src/main/qscripts + ${gatk.basedir}/public/gatk-queue-extensions-public/src/main/qscripts @@ -503,7 +517,7 @@ ${basedir}/private/scala/qscript - ${sting.basedir}/private/queue-private/src/main/qscripts + ${gatk.basedir}/private/gatk-queue-extensions-internal/src/main/qscripts @@ -518,7 +532,27 @@ ${basedir}/private/scala/qscript - ${sting.basedir}/private/queue-private/src/main/qscripts + ${gatk.basedir}/private/gatk-queue-extensions-internal/src/main/qscripts + + + + + + + link-extensions-sources + + link + + none + + + + ${project.build.directory}/generated-sources/gatk-queue-extensions-public-src-main-scala + ${gatk.basedir}/public/gatk-queue-extensions-public/src/main/scala @@ -532,7 +566,7 @@ - ${sting.basedir}/target/${sting.binary-dist.name}.${project.packaging} + ${gatk.basedir}/target/${gatk.binary-dist.name}.${project.packaging} ${project.build.directory}/${project.build.finalName}.${project.packaging} @@ -547,7 +581,7 @@ - ${project.build.directory}/${sting.binary-dist.name}-${build.version}.tar.bz2 + ${project.build.directory}/${gatk.binary-dist.name}-${build.version}.tar.bz2 ${project.build.directory}/${project.build.finalName}-binary-dist.tar.bz2 @@ -561,19 +595,19 @@ true false - ${sting.basedir}/public/package-tests/pom.xml + ${gatk.basedir}/public/package-tests/pom.xml true true - ${sting.basedir}/${maven.repo.local} + ${gatk.basedir}/${maven.repo.local} ${test} ${it.test} false false - ${sting.packagetests.artifactId} - ${project.build.testOutputDirectory} - ${project.basedir} - ${sting.queuetests.run} + ${gatk.packagetests.artifactId} + ${project.build.testOutputDirectory} + ${project.basedir} + ${gatk.queuetests.run} ${maven.surefire.debug} ${maven.failsafe.debug} @@ -599,10 +633,10 @@ test ${project.build.directory}/invoker-reports/unit/${test} - ${sting.packageunittests.skipped} + ${gatk.packageunittests.skipped} true - ${sting.packageunittests.skipped} + ${gatk.packageunittests.skipped} @@ -617,10 +651,10 @@ verify ${project.build.directory}/invoker-reports/integration/${it.test} - ${sting.packageintegrationtests.skipped} + ${gatk.packageintegrationtests.skipped} true - ${sting.packageintegrationtests.skipped} + ${gatk.packageintegrationtests.skipped} @@ -635,10 +669,10 @@ verify ${project.build.directory}/invoker-reports/queuetest/${it.test} - ${sting.packagequeuetests.skipped} + ${gatk.packagequeuetests.skipped} true - ${sting.packagequeuetests.skipped} + ${gatk.packagequeuetests.skipped} @@ -653,10 +687,10 @@ verify ${project.build.directory}/invoker-reports/largescale/${it.test} - ${sting.packagelargescaletests.skipped} + ${gatk.packagelargescaletests.skipped} true - ${sting.packagelargescaletests.skipped} + ${gatk.packagelargescaletests.skipped} @@ -671,10 +705,10 @@ verify ${project.build.directory}/invoker-reports/knowledgebase/${it.test} - ${sting.packageknowledgebasetests.skipped} + ${gatk.packageknowledgebasetests.skipped} true - ${sting.packageknowledgebasetests.skipped} + ${gatk.packageknowledgebasetests.skipped} @@ -776,7 +810,7 @@ false - org.broadinstitute.sting.utils.help.GATKDoclet + org.broadinstitute.gatk.utils.help.GATKDoclet ${project.groupId} gatk-package @@ -785,7 +819,7 @@ false true private - -build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${sting.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs + -build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${gatk.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs @@ -852,17 +886,17 @@ packagetests-enabled - sting.packagetests.enabled + gatk.packagetests.enabled true true - true - none - none - none - none + true + none + none + none + none diff --git a/protected/gatk-package-distribution/pom.xml b/protected/gatk-package-distribution/pom.xml index a8500815c..cc85fdaca 100644 --- a/protected/gatk-package-distribution/pom.xml +++ b/protected/gatk-package-distribution/pom.xml @@ -3,29 +3,44 @@ 4.0.0 - org.broadinstitute.sting - sting-aggregator + org.broadinstitute.gatk + gatk-aggregator 3.2-SNAPSHOT ../.. - gatk-package + gatk-package-distribution jar - GATK Package + GATK Package Distribution - ${project.basedir}/../.. - prepare-package - package - org.broadinstitute.sting.gatk.CommandLineGATK - GenomeAnalysisTK + ${project.basedir}/../.. + prepare-package + package + org.broadinstitute.gatk.engine.CommandLineGATK + GenomeAnalysisTK - + ${project.groupId} - gatk-framework + gatk-utils + ${project.version} + + + ${project.groupId} + gatk-engine + ${project.version} + + + ${project.groupId} + gatk-tools-public + ${project.version} + + + ${project.groupId} + gatk-tools-protected ${project.version} @@ -46,26 +61,29 @@ ${project.groupId} - gatk-framework + gatk-engine ${project.version} example-resources tar.bz2 + ${project.groupId} - gatk-framework + gatk-tools-public + ${project.version} + test-jar + test + + + ${project.groupId} + gatk-tools-protected ${project.version} test-jar test - - org.testng - testng - test - - + com.google.caliper caliper @@ -82,9 +100,9 @@ unit-tests - ${sting.serialunittests.skipped} + ${gatk.serialunittests.skipped} - org.broadinstitute.sting:.* + org.broadinstitute.gatk:.* @@ -98,36 +116,36 @@ integration-tests - ${sting.serialintegrationtests.skipped} + ${gatk.serialintegrationtests.skipped} - org.broadinstitute.sting:.* + org.broadinstitute.gatk:.* queue-tests - ${sting.serialqueuetests.skipped} + ${gatk.serialqueuetests.skipped} - org.broadinstitute.sting:.* + org.broadinstitute.gatk:.* large-scale-tests - ${sting.seriallargescaletests.skipped} + ${gatk.seriallargescaletests.skipped} - org.broadinstitute.sting:.* + org.broadinstitute.gatk:.* knowledge-base-tests - ${sting.serialknowledgebasetests.skipped} + ${gatk.serialknowledgebasetests.skipped} - org.broadinstitute.sting:.* + org.broadinstitute.gatk:.* @@ -140,7 +158,7 @@ unpack-direct-dependencies - ${sting.unpack.phase} + ${gatk.unpack.phase} @@ -150,8 +168,8 @@ maven-shade-plugin - sting-executable - ${sting.shade.phase} + gatk-executable + ${gatk.shade.phase} @@ -162,7 +180,7 @@ binary-dist - ${sting.shade.phase} + ${gatk.shade.phase} @@ -173,11 +191,11 @@ link-binary-jar - ${sting.shade.phase} + ${gatk.shade.phase} link-git-release - ${sting.shade.phase} + ${gatk.shade.phase} @@ -202,52 +220,12 @@ - protected + private-testdata - ${basedir}/../../protected/gatk-protected/pom.xml + ${basedir}/../../private/pom.xml - - - ${project.groupId} - gatk-protected - ${project.version} - true - - - ${project.groupId} - gatk-protected - ${project.version} - test-jar - test - true - - - - - private - - - ${basedir}/../../private/gatk-private/pom.xml - - - - - ${project.groupId} - gatk-private - ${project.version} - true - - - ${project.groupId} - gatk-private - ${project.version} - test-jar - test - true - - @@ -272,13 +250,13 @@ packagetests-enabled - sting.packagetests.enabled + gatk.packagetests.enabled true - none - none + none + none diff --git a/protected/gatk-package-distribution/src/main/assembly/binary-dist.xml b/protected/gatk-package-distribution/src/main/assembly/binary-dist.xml index adc52646c..11fb98e00 100644 --- a/protected/gatk-package-distribution/src/main/assembly/binary-dist.xml +++ b/protected/gatk-package-distribution/src/main/assembly/binary-dist.xml @@ -7,15 +7,15 @@ - org.broadinstitute.sting:gatk-package + org.broadinstitute.gatk:gatk-package-distribution - ${sting.binary-dist.name}.${artifact.extension} + ${gatk.binary-dist.name}.${artifact.extension} resources true - org.broadinstitute.sting:gatk-framework:tar.bz2:example-resources + org.broadinstitute.gatk:gatk-engine:tar.bz2:example-resources diff --git a/protected/gatk-queue-package-distribution/pom.xml b/protected/gatk-queue-package-distribution/pom.xml index 3a266236c..194e88781 100644 --- a/protected/gatk-queue-package-distribution/pom.xml +++ b/protected/gatk-queue-package-distribution/pom.xml @@ -3,34 +3,39 @@ 4.0.0 - org.broadinstitute.sting - sting-aggregator + org.broadinstitute.gatk + gatk-aggregator 3.2-SNAPSHOT ../.. - queue-package + gatk-queue-package-distribution jar - Queue Package + GATK Queue Package Distribution - ${project.basedir}/../.. - prepare-package - package - Queue - org.broadinstitute.sting.queue.QCommandLine + ${project.basedir}/../.. + prepare-package + package + Queue + org.broadinstitute.gatk.queue.QCommandLine ${project.groupId} - queue-framework + gatk-queue ${project.version} ${project.groupId} - gatk-package + gatk-package-distribution + ${project.version} + + + ${project.groupId} + gatk-queue-extensions-distribution ${project.version} @@ -75,41 +80,29 @@ ${project.groupId} - gatk-framework + gatk-engine ${project.version} example-resources tar.bz2 ${project.groupId} - queue-framework + gatk-queue-extensions-public ${project.version} example-resources tar.bz2 + ${project.groupId} - queue-framework + gatk-queue ${project.version} test-jar test - - ${project.groupId} - gatk-framework - ${project.version} - test-jar - test - - - - org.testng - testng - test - - + com.google.caliper caliper @@ -126,9 +119,9 @@ unit-tests - ${sting.serialunittests.skipped} + ${gatk.serialunittests.skipped} - org.broadinstitute.sting:.* + org.broadinstitute.gatk:.* @@ -142,36 +135,36 @@ integration-tests - ${sting.serialintegrationtests.skipped} + ${gatk.serialintegrationtests.skipped} - org.broadinstitute.sting:.* + org.broadinstitute.gatk:.* queue-tests - ${sting.serialqueuetests.skipped} + ${gatk.serialqueuetests.skipped} - org.broadinstitute.sting:.* + org.broadinstitute.gatk:.* large-scale-tests - ${sting.seriallargescaletests.skipped} + ${gatk.seriallargescaletests.skipped} - org.broadinstitute.sting:.* + org.broadinstitute.gatk:.* knowledge-base-tests - ${sting.serialknowledgebasetests.skipped} + ${gatk.serialknowledgebasetests.skipped} - org.broadinstitute.sting:.* + org.broadinstitute.gatk:.* @@ -184,7 +177,7 @@ unpack-direct-dependencies - ${sting.unpack.phase} + ${gatk.unpack.phase} @@ -194,8 +187,8 @@ maven-shade-plugin - sting-executable - ${sting.shade.phase} + gatk-executable + ${gatk.shade.phase} @@ -206,7 +199,7 @@ binary-dist - ${sting.shade.phase} + ${gatk.shade.phase} @@ -217,11 +210,11 @@ link-binary-jar - ${sting.shade.phase} + ${gatk.shade.phase} link-git-release - ${sting.shade.phase} + ${gatk.shade.phase} @@ -246,35 +239,19 @@ - private + private-testdata - ${basedir}/../../private/queue-private/pom.xml + ${basedir}/../../private/pom.xml - - - ${project.groupId} - queue-private - ${project.version} - true - - - ${project.groupId} - queue-private - ${project.version} - test-jar - test - true - - - com.pyx4j maven-junction-plugin + link-private-testdata process-test-resources @@ -300,13 +277,13 @@ packagetests-enabled - sting.packagetests.enabled + gatk.packagetests.enabled true - none - none + none + none diff --git a/protected/gatk-queue-package-distribution/src/main/assembly/binary-dist.xml b/protected/gatk-queue-package-distribution/src/main/assembly/binary-dist.xml index 6de236a56..daa974216 100644 --- a/protected/gatk-queue-package-distribution/src/main/assembly/binary-dist.xml +++ b/protected/gatk-queue-package-distribution/src/main/assembly/binary-dist.xml @@ -7,16 +7,16 @@ - org.broadinstitute.sting:queue-package + org.broadinstitute.gatk:gatk-queue-package-distribution - ${sting.binary-dist.name}.${artifact.extension} + ${gatk.binary-dist.name}.${artifact.extension} resources true - org.broadinstitute.sting:gatk-framework:tar.bz2:example-resources - org.broadinstitute.sting:queue-framework:tar.bz2:example-resources + org.broadinstitute.gatk:gatk-engine:tar.bz2:example-resources + org.broadinstitute.gatk:gatk-queue-extensions-public:tar.bz2:example-resources diff --git a/protected/gatk-tools-protected/pom.xml b/protected/gatk-tools-protected/pom.xml index b25f9406d..6708adedf 100644 --- a/protected/gatk-tools-protected/pom.xml +++ b/protected/gatk-tools-protected/pom.xml @@ -3,25 +3,31 @@ 4.0.0 - org.broadinstitute.sting - sting-aggregator + org.broadinstitute.gatk + gatk-aggregator 3.2-SNAPSHOT ../.. - gatk-protected + gatk-tools-protected jar - GATK Protected + GATK Tools Protected - ${project.basedir}/../.. - gatk-package + ${project.basedir}/../.. + gatk-package-distribution ${project.groupId} - gatk-framework + gatk-engine + ${project.version} + + + + ${project.groupId} + gatk-tools-public ${project.version} @@ -42,17 +48,12 @@ ${project.groupId} - gatk-framework + gatk-tools-public ${project.version} test-jar test - - org.testng - testng - test - com.google.caliper caliper @@ -108,10 +109,10 @@ - private + private-testdata - ${basedir}/../../private/gatk-private/pom.xml + ${basedir}/../../private/pom.xml diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardCallerArgumentCollection.java index dd61742d2..3e31636a4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardCallerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardCallerArgumentCollection.java @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.arguments; +package org.broadinstitute.gatk.engine.arguments; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypingOutputMode; -import org.broadinstitute.sting.gatk.walkers.genotyper.OutputMode; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; -import org.broadinstitute.sting.utils.collections.DefaultHashMap; -import org.broadinstitute.sting.utils.variant.HomoSapiensConstants; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode; +import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory; +import org.broadinstitute.gatk.utils.collections.DefaultHashMap; +import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants; import htsjdk.variant.variantcontext.VariantContext; import java.io.File; 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 d3ae6d710..1dfdb2aac 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 @@ -44,4 +44,4 @@ * 7.7 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.sting; +package org.broadinstitute.gatk; 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 2d2d57536..37fa85393 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.PileupElement; import java.util.*; 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 2722ef67a..30430d445 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 @@ -44,18 +44,18 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.variantcontext.VariantContext; 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 94cf7b97e..6c127669c 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.PileupElement; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.*; 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 5b4edad22..9464392f5 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFStandardHeaderLines; 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 9adc99e02..f3d53195d 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 @@ -44,22 +44,22 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFFormatHeaderLine; import htsjdk.variant.vcf.VCFStandardHeaderLines; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypeBuilder; 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 be3c176c6..0b93a6906 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypeBuilder; 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 22e85c8e5..40379b585 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 @@ -44,23 +44,23 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; import cern.jet.math.Arithmetic; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.QualityUtils; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; 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 42f6753fa..78d3e5a9e 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 @@ -44,21 +44,21 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.help.HelpConstants; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.help.HelpConstants; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; 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 a2e7f41fb..4ffffe9ab 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 @@ -44,17 +44,17 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFHeaderLineType; 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 31ec2c77a..ea9cda773 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 @@ -44,27 +44,27 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; @@ -261,7 +261,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot final byte[] b = haplotypeB.getBases(); if (a.length != b.length) { - throw new ReviewedStingException("Haplotypes a and b must be of same length"); + throw new ReviewedGATKException("Haplotypes a and b must be of same length"); } byte chA, chB; 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 fbc844fea..c970c0449 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 @@ -44,18 +44,18 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; import htsjdk.tribble.util.popgen.HardyWeinbergCalculation; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.WorkInProgressAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.QualityUtils; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.variantcontext.Genotype; 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 679a94f04..ac28e8715 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.GenomeLoc; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.variantcontext.VariantContext; 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 41db36e33..7fb2ef6ea 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 @@ -44,18 +44,18 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.variantcontext.Genotype; 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 69703178c..3e9bd960a 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; 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 b8ae2a17f..d537fa6a2 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 @@ -44,22 +44,21 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.samples.Trio; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.MendelianViolation; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.samples.Trio; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.RodRequiringAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.MendelianViolation; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import htsjdk.variant.variantcontext.VariantContext; import java.util.*; 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 824085008..043d3366a 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.pileup.PileupElement; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.*; 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 c940f469b..a44360f9d 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 @@ -44,22 +44,22 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFStandardHeaderLines; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; 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 429977344..efaafa94c 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 @@ -44,19 +44,19 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.variantcontext.Genotype; 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 d08dd2e14..86b123a8a 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 @@ -44,23 +44,23 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFStandardHeaderLines; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.VariantContext; import java.util.*; 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 06c146ed4..d51ddced2 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 @@ -44,24 +44,24 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.MannWhitneyU; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.MannWhitneyU; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypesContext; 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 77f5a7398..32e26797e 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 @@ -44,20 +44,20 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.util.*; 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 80beb2ccd..938b97337 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.vcf.VCFHeaderLineCount; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; 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 cec145e9c..0f9b5a64d 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.pileup.PileupElement; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.variantcontext.VariantContext; 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 1449dedc5..173580699 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.VariantContext; 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 4d1d5e015..474ab42cc 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypesContext; 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 e08907080..e204d9007 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; 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 16d9426f7..c90924715 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 @@ -44,17 +44,17 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.collections.Pair; import htsjdk.variant.vcf.VCFHeaderLineCount; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; 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 356b0c256..42bbee925 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 @@ -44,22 +44,22 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.samples.Sample; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.samples.Sample; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.RodRequiringAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.vcf.VCFHeaderLineCount; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import htsjdk.variant.variantcontext.VariantContext; import java.util.*; 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 cbb1d95f0..5934c0503 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 @@ -44,15 +44,15 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.IndelUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.IndelUtils; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.variantcontext.VariantContext; 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 c8c5eae0b..9df9d8cc9 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 @@ -43,24 +43,24 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.bqsr; +package org.broadinstitute.gatk.tools.walkers.bqsr; import com.google.java.contract.Requires; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.recalibration.RecalUtils; -import org.broadinstitute.sting.utils.recalibration.RecalibrationReport; -import org.broadinstitute.sting.utils.recalibration.BaseRecalibration; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Input; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.recalibration.RecalUtils; +import org.broadinstitute.gatk.utils.recalibration.RecalibrationReport; +import org.broadinstitute.gatk.utils.recalibration.BaseRecalibration; import java.io.File; import java.io.FileNotFoundException; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGatherer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGatherer.java index 84bf844f4..b4686166d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGatherer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGatherer.java @@ -44,15 +44,15 @@ * 7.7 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.sting.gatk.walkers.bqsr; +package org.broadinstitute.gatk.tools.walkers.bqsr; import org.apache.commons.collections.CollectionUtils; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.Gatherer; -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.recalibration.RecalibrationReport; +import org.broadinstitute.gatk.utils.commandline.Gatherer; +import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.recalibration.RecalibrationReport; import java.io.File; import java.io.FileNotFoundException; @@ -125,7 +125,7 @@ public class BQSRGatherer extends Gatherer { generalReport.combine(inputReport); } if (generalReport == null) - throw new ReviewedStingException(EMPTY_INPUT_LIST); + throw new ReviewedGATKException(EMPTY_INPUT_LIST); generalReport.calculateQuantizedQualities(); 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 96ebcf8e9..f36a1cdc7 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 @@ -44,34 +44,34 @@ * 7.7 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.sting.gatk.walkers.bqsr; +package org.broadinstitute.gatk.tools.walkers.bqsr; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.CigarElement; import htsjdk.samtools.SAMFileHeader; import htsjdk.tribble.Feature; -import org.broadinstitute.sting.commandline.Advanced; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.filters.*; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.clipping.ReadClipper; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.recalibration.*; -import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.commandline.Advanced; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.filters.*; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.baq.BAQ; +import org.broadinstitute.gatk.utils.clipping.ReadClipper; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.recalibration.*; +import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.io.IOException; import java.io.PrintStream; @@ -357,7 +357,7 @@ public class BaseRecalibrator extends ReadWalker implements NanoSche case P: break; default: - throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator()); + throw new ReviewedGATKException("Unsupported cigar operator: " + ce.getOperator()); } } return snp; @@ -400,7 +400,7 @@ public class BaseRecalibrator extends ReadWalker implements NanoSche case P: break; default: - throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator()); + throw new ReviewedGATKException("Unsupported cigar operator: " + ce.getOperator()); } } return indel; @@ -414,7 +414,7 @@ public class BaseRecalibrator extends ReadWalker implements NanoSche protected static double[] calculateFractionalErrorArray( final int[] errorArray, final byte[] baqArray ) { if(errorArray.length != baqArray.length ) { - throw new ReviewedStingException("Array length mismatch detected. Malformed read?"); + throw new ReviewedGATKException("Array length mismatch detected. Malformed read?"); } final int BLOCK_START_UNSET = -1; @@ -442,7 +442,7 @@ public class BaseRecalibrator extends ReadWalker implements NanoSche calculateAndStoreErrorsInBlock(iii-1, blockStartIndex, errorArray, fractionalErrors); } if( fractionalErrors.length != errorArray.length ) { - throw new ReviewedStingException("Output array length mismatch detected. Malformed read?"); + throw new ReviewedGATKException("Output array length mismatch detected. Malformed read?"); } return fractionalErrors; } 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 94d1c5501..01968db3e 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.bqsr; +package org.broadinstitute.gatk.tools.walkers.bqsr; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.recalibration.EventType; -import org.broadinstitute.sting.utils.recalibration.ReadCovariates; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.recalibration.EventType; +import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /** * Created with IntelliJ IDEA. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationArgumentCollection.java index 5bafba185..6d4f9a539 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationArgumentCollection.java @@ -44,15 +44,15 @@ * 7.7 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.sting.gatk.walkers.bqsr; +package org.broadinstitute.gatk.tools.walkers.bqsr; import com.google.java.contract.Requires; import htsjdk.tribble.Feature; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.report.GATKReportTable; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.recalibration.RecalUtils; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.recalibration.RecalUtils; import java.io.File; import java.io.PrintStream; @@ -407,7 +407,7 @@ public class RecalibrationArgumentCollection implements Cloneable { try { return (RecalibrationArgumentCollection) super.clone(); } catch (CloneNotSupportedException e) { - throw new StingException("Unreachable code clone not supported thrown when the class " + throw new GATKException("Unreachable code clone not supported thrown when the class " + this.getClass().getName() + " is cloneable ",e); } } 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 9f33234cf..5054cc6f9 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.gatk.walkers.bqsr; +package org.broadinstitute.gatk.tools.walkers.bqsr; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.collections.NestedIntegerArray; -import org.broadinstitute.sting.utils.recalibration.*; -import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; +import org.broadinstitute.gatk.utils.recalibration.*; +import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.io.PrintStream; import java.util.LinkedList; 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 417da9d79..4d0417daf 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 @@ -44,20 +44,20 @@ * 7.7 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.sting.gatk.walkers.diagnostics; +package org.broadinstitute.gatk.tools.walkers.diagnostics; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.engine.walkers.LocusWalker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; import java.io.PrintStream; import java.util.ArrayList; 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 bd69cbdbd..611c40f9c 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 @@ -44,22 +44,22 @@ * 7.7 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.sting.gatk.walkers.diagnostics; +package org.broadinstitute.gatk.tools.walkers.diagnostics; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionTraversalParameters; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; -import org.broadinstitute.sting.gatk.walkers.PartitionBy; -import org.broadinstitute.sting.gatk.walkers.PartitionType; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileState; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.ActiveRegionTraversalParameters; +import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker; +import org.broadinstitute.gatk.engine.walkers.PartitionBy; +import org.broadinstitute.gatk.engine.walkers.PartitionType; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; import java.io.PrintStream; @@ -126,7 +126,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker { } @Override - public GenomeLoc map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) { + public GenomeLoc map(final org.broadinstitute.gatk.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) { if ((!outputUncovered && activeRegion.isActive()) || (outputUncovered && !activeRegion.isActive())) return activeRegion.getLocation(); 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 ceccdcb2e..e1d9cbeab 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; import java.util.HashMap; import java.util.LinkedList; 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 d38736f4f..1577d8d0b 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * Short one line description of the walker. 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 cb824f0fe..a56462d6c 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 @@ -44,24 +44,24 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; import htsjdk.samtools.util.PeekableIterator; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.downsampling.DownsampleType; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.classloader.PluginManager; +import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; import htsjdk.variant.variantcontext.*; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.vcf.*; 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 50470a744..bb01840db 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * Created with IntelliJ IDEA. 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 cd38d28c6..fb6fba49b 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import java.util.*; @@ -103,7 +103,7 @@ final class IntervalStratification extends AbstractStratification { SampleStratification sampleStratification = (SampleStratification) samples.get(sample); if (sampleStratification == null) - throw new ReviewedStingException(String.format("Trying to add locus statistics to a sample (%s) that doesn't exist in the Interval.", sample)); + throw new ReviewedGATKException(String.format("Trying to add locus statistics to a sample (%s) that doesn't exist in the Interval.", sample)); sampleStratification.addLocus(context.getLocation(), samplePileup); } 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 9950b4e2d..77fda0730 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * Created with IntelliJ IDEA. 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 0973fef1e..b41c69e6b 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * User: carneiro 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 fbedc5404..ac5032344 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * User: carneiro 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 5b5015beb..a8b0df48f 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * User: carneiro 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 53c07d421..572361c35 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * User: carneiro 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 5902fce31..62cd711c7 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; import java.util.List; 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 6f13b9cac..2d66317cf 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * 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 7984ba7e7..cd3e75082 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; import java.util.Map; 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 8de33b269..6ca357df9 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * Created with IntelliJ IDEA. 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 cf5aac4a6..fe33358e8 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * User: carneiro 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 bf9e7420d..ee53147ec 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; /** * User: carneiro 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 0f84c7d22..b2afb58c2 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.ArrayList; import java.util.LinkedList; @@ -92,7 +92,7 @@ final class SampleStratification extends AbstractStratification { */ public void addLocus(GenomeLoc locus, ReadBackedPileup pileup) { if (!interval.containsP(locus)) - throw new ReviewedStingException(String.format("Locus %s is not part of the Interval %s", locus, interval)); + throw new ReviewedGATKException(String.format("Locus %s is not part of the Interval %s", locus, interval)); // a null pileup means there nothing to add if (pileup != null) { 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 b088951e5..35de956c8 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Output; import java.io.PrintStream; import java.util.LinkedList; 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 63c35fd65..632d98c7c 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.missing; +package org.broadinstitute.gatk.tools.walkers.diagnostics.missing; /** * Metrics class for the QualifyMissingInterval walker 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 54fc6e97e..73933dd0d 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 @@ -44,26 +44,26 @@ * 7.7 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.sting.gatk.walkers.diagnostics.missing; +package org.broadinstitute.gatk.tools.walkers.diagnostics.missing; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Gather; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.gatk.report.GATKReportGatherer; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Gather; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.engine.report.GATKReportGatherer; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocSortedSet; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.interval.IntervalUtils; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import java.io.PrintStream; import java.util.List; 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 0b019ef0e..7b81bc350 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; public enum BaseMismatchModel { THREE_STATE, 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 e19e9aba5..ad1a3011e 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 @@ -44,21 +44,21 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.clipping.ReadClipper; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.clipping.ReadClipper; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import htsjdk.variant.variantcontext.*; import java.util.*; 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 66ef8e8a5..5a26f830e 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 @@ -44,18 +44,18 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.SAMUtils; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.fragments.FragmentCollection; -import org.broadinstitute.sting.utils.fragments.FragmentUtils; -import org.broadinstitute.sting.utils.genotyper.DiploidGenotype; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.fragments.FragmentCollection; +import org.broadinstitute.gatk.utils.fragments.FragmentUtils; +import org.broadinstitute.gatk.utils.genotyper.DiploidGenotype; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import java.util.List; 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 fac0d64be..c636db4c0 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 @@ -44,17 +44,17 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import com.google.java.contract.Requires; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; 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 1c441f632..0495db541 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 @@ -44,17 +44,17 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.SAMUtils; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACcounts; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACcounts; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACset; +import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.vcf.VCFConstants; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypeLikelihoods; @@ -124,7 +124,7 @@ public abstract class GeneralPloidyGenotypeLikelihoods { Arrays.fill(log10Likelihoods, MIN_LIKELIHOOD); } else { if (logLikelihoods.length != likelihoodDim) - throw new ReviewedStingException("BUG: inconsistent parameters when creating GeneralPloidyGenotypeLikelihoods object"); + throw new ReviewedGATKException("BUG: inconsistent parameters when creating GeneralPloidyGenotypeLikelihoods object"); log10Likelihoods = logLikelihoods; //.clone(); // is clone needed? } @@ -192,7 +192,7 @@ public abstract class GeneralPloidyGenotypeLikelihoods { if (restrictSumTo > 0) { // check that desired vector is valid if (MathUtils.sum(stateVector) != restrictSumTo) - throw new ReviewedStingException("BUG: initial state vector nor compatible with sum iterator"); + throw new ReviewedGATKException("BUG: initial state vector nor compatible with sum iterator"); final int numAlleles = currentState.length; final int ploidy = restrictSumTo; @@ -200,7 +200,7 @@ public abstract class GeneralPloidyGenotypeLikelihoods { linearIndex = GeneralPloidyGenotypeLikelihoods.getLinearIndex(stateVector, numAlleles, ploidy); } else - throw new ReviewedStingException("BUG: Not supported"); + throw new ReviewedGATKException("BUG: Not supported"); } public void next() { 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 1f370c07c..b4c855577 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 @@ -44,21 +44,21 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.vcf.VCFConstants; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.*; import java.util.*; @@ -180,11 +180,11 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G final double topLogGL = mlACPair.second; if (sampleData.GL.getAlleles().size() != allAlleles.size()) - throw new ReviewedStingException("BUG: inconsistent size of alleles!"); + throw new ReviewedGATKException("BUG: inconsistent size of alleles!"); // ref allele is always first in array list if (sampleData.GL.alleles.get(0).isNonReference()) - throw new ReviewedStingException("BUG: first allele in list is not reference!"); + throw new ReviewedGATKException("BUG: first allele in list is not reference!"); double refGL = sampleData.GL.getLikelihoods()[REFERENCE_IDX]; @@ -219,7 +219,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G final List allAllelesToUse, final boolean useBAQedPileup, final GenomeLocParser locParser, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { HashMap perLaneErrorModels = getPerLaneErrorModels(tracker, ref, contexts); if (perLaneErrorModels == null && UAC.referenceSampleName != null) @@ -357,7 +357,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G final boolean useBQAedPileup, final ReferenceContext ref, final boolean ignoreLaneInformation, - final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap); + final org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap); protected abstract List getInitialAllelesToUse(final RefMetaDataTracker tracker, final ReferenceContext ref, 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 8efea2969..b1b29759c 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset; -import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACset; +import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.Allele; import java.util.*; @@ -73,7 +73,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype double[][] readHaplotypeLikelihoods; final byte refBase; - final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap; + final org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap; public GeneralPloidyIndelGenotypeLikelihoods(final List alleles, final double[] logLikelihoods, @@ -83,7 +83,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype final PairHMMIndelErrorModel pairModel, final LinkedHashMap haplotypeMap, final ReferenceContext referenceContext, - final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap) { + final org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap) { super(alleles, logLikelihoods, ploidy, perLaneErrorModels, ignoreLaneInformation); this.pairModel = pairModel; this.haplotypeMap = haplotypeMap; @@ -204,7 +204,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype } if (refAllele == null) - throw new ReviewedStingException("BUG: no ref alleles in passed in allele list!"); + throw new ReviewedGATKException("BUG: no ref alleles in passed in allele list!"); // count number of elements in pileup for (PileupElement elt : pileup) { 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 60b406119..d4fb08e3e 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; +import org.broadinstitute.gatk.utils.*; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; import htsjdk.variant.variantcontext.*; import java.util.*; @@ -96,7 +96,7 @@ public class GeneralPloidyIndelGenotypeLikelihoodsCalculationModel extends Gener final boolean useBQAedPileup, final ReferenceContext ref, final boolean ignoreLaneInformation, - final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){ + final org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){ return new GeneralPloidyIndelGenotypeLikelihoods(alleles, logLikelihoods, ploidy,perLaneErrorModels,ignoreLaneInformation, pairModel, haplotypeMap, ref, perReadAlleleLikelihoodMap); } 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 3c065abdb..2e2c959aa 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 @@ -44,18 +44,18 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.SAMUtils; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACset; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; import htsjdk.variant.variantcontext.Allele; import java.util.ArrayList; @@ -101,7 +101,7 @@ public class GeneralPloidySNPGenotypeLikelihoods extends GeneralPloidyGenotypeLi Allele refAllele = alleles.get(0); //sanity check: by construction, first allele should ALWAYS be the reference alleles if (!refAllele.isReference()) - throw new ReviewedStingException("BUG: First allele in list passed to GeneralPloidySNPGenotypeLikelihoods should be reference!"); + throw new ReviewedGATKException("BUG: First allele in list passed to GeneralPloidySNPGenotypeLikelihoods should be reference!"); refByte = refAllele.getBases()[0]; // by construction, first allele in list is always ref! 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 acd5fe4a1..cd59c0dec 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; /* * Copyright (c) 2010. * @@ -72,13 +72,13 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.*; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils; import htsjdk.variant.variantcontext.*; import java.util.*; @@ -98,7 +98,7 @@ public class GeneralPloidySNPGenotypeLikelihoodsCalculationModel extends General final boolean useBQAedPileup, final ReferenceContext ref, final boolean ignoreLaneInformation, - final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){ + final org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){ return new GeneralPloidySNPGenotypeLikelihoods(alleles, null, UAC.samplePloidy, perLaneErrorModels, useBQAedPileup, UAC.IGNORE_LANE_INFO); } 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 faf8ad6c6..09d80912b 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 @@ -44,18 +44,18 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; @@ -88,7 +88,7 @@ public abstract class GenotypeLikelihoodsCalculationModel { * @param UAC unified arg collection */ protected GenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) { - if ( logger == null || UAC == null ) throw new ReviewedStingException("Bad arguments"); + if ( logger == null || UAC == null ) throw new ReviewedGATKException("Bad arguments"); this.UAC = UAC; this.logger = logger; } @@ -112,7 +112,7 @@ public abstract class GenotypeLikelihoodsCalculationModel { final List allAllelesToUse, final boolean useBAQedPileup, final GenomeLocParser locParser, - final Map perReadAlleleLikelihoodMap); + final Map perReadAlleleLikelihoodMap); protected int getFilteredDepth(ReadBackedPileup pileup) { 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 80982a07f..419decd1b 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; public interface GenotypePriors { 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 870b85610..0a53a5fae 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 @@ -44,29 +44,29 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalc; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalc; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcResult; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFConstants; @@ -228,7 +228,7 @@ public abstract class GenotypingEngine stratifiedContexts, final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, final boolean inheritAttributesFromInputVC, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { final boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null; // if input VC can't be genotyped, exit with either null VCC or, in case where we need to emit all sites, an empty call @@ -653,7 +653,7 @@ public abstract class GenotypingEngine composeCallAttributes(final boolean inheritAttributesFromInputVC, final VariantContext vc, final AlignmentContext rawContext, final Map stratifiedContexts, final RefMetaDataTracker tracker, final ReferenceContext refContext, final List alleleCountsofMLE, final boolean bestGuessIsRef, final AFCalcResult AFresult, final List allAllelesToUse, final GenotypesContext genotypes, - final GenotypeLikelihoodsCalculationModel.Model model, final Map perReadAlleleLikelihoodMap) { + final GenotypeLikelihoodsCalculationModel.Model model, final Map perReadAlleleLikelihoodMap) { final HashMap attributes = new HashMap<>(); final boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null; 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 f8860ac5a..39aeeff6c 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; /** * Enumeration of possible genotyping modes. 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 a34c157e4..73b2d5e99 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 @@ -44,21 +44,21 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.*; import java.util.*; 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 72918e914..782b116aa 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; /** * TODO document this. 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 609339d0c..0ce1a4015 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.tools.walkers.indels.HaplotypeIndelErrorModel; +import org.broadinstitute.gatk.utils.MathUtils; public class PoolGenotypePriors implements GenotypePriors { private final double[] flatPriors; 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 ef39e26e8..5bd7061cb 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.Arrays; @@ -75,7 +75,7 @@ public class ProbabilityVector { int maxValIdx = MathUtils.maxElementIndex(vec); double maxv = vec[maxValIdx]; if (maxv > 0.0) - throw new ReviewedStingException("BUG: Attempting to create a log-probability vector with positive elements"); + throw new ReviewedGATKException("BUG: Attempting to create a log-probability vector with positive elements"); if (compressRange) { minVal = getMinIdx(vec, maxValIdx); 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 85d34864c..5e8914c8e 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 @@ -44,25 +44,25 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.genotyper.DiploidGenotype; -import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.baq.BAQ; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.genotyper.DiploidGenotype; +import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; import htsjdk.variant.variantcontext.*; import java.util.*; 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 6b879cb47..e8dddaaaf 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection; -import org.broadinstitute.sting.utils.pairhmm.PairHMM; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.utils.pairhmm.PairHMM; import htsjdk.variant.variantcontext.VariantContext; public class UnifiedArgumentCollection extends StandardCallerArgumentCollection { 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 d76bd2c2d..bf26c18f3 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 @@ -44,29 +44,29 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils; -import org.broadinstitute.sting.gatk.downsampling.DownsampleType; -import org.broadinstitute.sting.gatk.filters.BadMateFilter; -import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtils; +import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.engine.filters.BadMateFilter; +import org.broadinstitute.gatk.engine.filters.MappingQualityUnavailableFilter; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.baq.BAQ; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.*; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.GenotypeLikelihoods; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.VariantContextWriter; @@ -179,7 +179,7 @@ public class UnifiedGenotyper extends LocusWalker, Unif /** * A raw, unfiltered, highly sensitive callset in VCF format. */ - //@Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer") + //@Gather(className = "org.broadinstitute.gatk.queue.extensions.gatk.CatVariantsGatherer") @Output(doc="File to which variants should be written") protected VariantContextWriter writer = null; 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 2cd019aaf..3fd51c21d 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 @@ -43,25 +43,25 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcResult; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.baq.BAQ; +import org.broadinstitute.gatk.utils.classloader.PluginManager; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; @@ -173,7 +173,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine models = getGLModelsToUse(tracker, rawContext); - final Map perReadAlleleLikelihoodMap = new HashMap<>(); + final Map perReadAlleleLikelihoodMap = new HashMap<>(); final VariantCallContext defaultResult = configuration.outputMode == OutputMode.EMIT_ALL_SITES && configuration.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES @@ -237,7 +237,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { final List models = getGLModelsToUse(tracker, rawContext); if ( models.isEmpty() ) { return null; @@ -303,7 +303,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine alternateAllelesToUse, final boolean useBAQedPileup, final GenotypeLikelihoodsCalculationModel.Model model, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { return glcm.get().get(model.name()).getLikelihoods(tracker, refContext, stratifiedContexts, type, alternateAllelesToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser, perReadAlleleLikelihoodMap); } @@ -319,7 +319,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine stratifiedContexts, final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false, perReadAlleleLikelihoodMap); } @@ -333,7 +333,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine stratifiedContexts, final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, final boolean inheritAttributesFromInputVC, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap) { boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null; final VariantCallContext result = super.calculateGenotypes(tracker,refContext,rawContext,stratifiedContexts,vc,model,inheritAttributesFromInputVC,perReadAlleleLikelihoodMap); if ( verboseWriter != null && !limitedContext ) @@ -356,7 +356,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine composeCallAttributes(final boolean inheritAttributesFromInputVC, final VariantContext vc, final AlignmentContext rawContext, final Map stratifiedContexts, final RefMetaDataTracker tracker, final ReferenceContext refContext, final List alleleCountsofMLE, final boolean bestGuessIsRef, final AFCalcResult AFresult, final List allAllelesToUse, final GenotypesContext genotypes, - final GenotypeLikelihoodsCalculationModel.Model model, final Map perReadAlleleLikelihoodMap) { + final GenotypeLikelihoodsCalculationModel.Model model, final Map perReadAlleleLikelihoodMap) { final Map result = super.composeCallAttributes(inheritAttributesFromInputVC, vc,rawContext,stratifiedContexts,tracker,refContext,alleleCountsofMLE,bestGuessIsRef, AFresult,allAllelesToUse,genotypes,model,perReadAlleleLikelihoodMap); 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 7efc39e03..84d4b8bd3 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalc.java index 1b94c024d..ade6de0d6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalc.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalc.java @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.SimpleTimer; +import org.broadinstitute.gatk.utils.SimpleTimer; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java index 0af4c520e..b904837c5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.classloader.PluginManager; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.lang.reflect.Constructor; import java.util.LinkedList; @@ -247,7 +247,7 @@ public class AFCalcFactory { Constructor c = afClass.getDeclaredConstructor(int.class, int.class, int.class); return (AFCalc)c.newInstance(args); } catch (Exception e) { - throw new ReviewedStingException("Could not instantiate AFCalc " + calc, e); + throw new ReviewedGATKException("Could not instantiate AFCalc " + calc, e); } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceTest.java index dd268e19d..4895ab303 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceTest.java @@ -44,18 +44,18 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import org.apache.log4j.ConsoleAppender; import org.apache.log4j.Logger; import org.apache.log4j.TTCCLayout; -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.gatk.report.GATKReportTable; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.SimpleTimer; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.SimpleTimer; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResult.java index d72877cbe..b4d22592e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResult.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResult.java @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; import htsjdk.variant.variantcontext.Allele; import java.util.*; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcTestBuilder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcTestBuilder.java index 46587d90b..9e8d18ddf 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcTestBuilder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcTestBuilder.java @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import org.apache.commons.lang.ArrayUtils; -import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypingEngine; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; import htsjdk.variant.variantcontext.*; import java.util.ArrayList; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalc.java index 5f6d15c73..98268c2bf 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalc.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalc.java @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypeLikelihoods; import htsjdk.variant.variantcontext.GenotypesContext; 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 8aa8806d9..fb1d084d5 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import java.util.Arrays; 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 6b412720f..ca067e810 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.utils.MathUtils; import java.util.Arrays; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalc.java index 2245ff4a7..d1aa86bfe 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalc.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalc.java @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import java.util.*; @@ -58,7 +58,7 @@ import java.util.*; abstract class ExactAFCalc extends AFCalc { protected static final int HOM_REF_INDEX = 0; // AA likelihoods are always first /** - * Sorts {@link org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with higher likelihood are first. + * Sorts {@link org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with higher likelihood are first. */ protected static final Comparator LIKELIHOOD_SUM_COMPARATOR = new Comparator() { @@ -68,7 +68,7 @@ abstract class ExactAFCalc extends AFCalc { } }; /** - * Sorts {@link org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with higher likelihood are first but make sure that + * Sorts {@link org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with higher likelihood are first but make sure that * NON_REF alleles are place are last. */ protected static final Comparator LIKELIHOOD_NON_REF_THEN_SUM_COMPARATOR = new Comparator() { @@ -83,7 +83,7 @@ abstract class ExactAFCalc extends AFCalc { } }; /** - * Sorts {@link org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with lower alternative allele index are first regardless of + * Sorts {@link org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with lower alternative allele index are first regardless of * the likelihood sum. */ protected static final Comparator LIKELIHOOD_INDEX_COMPARATOR = new Comparator() { 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 374177769..a6b936e61 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import com.google.java.contract.Requires; import org.apache.commons.lang.ArrayUtils; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.*; +import org.broadinstitute.gatk.utils.exceptions.UserException; import htsjdk.variant.variantcontext.*; import java.io.*; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java index 74dd447f0..500cdf4ce 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java @@ -44,13 +44,13 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; -import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyGenotypeLikelihoods; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import htsjdk.variant.variantcontext.*; import java.util.*; @@ -306,7 +306,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc { // final int dim2 = GenotypeLikelihoods.numLikelihoods(numAlleles, ploidy2); // // if (dim1 != originalPool.getLength() || dim2 != yy.length) -// throw new ReviewedStingException("BUG: Inconsistent vector length"); +// throw new ReviewedGATKException("BUG: Inconsistent vector length"); // // if (ploidy2 == 0) // return; @@ -367,7 +367,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc { // sanity check int totalAltK = set.getACsum(); if (newPloidy != totalAltK) - throw new ReviewedStingException("BUG: inconsistent sizes of set.getACsum and passed ploidy values"); + throw new ReviewedGATKException("BUG: inconsistent sizes of set.getACsum and passed ploidy values"); totalAltK -= set.getACcounts().getCounts()[0]; // totalAltK has sum of alt alleles of conformation now diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java index 669094007..6a740164f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java index 452eeb70b..bd6b0de84 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.collections.Pair; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java index 909d4c8bb..955fa86f2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; public class ReferenceDiploidExactAFCalc extends DiploidExactAFCalc { protected ReferenceDiploidExactAFCalc(int nSamples, int maxAltAlleles, final int ploidy) { 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 6f838e538..51f5daffc 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.variantcontext.Allele; import java.util.Arrays; 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 f83f69cfb..4f72c5ffd 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 @@ -43,16 +43,16 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Hidden; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.UserException; import htsjdk.variant.variantcontext.VariantContext; import java.util.*; 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 658ffc10e..f29fcf4e5 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.SeqGraph; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.SeqGraph; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph; /** * Result of assembling, with the resulting graph and status 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 97b922d83..31c8cb22b 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.collections.CountSet; -import org.broadinstitute.sting.utils.haplotype.EventMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.haplotype.HaplotypeSizeAndBaseComparator; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.collections.CountSet; +import org.broadinstitute.gatk.utils.haplotype.EventMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotype.HaplotypeSizeAndBaseComparator; import htsjdk.variant.variantcontext.VariantContext; import java.io.PrintWriter; 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 be7305085..4c3655c72 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 @@ -43,12 +43,12 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Route; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.MultiSampleEdge; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.Route; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; import java.util.*; 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 ca4985cef..5ad63af82 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 @@ -43,15 +43,15 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Requires; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; -import org.broadinstitute.sting.utils.collections.CountSet; -import org.broadinstitute.sting.utils.collections.CountSet; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.MultiSampleEdge; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; +import org.broadinstitute.gatk.utils.collections.CountSet; +import org.broadinstitute.gatk.utils.collections.CountSet; +import org.broadinstitute.gatk.utils.collections.Pair; import java.util.*; 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 18341e185..cfb1b957a 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 @@ -43,17 +43,17 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.SeqGraph; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.pairhmm.FlexibleHMM; -import org.broadinstitute.sting.utils.pairhmm.FastLoglessPairHMM; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.SeqGraph; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.pairhmm.FlexibleHMM; +import org.broadinstitute.gatk.utils.pairhmm.FastLoglessPairHMM; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.io.File; import java.io.FileWriter; @@ -151,7 +151,7 @@ public class GraphBasedLikelihoodCalculationEngine implements ReadLikelihoodCalc pw.close(); fw.close(); } catch (Exception ex) { - throw new StingException("", ex); + throw new GATKException("", ex); } } } 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 beb161939..50e12842a 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 @@ -44,22 +44,22 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Path; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Route; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.CountSet; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.pairhmm.FlexibleHMM; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.MultiSampleEdge; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.Path; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.Route; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.CountSet; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.pairhmm.FlexibleHMM; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import java.util.*; 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 3685936a8..5c1820324 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 @@ -44,54 +44,54 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Ensures; import htsjdk.samtools.SAMFileWriter; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils; -import org.broadinstitute.sting.gatk.downsampling.DownsampleType; -import org.broadinstitute.sting.gatk.downsampling.DownsamplingUtils; -import org.broadinstitute.sting.gatk.filters.BadMateFilter; -import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.genotyper.*; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingAssembler; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileState; -import org.broadinstitute.sting.utils.clipping.ReadClipper; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.fragments.FragmentCollection; -import org.broadinstitute.sting.utils.fragments.FragmentUtils; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; -import org.broadinstitute.sting.utils.gvcf.GVCFWriter; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.haplotype.LDMerger; -import org.broadinstitute.sting.utils.haplotype.MergeVariantsAcrossHaplotypes; -import org.broadinstitute.sting.utils.haplotypeBAMWriter.HaplotypeBAMWriter; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.pairhmm.PairHMM; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variant.GATKVCFIndexType; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtils; +import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.engine.downsampling.DownsamplingUtils; +import org.broadinstitute.gatk.engine.filters.BadMateFilter; +import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.genotyper.*; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegionReadState; +import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState; +import org.broadinstitute.gatk.utils.clipping.ReadClipper; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.fragments.FragmentCollection; +import org.broadinstitute.gatk.utils.fragments.FragmentUtils; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils; +import org.broadinstitute.gatk.utils.gvcf.GVCFWriter; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotype.LDMerger; +import org.broadinstitute.gatk.utils.haplotype.MergeVariantsAcrossHaplotypes; +import org.broadinstitute.gatk.utils.haplotypeBAMWriter.HaplotypeBAMWriter; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.pairhmm.PairHMM; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType; import htsjdk.variant.variantcontext.*; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.vcf.*; @@ -195,7 +195,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In */ @Advanced @Output(fullName="bamOutput", shortName="bamout", doc="File to which assembled haplotypes should be written", required = false, defaultToStdout = false) - protected StingSAMFileWriter bamWriter = null; + protected GATKSAMFileWriter bamWriter = null; private HaplotypeBAMWriter haplotypeBAMWriter; /** 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 1224ed6f7..321c48166 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 @@ -43,11 +43,11 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.commandline.Advanced; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.utils.commandline.Advanced; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; /** * Set of arguments for the {@link HaplotypeCaller} 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 478b6888f..86548796e 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 @@ -44,26 +44,26 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypingEngine; -import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypingOutputMode; -import org.broadinstitute.sting.gatk.walkers.genotyper.OutputMode; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.DefaultHashMap; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.EventMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.haplotype.MergeVariantsAcrossHaplotypes; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode; +import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.DefaultHashMap; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.EventMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotype.MergeVariantsAcrossHaplotypes; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import java.util.*; 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 2daf25420..712da91e5 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 @@ -44,29 +44,29 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.Reference; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.Window; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment; -import org.broadinstitute.sting.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Input; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.utils.commandline.RodBinding; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.Reference; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.engine.walkers.Window; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment; +import org.broadinstitute.gatk.utils.help.HelpConstants; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; 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 5887864e3..63e3f8933 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 @@ -43,11 +43,11 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Route; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.MultiSampleEdge; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.Route; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; import java.util.*; 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 b56d942ae..42dd7fab4 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; /** * How to resolve the haplotype graph when haplotypes where generated from a mixture of different kmerSizes. 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 aad8407dd..a6f8cdfc1 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import java.util.*; 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 056f7991f..761ed8378 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Requires; 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 78c927877..3ba8d89b5 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; import java.lang.reflect.Array; import java.util.*; 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 d71f99116..5a4a65b43 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.BaseEdge; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.BaseVertex; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.KmerSearchableGraph; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.BaseEdge; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.BaseVertex; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.KmerSearchableGraph; import java.util.List; import java.util.Map; 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 d0b53f20f..2ae031f4b 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; @@ -52,13 +52,13 @@ import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.CigarUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.*; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.CigarUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.VariantContext; import java.io.File; @@ -201,7 +201,7 @@ public abstract class LocalAssemblyEngine { final KBestHaplotype kBestHaplotype = bestHaplotypes.next(); final Haplotype h = kBestHaplotype.haplotype(); if( !returnHaplotypes.contains(h) ) { - final Cigar cigar = CigarUtils.calculateCigar(refHaplotype.getBases(),h.getBases()); + final Cigar cigar = CigarUtils.calculateCigar(refHaplotype.getBases(), h.getBases()); if ( cigar == null ) { // couldn't produce a meaningful alignment of haplotype to reference, fail quietly 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 9d5044957..3b84f53f4 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 @@ -44,21 +44,21 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import htsjdk.samtools.SAMUtils; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.pairhmm.*; -import org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate; -import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.pairhmm.*; +import org.broadinstitute.gatk.utils.recalibration.covariates.RepeatCovariate; +import org.broadinstitute.gatk.utils.recalibration.covariates.RepeatLengthCovariate; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.*; import java.io.File; @@ -586,7 +586,7 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula // } // // /** -// * Find the haplotype that isRef(), or @throw ReviewedStingException if one isn't found +// * Find the haplotype that isRef(), or @throw ReviewedGATKException if one isn't found // * @param haplotypes non-null list of haplotypes // * @return the reference haplotype // */ @@ -594,7 +594,7 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula // for( final Haplotype h : haplotypes ) { // if( h.isReference() ) return h; // } -// throw new ReviewedStingException( "No reference haplotype found in the list of haplotypes!" ); +// throw new ReviewedGATKException( "No reference haplotype found in the list of haplotypes!" ); // } // -------------------------------------------------------------------------------- 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 c6dd7aa0f..7edcfde39 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 @@ -43,12 +43,12 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import java.util.HashMap; 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 b4d2e1a2f..1396a6a46 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 @@ -43,15 +43,15 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Path; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.MultiSampleEdge; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.Path; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.*; 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 6fc784799..b92723d11 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 @@ -43,10 +43,10 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Comparator; 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 a48ac9ee0..d7f3583fa 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.clipping.ReadClipper; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.clipping.ReadClipper; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.*; 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 98d76b356..535ca813f 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.List; import java.util.Map; 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 2efe42337..b95393eb6 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import java.util.Comparator; 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 b362dcb76..8c5db2760 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 @@ -43,13 +43,13 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Route; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.MultiSampleEdge; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.Route; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.concurrent.atomic.AtomicLong; 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 8fb7afec7..8726c9365 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; /** * Holds information about a genotype call of a single sample reference vs. any non-ref event 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 ce40fbc05..1d98e508e 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; /** * Reference confidence emission modes. 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 07c355355..63543c5c2 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 @@ -44,27 +44,27 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.samtools.*; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.haplotypeBAMWriter.HaplotypeBAMWriter; -import org.broadinstitute.sting.utils.haplotypeBAMWriter.ReadDestination; -import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotypeBAMWriter.HaplotypeBAMWriter; +import org.broadinstitute.gatk.utils.haplotypeBAMWriter.ReadDestination; +import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFSimpleHeaderLine; 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 d981e6eeb..ef69617c2 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 @@ -43,9 +43,9 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.collections.Pair; import java.util.*; 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 a6ef0d1c2..1f5a1da10 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import java.io.Serializable; import java.util.Collection; 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 3abd2e4bc..c31ef8469 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; 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 ee198185d..8c474418f 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import java.util.HashSet; import java.util.Iterator; 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 63f087979..5f3289333 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import com.google.java.contract.Ensures; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph; import java.util.Arrays; 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 71ce9929b..263ef6b35 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import com.google.java.contract.Requires; 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 cf95f6a5a..3a164a3f0 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import com.google.java.contract.Ensures; 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 5ceaa29c5..a0bcb2fb5 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 @@ -43,9 +43,9 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.collections.Pair; import java.util.Collections; import java.util.Set; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java index 1a642d200..6d0b7a693 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java @@ -43,10 +43,10 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.Pair; import java.util.Collections; import java.util.Set; 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 73a1daa3e..273cc1c5e 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.collections.PrimitivePair; +import org.broadinstitute.gatk.utils.collections.PrimitivePair; import java.util.ArrayList; import java.util.Collection; 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 d1b5bd614..7dd84849a 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 @@ -43,9 +43,9 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; /** * Represents a result from a K-best haplotype search. 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 5e971792c..1650cfd24 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 @@ -43,10 +43,10 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; import org.jgrapht.alg.CycleDetector; import java.io.File; 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 eb3360500..1cc75d18b 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 @@ -43,9 +43,9 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.collections.Pair; import java.util.Set; 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 94dc98b6c..810a44e0e 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Kmer; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer; /** * Common interface for those graphs that implement vertex by kmer look-up. 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 520267dee..2716dc8d6 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import java.util.*; 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 657ecfd85..c320addea 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import java.util.PriorityQueue; 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 4ec950623..36789a459 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import com.google.java.contract.Ensures; import htsjdk.samtools.Cigar; import org.apache.commons.lang.ArrayUtils; -import org.broadinstitute.sting.utils.sam.CigarUtils; +import org.broadinstitute.gatk.utils.sam.CigarUtils; import java.util.*; 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 fe85befef..c4111c030 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 @@ -43,10 +43,10 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.Pair; import java.util.*; 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 4eeb18eb6..44615ae42 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import java.util.List; 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 ac6837d33..5df2205d8 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 @@ -43,10 +43,10 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.KmerSequence; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.KmerSequence; +import org.broadinstitute.gatk.utils.collections.Pair; import java.util.Stack; 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 087c07be7..533151076 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; @@ -302,7 +302,7 @@ public class SeqGraph extends BaseGraph { protected SeqVertex mergeLinearChainVertices(final List vertices) { final List seqs = new LinkedList(); for ( SeqVertex v : vertices ) seqs.add(v.getSequence()); - final byte[] seqsCat = org.broadinstitute.sting.utils.Utils.concat(seqs.toArray(new byte[][]{})); + final byte[] seqsCat = org.broadinstitute.gatk.utils.Utils.concat(seqs.toArray(new byte[][]{})); return new SeqVertex( seqsCat ); } 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 ee1ece3f3..203f7cdee 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import com.google.java.contract.Requires; 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 5d725b1dd..b9cacfb5a 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import org.apache.commons.lang.ArrayUtils; 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 401cbf18c..192304f68 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.collections.Pair; import java.util.*; 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 8c79a5efe..9e7328f6e 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import com.google.java.contract.Ensures; import org.jgrapht.EdgeFactory; 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 2b58fcbf0..1b51175ca 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; /** * Indicate a SeqGraph vertex topological order between to vertices. 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 0a4264046..09a5a001f 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 @@ -44,15 +44,15 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.readthreading; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; import com.google.java.contract.Ensures; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.smithwaterman.*; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.*; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.smithwaterman.*; import org.jgrapht.EdgeFactory; import java.util.*; 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 150cdc826..17b43cb35 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 @@ -44,17 +44,17 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.readthreading; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeRoute; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Kmer; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; -import org.broadinstitute.sting.utils.SequenceComplexity; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.CountSet; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeRoute; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.*; +import org.broadinstitute.gatk.utils.SequenceComplexity; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.CountSet; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; import java.io.File; import java.io.PrintStream; 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 ef8c74d0b..66e702179 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.readthreading; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.DeBruijnVertex; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.DeBruijnVertex; +import org.broadinstitute.gatk.utils.Utils; import java.util.LinkedList; import java.util.List; 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 fc5d22fd7..77cc81b48 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 @@ -44,15 +44,15 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.readthreading; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.AssemblyResult; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.LocalAssemblyEngine; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResult; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.LocalAssemblyEngine; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.*; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.io.File; import java.util.Arrays; 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 06ee15a47..d34b66873 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.readthreading; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.KMerCounter; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Kmer; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.KMerCounter; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.*; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.io.File; import java.util.*; 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 e55772657..bafe1ea51 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.readthreading; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; /** * Keeps track of the information needed to add a sequence to the read threading assembly graph 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 233445b18..3e7c686f5 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; import htsjdk.samtools.SamPairUtil; import htsjdk.samtools.SAMFileWriter; @@ -52,10 +52,10 @@ import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMRecordComparator; import htsjdk.samtools.SAMRecordCoordinateComparator; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.*; 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 c299462ba..588b3a907 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 @@ -44,15 +44,15 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import htsjdk.variant.variantcontext.Allele; import java.util.Arrays; 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 ea0f53579..75d55c6f6 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 @@ -44,41 +44,41 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; import htsjdk.samtools.*; import htsjdk.samtools.util.RuntimeIOException; import htsjdk.samtools.util.SequenceUtil; import htsjdk.samtools.util.StringUtil; import htsjdk.tribble.Feature; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.BAQMode; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.smithwaterman.Parameters; -import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter; -import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.text.TextFormattingUtils; -import org.broadinstitute.sting.utils.text.XReadLines; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.BAQMode; +import org.broadinstitute.gatk.engine.walkers.ReadWalker; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.smithwaterman.Parameters; +import org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.baq.BAQ; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.NWaySAMFileWriter; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.text.TextFormattingUtils; +import org.broadinstitute.gatk.utils.text.XReadLines; import htsjdk.variant.variantcontext.VariantContext; import java.io.File; @@ -191,7 +191,7 @@ public class IndelRealigner extends ReadWalker { * The realigned bam file. */ @Output(required=false, doc="Output bam", defaultToStdout=false) - protected StingSAMFileWriter writer = null; + protected GATKSAMFileWriter writer = null; protected ConstrainedMateFixingManager manager = null; protected SAMFileWriter writerToUse = null; @@ -372,7 +372,7 @@ public class IndelRealigner extends ReadWalker { fname_map.put(fields[0],fields[1]); } } catch (IOException e) { - throw new StingException("I/O Error while reading input-output map file "+N_WAY_OUT+": "+e.getMessage()); + throw new GATKException("I/O Error while reading input-output map file "+N_WAY_OUT+": "+e.getMessage()); } return fname_map; } @@ -472,9 +472,9 @@ public class IndelRealigner extends ReadWalker { if ( NO_PG_TAG ) return null; final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME); - final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText"); + final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText"); try { - final String version = headerInfo.getString("org.broadinstitute.sting.gatk.version"); + final String version = headerInfo.getString("org.broadinstitute.gatk.tools.version"); programRecord.setProgramVersion(version); } catch (MissingResourceException e) { // this is left empty on purpose (perhaps Andrey knows why?) @@ -588,7 +588,7 @@ public class IndelRealigner extends ReadWalker { currentInterval = intervals.hasNext() ? intervals.next() : null; } while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) ); - } catch (ReviewedStingException e) { + } catch (ReviewedGATKException e) { throw new UserException.MissortedFile(new File(intervalsFile.getSource()), " *** Are you sure that your interval file is sorted? If not, you must use the --targetIntervalsAreNotSorted argument. ***", e); } sawReadInCurrentInterval = false; 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 4a3e65d02..4f3988584 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 @@ -44,20 +44,20 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; import htsjdk.samtools.Cigar; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.ReadWalker; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /** @@ -92,7 +92,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; public class LeftAlignIndels extends ReadWalker { @Output(required=false, doc="Output bam") - protected StingSAMFileWriter writer = null; + protected GATKSAMFileWriter writer = null; public void initialize() {} 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 27ce8c0af..32e1dcd0e 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 @@ -44,23 +44,23 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; import com.google.java.contract.Ensures; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.clipping.ReadClipper; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.pairhmm.ArrayLoglessPairHMM; -import org.broadinstitute.sting.utils.pairhmm.Log10PairHMM; -import org.broadinstitute.sting.utils.pairhmm.LoglessPairHMM; -import org.broadinstitute.sting.utils.pairhmm.PairHMM; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.clipping.ReadClipper; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.pairhmm.ArrayLoglessPairHMM; +import org.broadinstitute.gatk.utils.pairhmm.Log10PairHMM; +import org.broadinstitute.gatk.utils.pairhmm.LoglessPairHMM; +import org.broadinstitute.gatk.utils.pairhmm.PairHMM; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import htsjdk.variant.variantcontext.Allele; import java.util.Arrays; 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 b086568e6..853839cfa 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.HasGenomeLocation; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.ArrayList; import java.util.List; 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 f87823735..998b8acab 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 @@ -44,25 +44,25 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.filters.*; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Input; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.utils.commandline.RodBinding; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.filters.*; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.VariantContext; import java.io.PrintStream; 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 259734ab9..d8b3dfcab 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; @@ -59,7 +59,7 @@ public class AllelePair { public AllelePair(Genotype gt) { if (gt.getPloidy() != 2) - throw new ReviewedStingException("AllelePair must have ploidy of 2! incoming gt was"+gt.toBriefString()); + throw new ReviewedGATKException("AllelePair must have ploidy of 2! incoming gt was"+gt.toBriefString()); this.top = gt.getAllele(0); this.bottom = gt.getAllele(1); 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 cbc6a1f94..69f49ea30 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.gatk.utils.BaseUtils; import java.util.Arrays; import java.util.LinkedList; 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 b4cf83b06..a8fd68f6e 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.Iterator; @@ -75,7 +75,7 @@ class CardinalityCounter implements Iterator, Iterable { public int[] next() { if (!hasNext()) - throw new ReviewedStingException("CANNOT iterate past end!"); + throw new ReviewedGATKException("CANNOT iterate past end!"); // Copy the assignment to be returned: int[] nextList = new int[valList.length]; 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 41a8b0ae9..778e19b15 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; import java.util.NoSuchElementException; 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 037e24cc8..f87836a16 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; import java.util.Collection; import java.util.Set; 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 b39aa1b42..9afc22bfb 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.Arrays; import java.util.LinkedList; @@ -70,12 +70,12 @@ class Haplotype extends BaseArray implements Cloneable { super(baseArr.bases); if (baseArr.getNonNullIndices().length != baseArr.bases.length) - throw new ReviewedStingException("Should NEVER call Haplotype ctor with null bases!"); + throw new ReviewedGATKException("Should NEVER call Haplotype ctor with null bases!"); } public void updateBase(int index, Byte base) { if (base == null) { - throw new ReviewedStingException("Internal error: CANNOT have null for a missing Haplotype base!"); + throw new ReviewedGATKException("Internal error: CANNOT have null for a missing Haplotype base!"); } super.updateBase(index, base); } 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 cc2a19131..7f1ad70b8 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 @@ -44,18 +44,18 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; import htsjdk.samtools.reference.ReferenceSequenceFile; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import htsjdk.variant.variantcontext.*; import java.io.File; @@ -154,7 +154,7 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter logger.debug("NOT Waiting to merge..."); if (!filteredVcfrList.isEmpty()) - throw new ReviewedStingException("filteredVcfrList should be empty if not waiting to merge a vc!"); + throw new ReviewedGATKException("filteredVcfrList should be empty if not waiting to merge a vc!"); if (curVcIsNotFiltered) { // still need to wait before can release vc logger.debug("Waiting for new variant " + GATKVariantContextUtils.getLocation(genomeLocParser, vc)); @@ -225,7 +225,7 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter private void stopWaitingToMerge() { if (vcfrWaitingToMerge == null) { if (!filteredVcfrList.isEmpty()) - throw new ReviewedStingException("filteredVcfrList should be empty if not waiting to merge a vc!"); + throw new ReviewedGATKException("filteredVcfrList should be empty if not waiting to merge a vc!"); return; } @@ -402,7 +402,7 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter if (containsRefAllele(site1Alleles) && containsRefAllele(site2Alleles)) { logger.debug("HET-HET for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2)); if (logger.isDebugEnabled() && !(gt1.isHet() && gt2.isHet())) - throw new ReviewedStingException("Since !gt1.isHomRef() && !gt2.isHomRef(), yet both have ref alleles, they BOTH must be hets!"); + throw new ReviewedGATKException("Since !gt1.isHomRef() && !gt2.isHomRef(), yet both have ref alleles, they BOTH must be hets!"); // There's the potential to only have REF-ALT, ALT-REF (CHet), or possibly ALT-ALT together (MNP) boolean hasMNP = false; 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 ed39a2896..87da9ce25 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 @@ -44,27 +44,27 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.samples.Sample; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.samples.Sample; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.*; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import htsjdk.variant.variantcontext.*; import java.io.PrintStream; 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 456a4913c..01b6903b8 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; import java.util.*; 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 a0a79d579..7a43fb42a 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; /* Edge class for PhasingGraph 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 a04789f61..3ed730b98 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.Arrays; @@ -94,7 +94,7 @@ class PhasingRead extends BaseArray { int sz = this.bases.length; if (sz != hap.bases.length) - throw new ReviewedStingException("Read and Haplotype should have same length to be compared!"); + throw new ReviewedGATKException("Read and Haplotype should have same length to be compared!"); // Technically, this HAS NO EFFECT since it is multiplied in for ALL haplotype pairs, but do so for completeness: score.timesEqual(mappingProb); 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 b5a6a5f69..246bd5257 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.samtools.util.StringUtil; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import htsjdk.variant.variantcontext.*; import java.util.*; @@ -188,10 +188,10 @@ class PhasingUtils { GenomeLoc loc2 = GATKVariantContextUtils.getLocation(genomeLocParser, vc2); if (!loc1.onSameContig(loc2)) - throw new ReviewedStingException("Can only merge vc1, vc2 if on the same chromosome"); + throw new ReviewedGATKException("Can only merge vc1, vc2 if on the same chromosome"); if (!loc1.isBefore(loc2)) - throw new ReviewedStingException("Can only merge if vc1 is BEFORE vc2"); + throw new ReviewedGATKException("Can only merge if vc1 is BEFORE vc2"); if (vc1.isFiltered() || vc2.isFiltered()) return false; @@ -243,7 +243,7 @@ class PhasingUtils { return new PhaseAndQuality(gt1); // maintain the phase of gt1 if (!gt1.isHom()) - throw new ReviewedStingException("alleleSegregationIsKnown(gt1, gt2) implies: gt2.genotypesArePhased() || gt2.isHom() || gt1.isHom()"); + throw new ReviewedGATKException("alleleSegregationIsKnown(gt1, gt2) implies: gt2.genotypesArePhased() || gt2.isHom() || gt1.isHom()"); /* We're dealing with: gt1.isHom(), gt2.isHet(), !gt2.genotypesArePhased(); so, the merged (het) Genotype is not phased relative to the previous Genotype 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 2a2b2618f..3c841f03e 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; /* PreciseNonNegativeDouble permits arithmetic operations on NON-NEGATIVE double values with precision (prevents underflow by representing in log10 space). 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 79255c7f8..319f20f68 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 @@ -44,32 +44,32 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.HasGenomeLocation; -import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; +import org.broadinstitute.gatk.utils.commandline.Hidden; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.filters.MappingQualityZeroFilter; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.SampleUtils; import htsjdk.variant.vcf.*; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.*; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; @@ -77,7 +77,7 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.*; import java.util.*; -import static org.broadinstitute.sting.utils.variant.GATKVCFUtils.getVCFHeadersFromRods; +import static org.broadinstitute.gatk.utils.variant.GATKVCFUtils.getVCFHeadersFromRods; /** * Walks along all variant ROD loci, caching a user-defined window of VariantContext sites, and then finishes phasing them when they go out of range (using upstream and downstream reads). @@ -441,7 +441,7 @@ public class ReadBackedPhasing extends RodWalker prevHetGenotypes, int goBackFromEndOfPrevHets) { if (prevHetGenotypes.isEmpty() || goBackFromEndOfPrevHets >= prevHetGenotypes.size()) // no previous sites against which to phase - throw new ReviewedStingException("Should never get empty set of previous sites to phase against"); + throw new ReviewedGATKException("Should never get empty set of previous sites to phase against"); // Include these previously phased sites in the phasing computation: List listHetGenotypes = new LinkedList(prevHetGenotypes); @@ -1102,7 +1102,7 @@ public class ReadBackedPhasing extends RodWalker 2!"); + throw new ReviewedGATKException("LOGICAL ERROR: Only considering haplotypes of length > 2!"); String[] curPairNames = prevPairNames; @@ -1441,7 +1441,7 @@ public class ReadBackedPhasing extends RodWalker { * The simulated reads will be written to a BAM file. */ @Output(doc="Reads corresponding to variants", required=true) - protected StingSAMFileWriter readWriter; + protected GATKSAMFileWriter readWriter; /** * Use this argument to set the desired target read depth. See the readSamplingMode argument for options that * determine whether coverage distribution will be exactly this value or an approximation. @@ -213,8 +215,8 @@ public class SimulateReadsForVariants extends RodWalker { final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME); if ( !NO_PG_TAG ) { - final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText"); - programRecord.setProgramVersion(headerInfo.getString("org.broadinstitute.sting.gatk.version")); + final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText"); + programRecord.setProgramVersion(headerInfo.getString("org.broadinstitute.gatk.tools.version")); programRecord.setCommandLine(getToolkit().createApproximateCommandLineArgumentString(getToolkit(), this)); } header.setProgramRecords(Arrays.asList(programRecord)); 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 288bcb6d8..fd8c62c90 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 @@ -44,22 +44,22 @@ * 7.7 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.sting.gatk.walkers.validation; +package org.broadinstitute.gatk.tools.walkers.validation; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.gatk.walkers.genotyper.*; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.genotyper.*; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; import htsjdk.variant.variantcontext.writer.VariantContextWriter; @@ -68,7 +68,7 @@ import htsjdk.variant.vcf.VCFUtils; import java.util.Map; import java.util.Set; -import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel; +import static org.broadinstitute.gatk.utils.IndelUtils.isInsideExtendedIndel; /** * Genotypes a dataset and validates the calls of another dataset using the Unified Genotyper. 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 5fbededeb..73ab5c9d4 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.validation.validationsiteselector; +package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocParser; import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; 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 6a0d1a956..e69d5995b 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.validation.validationsiteselector; +package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalc; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; -import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalc; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcResult; import htsjdk.variant.variantcontext.VariantContext; import java.util.TreeSet; 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 7bb59e721..c10170189 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.validation.validationsiteselector; +package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; import htsjdk.variant.variantcontext.VariantContext; 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 954398c4f..ee3b8441f 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.validation.validationsiteselector; +package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; @@ -77,7 +77,7 @@ public class GenomeEvent implements Comparable { } public int compareTo(final Object o) { if (!(o instanceof GenomeEvent)) - throw new ReviewedStingException("BUG: comparing variant context with non-VC object"); + throw new ReviewedGATKException("BUG: comparing variant context with non-VC object"); GenomeEvent otherEvent = (GenomeEvent)o; 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 af9aa05e9..4e10a8210 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.validation.validationsiteselector; +package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextUtils; 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 c88b70c8f..ebe4d4ba5 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.validation.validationsiteselector; +package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; import htsjdk.variant.variantcontext.VariantContext; import java.util.TreeSet; 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 552f48499..ab582c172 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.validation.validationsiteselector; +package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; import htsjdk.variant.variantcontext.VariantContext; import java.util.TreeSet; 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 8de485ef2..131533452 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.validation.validationsiteselector; +package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextUtils; 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 53d367810..4054d9d9a 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 @@ -44,22 +44,22 @@ * 7.7 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.sting.gatk.walkers.validation.validationsiteselector; +package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.VariantContextWriter; 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 95fcc6728..b66288458 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 @@ -44,24 +44,23 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; -import org.apache.commons.math.util.MathUtils; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.PartitionBy; -import org.broadinstitute.sting.gatk.walkers.PartitionType; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.PartitionBy; +import org.broadinstitute.gatk.engine.walkers.PartitionType; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.engine.walkers.TreeReducible; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import htsjdk.variant.vcf.*; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; import htsjdk.variant.variantcontext.writer.VariantContextWriter; 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 9e36e5dbe..1bbdd3df4 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import Jama.Matrix; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.MathUtils; import java.util.ArrayList; import java.util.Arrays; 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 1b1656a10..765eafcde 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import Jama.Matrix; import org.apache.commons.math.special.Gamma; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.collections.ExpandingArrayList; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.collections.ExpandingArrayList; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.util.Arrays; import java.util.List; 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 545b616d2..e3d5caf32 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.commandline.Tags; +import org.broadinstitute.gatk.utils.commandline.RodBinding; +import org.broadinstitute.gatk.utils.commandline.Tags; import htsjdk.variant.variantcontext.VariantContext; /** 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 3741ce12d..00e4cc836 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.text.XReadLines; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.text.XReadLines; import java.io.*; import java.util.*; @@ -91,10 +91,10 @@ public class Tranche { throw new UserException("Target FDR is unreasonable " + ts); if ( numKnown < 0 || numNovel < 0) - throw new ReviewedStingException("Invalid tranche - no. variants is < 0 : known " + numKnown + " novel " + numNovel); + throw new ReviewedGATKException("Invalid tranche - no. variants is < 0 : known " + numKnown + " novel " + numNovel); if ( name == null ) - throw new ReviewedStingException("BUG -- name cannot be null"); + throw new ReviewedGATKException("BUG -- name cannot be null"); } private double getTruthSensitivity() { 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 ab6b4adda..04ff505c4 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.File; import java.io.FileNotFoundException; 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 9caef9248..d0fb51318 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 @@ -44,21 +44,21 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import it.unimi.dsi.fastutil.booleans.BooleanLists; import org.apache.commons.lang.ArrayUtils; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import htsjdk.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.collections.ExpandingArrayList; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.collections.ExpandingArrayList; +import org.broadinstitute.gatk.utils.exceptions.UserException; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; @@ -404,7 +404,7 @@ public class VariantDataManager { case BOTH: return true; default: - throw new ReviewedStingException( "Encountered unknown recal mode: " + mode ); + throw new ReviewedGATKException( "Encountered unknown recal mode: " + mode ); } } 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 41b27949d..68e274c00 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; -import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLoc; import java.io.Serializable; import java.util.Comparator; 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 cb73cacb6..74c00290b 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 @@ -44,29 +44,29 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.PartitionBy; -import org.broadinstitute.sting.gatk.walkers.PartitionType; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.R.RScriptExecutor; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.PartitionBy; +import org.broadinstitute.gatk.engine.walkers.PartitionType; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.engine.walkers.TreeReducible; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.R.RScriptExecutor; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.collections.ExpandingArrayList; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.io.Resource; +import org.broadinstitute.gatk.utils.collections.ExpandingArrayList; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.io.Resource; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.VariantContextWriter; 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 81067e695..800e93a87 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; -import org.broadinstitute.sting.commandline.Advanced; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.commandline.Advanced; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Hidden; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; /** * Created by IntelliJ IDEA. @@ -69,7 +69,7 @@ public class VariantRecalibratorArgumentCollection { if( input.equals("SNP") ) { return Mode.SNP; } if( input.equals("INDEL") ) { return Mode.INDEL; } if( input.equals("BOTH") ) { return Mode.BOTH; } - throw new ReviewedStingException("VariantRecalibrator mode string is unrecognized, input = " + input); + throw new ReviewedGATKException("VariantRecalibrator mode string is unrecognized, input = " + input); } @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels (emitting SNPs untouched in the output VCF); and 3.) BOTH for recalibrating both SNPs and indels simultaneously (for testing purposes only, not recommended for general use).", required = false) 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 dae3bffa5..13a9e115f 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import java.util.List; 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 cf600ed4c..c9e97f405 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 @@ -44,22 +44,22 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.sting.utils.variant.HomoSapiensConstants; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.vcf.*; 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 98c8922f5..22eae02cb 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 @@ -44,23 +44,23 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.Reference; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.Window; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.Reference; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.engine.walkers.Window; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.vcf.*; 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 cdd6f7f5d..b0b7eeddc 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 @@ -44,28 +44,28 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.Reference; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.gatk.walkers.Window; -import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; -import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotypingEngine; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.Reference; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.engine.walkers.TreeReducible; +import org.broadinstitute.gatk.engine.walkers.Window; +import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedArgumentCollection; +import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.vcf.*; 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 f5f3a40b0..4c7a535fe 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFConstants; 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 14ced08b0..50e8bd416 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 @@ -44,22 +44,22 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.gatk.walkers.genotyper.*; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.engine.walkers.TreeReducible; +import org.broadinstitute.gatk.tools.walkers.genotyper.*; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; 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 8040ca62a..f40a9d5b0 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.utils; +package org.broadinstitute.gatk.utils; /** * Helper class to handle sequence complexity analyses. 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 5c7dbd505..61b7b7070 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.utils.collections; +package org.broadinstitute.gatk.utils.collections; import com.google.java.contract.Requires; 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 a3ef22cfc..4c561db1b 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 @@ -43,14 +43,14 @@ * 7.6 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. * 7.7 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.sting.utils.gga; +package org.broadinstitute.gatk.utils.gga; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.commandline.RodBinding; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; 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 ca49751a0..e55bf4fa0 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.utils.gvcf; +package org.broadinstitute.gatk.utils.gvcf; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.VariantContext; 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 1307cbf21..179217b91 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.utils.gvcf; +package org.broadinstitute.gatk.utils.gvcf; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java index 81c4ede80..ac33221d5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java @@ -44,12 +44,12 @@ * 7.7 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.sting.utils.haplotype; +package org.broadinstitute.gatk.utils.haplotype; import com.google.java.contract.Requires; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/LDMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/LDMerger.java index 02bf2a675..710fbc32c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/LDMerger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/LDMerger.java @@ -44,12 +44,12 @@ * 7.7 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.sting.utils.haplotype; +package org.broadinstitute.gatk.utils.haplotype; import org.apache.commons.lang.ArrayUtils; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/MergeVariantsAcrossHaplotypes.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/MergeVariantsAcrossHaplotypes.java index fc47807e0..f3565e4b8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/MergeVariantsAcrossHaplotypes.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/MergeVariantsAcrossHaplotypes.java @@ -44,10 +44,10 @@ * 7.7 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.sting.utils.haplotype; +package org.broadinstitute.gatk.utils.haplotype; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import java.util.List; import java.util.Map; 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 b5fe31255..019243364 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.utils.haplotypeBAMWriter; +package org.broadinstitute.gatk.utils.haplotypeBAMWriter; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import java.util.*; 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 82bfdabe0..4b8075a27 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.utils.haplotypeBAMWriter; +package org.broadinstitute.gatk.utils.haplotypeBAMWriter; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import java.util.Collection; 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 6625c4434..704c62a5b 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 @@ -44,20 +44,20 @@ * 7.7 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.sting.utils.haplotypeBAMWriter; +package org.broadinstitute.gatk.utils.haplotypeBAMWriter; import htsjdk.samtools.Cigar; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMTag; -import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.CigarUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment; +import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.CigarUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment; import java.util.Collection; import java.util.HashSet; @@ -109,7 +109,7 @@ public abstract class HaplotypeBAMWriter { * @param header the header of the input BAMs used to make calls, must not be null * @return a new HaplotypeBAMWriter */ - public static HaplotypeBAMWriter create(final Type type, final StingSAMFileWriter stingSAMWriter, final SAMFileHeader header) { + public static HaplotypeBAMWriter create(final Type type, final GATKSAMFileWriter stingSAMWriter, final SAMFileHeader header) { if ( type == null ) throw new IllegalArgumentException("type cannot be null"); final ReadDestination toBam = new ReadDestination.ToBAM(stingSAMWriter, header, READ_GROUP_ID); 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 7c75fca12..386723c6b 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.utils.haplotypeBAMWriter; +package org.broadinstitute.gatk.utils.haplotypeBAMWriter; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileWriter; import htsjdk.samtools.SAMReadGroupRecord; -import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.ArrayList; import java.util.LinkedList; @@ -94,7 +94,7 @@ public abstract class ReadDestination { /** * Create a ReadDestination that writes to a BAM file */ - public ToBAM(final StingSAMFileWriter stingSAMWriter, final SAMFileHeader header, final String readGroupID) { + public ToBAM(final GATKSAMFileWriter stingSAMWriter, final SAMFileHeader header, final String readGroupID) { super(header, readGroupID); if ( stingSAMWriter == null ) throw new IllegalArgumentException("writer cannot be null"); 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 e818c9899..598e103f3 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 @@ -44,15 +44,15 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.utils.QualityUtils; import java.util.Arrays; -import static org.broadinstitute.sting.utils.pairhmm.PairHMMModel.*; +import static org.broadinstitute.gatk.utils.pairhmm.PairHMMModel.*; /** * Created with IntelliJ IDEA. 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 fc615b608..80be36f02 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import java.io.File; 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 ff26f1095..89c94a3e2 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 @@ -44,18 +44,18 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.utils.QualityUtils; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; -import org.broadinstitute.sting.utils.exceptions.UserException; -import static org.broadinstitute.sting.utils.pairhmm.PairHMMModel.*; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import static org.broadinstitute.gatk.utils.pairhmm.PairHMMModel.*; import java.util.List; import java.util.Map; 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 f6c746b32..93a45b394 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 @@ -44,17 +44,17 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Arrays; import java.util.HashMap; import java.util.Map; -import static org.broadinstitute.sting.utils.pairhmm.PairHMMModel.*; +import static org.broadinstitute.gatk.utils.pairhmm.PairHMMModel.*; /** * Fast partial PairHMM backed on the standard Logless PairHMM 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 152274947..0cf01e07a 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /** * API for the fast (partial) HMM calculation engine. 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 e6b9f0469..0106bce66 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; -import org.broadinstitute.sting.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; import java.util.HashMap; 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 2408f34c1..8cf636a8c 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.utils.QualityUtils; -import static org.broadinstitute.sting.utils.pairhmm.PairHMMModel.*; +import static org.broadinstitute.gatk.utils.pairhmm.PairHMMModel.*; /** 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 e7ce367ce..df78c89f6 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 @@ -44,15 +44,15 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.utils.QualityUtils; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import java.util.List; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRReadTransformer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRReadTransformer.java index 3f8fd0e88..0d5da3227 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRReadTransformer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRReadTransformer.java @@ -44,13 +44,13 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.WalkerManager; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.WalkerManager; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /** * A ReadTransformer that applies BQSR on the fly to reads diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BaseRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BaseRecalibration.java index cb1de0fb6..275223dee 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BaseRecalibration.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BaseRecalibration.java @@ -44,17 +44,17 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; import com.google.java.contract.Ensures; import htsjdk.samtools.SAMTag; import htsjdk.samtools.SAMUtils; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.io.File; import java.util.ArrayList; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizer.java index 85379b900..2689fea36 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizer.java @@ -44,17 +44,17 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.gatk.report.GATKReportTable; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.PrintStream; import java.util.*; @@ -139,9 +139,9 @@ public class QualQuantizer { this.minInterestingQual = minInterestingQual; // some sanity checking - if ( Collections.min(nObservationsPerQual) < 0 ) throw new ReviewedStingException("Quality score histogram has negative values at: " + Utils.join(", ", nObservationsPerQual)); - if ( nLevels < 0 ) throw new ReviewedStingException("nLevels must be >= 0"); - if ( minInterestingQual < 0 ) throw new ReviewedStingException("minInterestingQual must be >= 0"); + if ( Collections.min(nObservationsPerQual) < 0 ) throw new ReviewedGATKException("Quality score histogram has negative values at: " + Utils.join(", ", nObservationsPerQual)); + if ( nLevels < 0 ) throw new ReviewedGATKException("nLevels must be >= 0"); + if ( minInterestingQual < 0 ) throw new ReviewedGATKException("minInterestingQual must be >= 0"); // actually run the quantizer this.quantizedIntervals = quantize(); @@ -272,7 +272,7 @@ public class QualQuantizer { final QualInterval right = this.compareTo(toMerge) < 0 ? toMerge : this; if ( left.qEnd + 1 != right.qStart ) - throw new ReviewedStingException("Attempting to merge non-contiguous intervals: left = " + left + " right = " + right); + throw new ReviewedGATKException("Attempting to merge non-contiguous intervals: left = " + left + " right = " + right); final long nCombinedObs = left.nObservations + right.nObservations; final long nCombinedErr = left.nErrors + right.nErrors; @@ -415,7 +415,7 @@ public class QualQuantizer { } if ( Collections.min(map) == Byte.MIN_VALUE ) - throw new ReviewedStingException("quantized quality score map contains an un-initialized value"); + throw new ReviewedGATKException("quantized quality score map contains an un-initialized value"); return map; } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QuantizationInfo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QuantizationInfo.java index 464390b99..6be4e44cc 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QuantizationInfo.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QuantizationInfo.java @@ -44,12 +44,12 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.gatk.report.GATKReportTable; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.collections.NestedIntegerArray; +import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; import java.util.Arrays; import java.util.List; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariates.java index 6efed2689..f657dcc8b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariates.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariates.java @@ -44,10 +44,10 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.LRUCache; +import org.broadinstitute.gatk.utils.LRUCache; /** * The object temporarily held by a read that describes all of it's covariates. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatum.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatum.java index 542f07679..7b76d7d5f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatum.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatum.java @@ -44,7 +44,7 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; /* * Copyright (c) 2009 The Broad Institute @@ -76,8 +76,8 @@ import com.google.java.contract.Invariant; import com.google.java.contract.Requires; import htsjdk.samtools.SAMUtils; import org.apache.commons.math.optimization.fitting.GaussianFunction; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; /** diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumNode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumNode.java index 637d9fb2d..93c647779 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumNode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumNode.java @@ -44,15 +44,15 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.commons.math.MathException; import org.apache.commons.math.stat.inference.ChiSquareTestImpl; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.Collection; import java.util.HashSet; @@ -320,11 +320,11 @@ public class RecalDatumNode { // make sure things are reasonable and fail early if not if (Double.isInfinite(penalty) || Double.isNaN(penalty)) - throw new ReviewedStingException("chi2 value is " + chi2PValue + " at " + getRecalDatum()); + throw new ReviewedGATKException("chi2 value is " + chi2PValue + " at " + getRecalDatum()); return penalty; } catch ( MathException e ) { - throw new ReviewedStingException("Failed in calculating chi2 value", e); + throw new ReviewedGATKException("Failed in calculating chi2 value", e); } } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalUtils.java index b4849ca33..ca538322c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalUtils.java @@ -44,29 +44,29 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.gatk.report.GATKReportTable; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.classloader.JVMUtils; -import org.broadinstitute.sting.utils.recalibration.covariates.*; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.R.RScriptExecutor; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.collections.NestedIntegerArray; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.io.Resource; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.classloader.JVMUtils; +import org.broadinstitute.gatk.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.R.RScriptExecutor; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.classloader.PluginManager; +import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.io.Resource; +import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.io.*; import java.util.*; @@ -181,7 +181,7 @@ public class RecalUtils { private static ArrayList addRequiredCovariatesToList(List> classes) { ArrayList dest = new ArrayList(classes.size()); if (classes.size() != 2) - throw new ReviewedStingException("The number of required covariates has changed, this is a hard change in the code and needs to be inspected"); + throw new ReviewedGATKException("The number of required covariates has changed, this is a hard change in the code and needs to be inspected"); dest.add(new ReadGroupCovariate()); // enforce the order with RG first and QS next. dest.add(new QualityScoreCovariate()); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReport.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReport.java index 0ff5e5de5..cbd50b649 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReport.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReport.java @@ -44,16 +44,16 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.gatk.report.GATKReportTable; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.collections.NestedIntegerArray; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; import java.io.*; import java.util.*; @@ -260,7 +260,7 @@ public class RecalibrationReport { else if ( o instanceof Long ) return (Long)o; else - throw new ReviewedStingException("Object " + o + " is expected to be either a double, long or integer but it's not either: " + o.getClass()); + throw new ReviewedGATKException("Object " + o + " is expected to be either a double, long or integer but it's not either: " + o.getClass()); } private long asLong(final Object o) { @@ -271,7 +271,7 @@ public class RecalibrationReport { else if ( o instanceof Double ) return ((Double)o).longValue(); else - throw new ReviewedStingException("Object " + o + " is expected to be a long but it's not: " + o.getClass()); + throw new ReviewedGATKException("Object " + o + " is expected to be a long but it's not: " + o.getClass()); } private RecalDatum getRecalDatum(final GATKReportTable reportTable, final int row, final boolean hasEstimatedQReportedColumn) { diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTables.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTables.java index 7d1a9f956..7242fa6fe 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTables.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTables.java @@ -44,12 +44,12 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; import com.google.java.contract.Ensures; -import org.broadinstitute.sting.utils.collections.LoggingNestedIntegerArray; -import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; -import org.broadinstitute.sting.utils.collections.NestedIntegerArray; +import org.broadinstitute.gatk.utils.collections.LoggingNestedIntegerArray; +import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; import java.io.PrintStream; import java.util.ArrayList; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ContextCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ContextCovariate.java index 79ffa50a3..da8486ae1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ContextCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ContextCovariate.java @@ -44,17 +44,17 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; -import org.broadinstitute.sting.utils.clipping.ReadClipper; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.recalibration.ReadCovariates; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.clipping.ClippingRepresentation; +import org.broadinstitute.gatk.utils.clipping.ReadClipper; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.ArrayList; @@ -267,7 +267,7 @@ public class ContextCovariate implements StandardCovariate { */ public static String contextFromKey(final int key) { if (key < 0) - throw new ReviewedStingException("dna conversion cannot handle negative numbers. Possible overflow?"); + throw new ReviewedGATKException("dna conversion cannot handle negative numbers. Possible overflow?"); final int length = key & LENGTH_MASK; // the first bits represent the length (in bp) of the context int mask = 48; // use the mask to pull out bases diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/Covariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/Covariate.java index b884f5445..59333242c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/Covariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/Covariate.java @@ -44,11 +44,11 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; -import org.broadinstitute.sting.utils.recalibration.ReadCovariates; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /* * Copyright (c) 2009 The Broad Institute diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/CycleCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/CycleCovariate.java index f585299f4..196883513 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/CycleCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/CycleCovariate.java @@ -44,14 +44,14 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; -import org.broadinstitute.sting.utils.recalibration.ReadCovariates; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.NGSPlatform; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.NGSPlatform; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.EnumSet; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ExperimentalCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ExperimentalCovariate.java index a16fdcaa1..88e0026b9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ExperimentalCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ExperimentalCovariate.java @@ -44,7 +44,7 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; /** * [Short one sentence description of this walker] diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/QualityScoreCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/QualityScoreCovariate.java index 46284b27e..326cb23ad 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/QualityScoreCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/QualityScoreCovariate.java @@ -44,12 +44,12 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; -import org.broadinstitute.sting.utils.recalibration.ReadCovariates; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /* * Copyright (c) 2009 The Broad Institute diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ReadGroupCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ReadGroupCovariate.java index 664c1786e..dda0a6caa 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ReadGroupCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ReadGroupCovariate.java @@ -44,12 +44,12 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.recalibration.ReadCovariates; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.HashMap; import java.util.Map; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatCovariate.java index 943e87461..1e8a5fbdf 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatCovariate.java @@ -44,16 +44,16 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.recalibration.ReadCovariates; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.collections.Pair; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatLengthCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatLengthCovariate.java index 48f3d4b60..7183fa6ec 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatLengthCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatLengthCovariate.java @@ -44,7 +44,7 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java index c4fdaad8b..3030d51b4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java @@ -44,7 +44,7 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitCovariate.java index ef0d3fc62..5e6fcfd1b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitCovariate.java @@ -44,7 +44,7 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; /** * Created with IntelliJ IDEA. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RequiredCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RequiredCovariate.java index 4267c1ffd..b52bfc15a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RequiredCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RequiredCovariate.java @@ -44,7 +44,7 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; /** * [Short one sentence description of this walker] diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/StandardCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/StandardCovariate.java index 045b21527..2f0c46dab 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/StandardCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/StandardCovariate.java @@ -44,7 +44,7 @@ * 7.7 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.sting.utils.recalibration.covariates; +package org.broadinstitute.gatk.utils.recalibration.covariates; /** * [Short one sentence description of this walker] 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 e42f109b2..61d72b3ce 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.utils.sam; +package org.broadinstitute.gatk.utils.sam; import java.util.Arrays; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngineUnitTest.java index cb9a9aada..b05f1309b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngineUnitTest.java @@ -44,12 +44,16 @@ * 7.7 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.sting.gatk.walkers.diffengine; +package org.broadinstitute.gatk.engine.walkers.diffengine; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffElement; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffEngine; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffNode; +import org.broadinstitute.gatk.engine.walkers.diffengine.Difference; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNodeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNodeUnitTest.java index 2ecc1f6cf..6acfb3ed4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNodeUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNodeUnitTest.java @@ -44,13 +44,16 @@ * 7.7 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.sting.gatk.walkers.diffengine; +package org.broadinstitute.gatk.engine.walkers.diffengine; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffElement; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffNode; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffValue; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjectsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjectsIntegrationTest.java index 5a308928d..7cc7a28a0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjectsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjectsIntegrationTest.java @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.diffengine; +package org.broadinstitute.gatk.engine.walkers.diffengine; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReaderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReaderUnitTest.java index 49f41d613..40b17db62 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReaderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReaderUnitTest.java @@ -44,13 +44,17 @@ * 7.7 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.sting.gatk.walkers.diffengine; +package org.broadinstitute.gatk.engine.walkers.diffengine; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffElement; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffEngine; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffNode; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffableReader; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DifferenceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DifferenceUnitTest.java index 4f08a057b..48073c561 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DifferenceUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DifferenceUnitTest.java @@ -44,23 +44,20 @@ * 7.7 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.sting.gatk.walkers.diffengine; +package org.broadinstitute.gatk.engine.walkers.diffengine; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffElement; +import org.broadinstitute.gatk.engine.walkers.diffengine.DiffNode; +import org.broadinstitute.gatk.engine.walkers.diffengine.Difference; import org.testng.Assert; -import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; - /** * Basic unit test for DifferableReaders in reduced reads */ 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 1e4d6fbf2..6f0029cb2 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers; +package org.broadinstitute.gatk.tools.walkers; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 775897223..73abacdda 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; import htsjdk.variant.variantcontext.*; import org.testng.Assert; 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 a02530c83..70c3a2b2b 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.DataProvider; 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 0ec1dd996..3656853d3 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.MannWhitneyU; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.MannWhitneyU; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; 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 2610f5008..50acc7e44 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; import org.testng.Assert; import org.testng.annotations.Test; -import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff.SnpEffEffect; +import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff.SnpEffEffect; public class SnpEffUnitTest { 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 562736f0a..aa52c1577 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; import org.testng.Assert; import org.testng.annotations.DataProvider; 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 60122047d..41631d62b 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; import htsjdk.tribble.readers.LineIterator; import htsjdk.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFCodec; import org.testng.Assert; 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 6bec5c6ec..d6ebad43d 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.annotator; +package org.broadinstitute.gatk.tools.walkers.annotator; import htsjdk.samtools.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.commandline.RodBinding; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; import htsjdk.variant.vcf.VCFConstants; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleIntegrationTest.java index 5601d66fb..fe9471591 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleIntegrationTest.java @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.beagle; +package org.broadinstitute.gatk.tools.walkers.beagle; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 95ce80848..77a941dd1 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 @@ -43,11 +43,11 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.bqsr; +package org.broadinstitute.gatk.tools.walkers.bqsr; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 7bfb2d86c..83f8faea7 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.bqsr; +package org.broadinstitute.gatk.tools.walkers.bqsr; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.gatk.report.GATKReportTable; -import org.broadinstitute.sting.utils.recalibration.RecalUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.recalibration.RecalUtils; import org.testng.Assert; import org.testng.annotations.Test; 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 05183a521..45a29e3e6 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.bqsr; +package org.broadinstitute.gatk.tools.walkers.bqsr; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 dce7f983e..d569dc13a 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.bqsr; +package org.broadinstitute.gatk.tools.walkers.bqsr; import htsjdk.samtools.SAMUtils; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.recalibration.EventType; -import org.broadinstitute.sting.utils.recalibration.ReadCovariates; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.recalibration.EventType; +import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.DataProvider; 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 27f140337..b54288ccb 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.diagnostics; +package org.broadinstitute.gatk.tools.walkers.diagnostics; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 84020e2d0..7fe58f23d 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.diagnostics; +package org.broadinstitute.gatk.tools.walkers.diagnostics; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 ff784cea2..3b3de3b2d 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.diagnostics; +package org.broadinstitute.gatk.tools.walkers.diagnostics; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 0259e9685..f4878c8da 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 fe3010e02..3147c90c9 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets; +package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; import org.testng.Assert; import org.testng.annotations.BeforeClass; 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 7ab891bd0..ec60d3b81 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.gatk.walkers.diagnostics.missing; +package org.broadinstitute.gatk.tools.walkers.diagnostics.missing; import it.unimi.dsi.fastutil.objects.ObjectArrayList; import java.util.List; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.UnvalidatingGenomeLoc; import org.testng.Assert; import org.testng.annotations.Test; 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 8130fa07b..6786149cd 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.fasta; +package org.broadinstitute.gatk.tools.walkers.fasta; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.util.Arrays; 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 6a29ff255..acef290f0 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.filters; +package org.broadinstitute.gatk.tools.walkers.filters; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.util.Arrays; 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 4fcb7698a..c49b87092 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 @@ -44,24 +44,24 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMReadGroupRecord; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.*; 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 2846352ca..737e586ed 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.SAMUtils; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.Test; 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 7bd75353d..bf9b54be8 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.walkers.Walker; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.engine.walkers.Walker; import htsjdk.variant.variantcontext.Allele; import java.util.*; 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 a09a36291..67c7ae889 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 @@ -43,12 +43,12 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import junit.framework.Assert; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCallerArgumentCollection; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection; import org.testng.SkipException; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 205390c41..d17c12b30 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 @@ -44,17 +44,17 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypeLikelihoods; import htsjdk.variant.variantcontext.VariantContext; 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 8f71c35be..a898266e2 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; -import static org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperGeneralPloidyTestExecutor.LSV_ALLELES; +import static org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyperGeneralPloidyTestExecutor.LSV_ALLELES; /** * Created by IntelliJ IDEA. 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 e16ca154f..9f82df1df 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; -import static org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperGeneralPloidyTestExecutor.CEUTRIO_BAM; -import static org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperGeneralPloidyTestExecutor.NA12891_CALLS; +import static org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyperGeneralPloidyTestExecutor.CEUTRIO_BAM; +import static org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyperGeneralPloidyTestExecutor.NA12891_CALLS; public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTest { 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 53d32832b..c8bae9fe8 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import java.util.Arrays; 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 3aee7a5b8..54f262f55 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.io.File; 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 605d4a226..8a6529189 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.util.BlockCompressedInputStream; import htsjdk.tribble.readers.AsciiLineReader; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; 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 eecb2987e..756601ddd 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.ArrayList; 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 29b93e427..6326e00d3 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java index fc354d875..bdbc475a6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.Pair; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResultUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResultUnitTest.java index a79d48346..644df8ea6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResultUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResultUnitTest.java @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.Utils; import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcUnitTest.java index 8cd96e7eb..0bbc0ecfa 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcUnitTest.java @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import org.apache.commons.lang.ArrayUtils; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotypingEngine; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.Utils; import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeSuite; 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 1b2dfe6e7..f2658a4c5 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyGenotypeLikelihoods; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypeBuilder; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java index a3a70d91c..756b6dce3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.genotyper.afcalc; +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; 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 d8c3a3ebd..165bebacb 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.caliper.Param; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.pairhmm.ActiveRegionTestDataSet; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 329fc54d8..c8da244c8 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 @@ -43,19 +43,19 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.samtools.SAMFileHeader; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.SeqGraph; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.RandomDNA; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.pairhmm.ActiveRegionTestDataSet; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.SeqGraph; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.RandomDNA; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; 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 05de40cee..2930dd599 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Requires; import htsjdk.samtools.Cigar; 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 10f9a3803..3f3708e8b 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 @@ -43,9 +43,9 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 a98c4e03a..dc878a9d3 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 @@ -43,13 +43,13 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; -import org.broadinstitute.sting.utils.pairhmm.ActiveRegionTestDataSet; -import org.broadinstitute.sting.utils.pairhmm.FastLoglessPairHMM; -import org.broadinstitute.sting.utils.pairhmm.PairHMM; +import org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet; +import org.broadinstitute.gatk.utils.pairhmm.FastLoglessPairHMM; +import org.broadinstitute.gatk.utils.pairhmm.PairHMM; import java.util.Collections; import java.util.Random; @@ -62,7 +62,7 @@ import java.util.Random; * To change this template use File | Settings | File Templates. */ public class HCLikelihoodCalculationEnginesBenchmark extends SimpleBenchmark { -// ./private/shell/googleCaliperCommand.csh org.broadinstitute.sting.gatk.walkers.haplotypecaller.HCLikelihoodCalculationEnginesBenchmark --saveResults build/benchmark/HCLikelihoodCalculationEnginesBenchmark +// ./private/shell/googleCaliperCommand.csh org.broadinstitute.gatk.tools.walkers.haplotypecaller.HCLikelihoodCalculationEnginesBenchmark --saveResults build/benchmark/HCLikelihoodCalculationEnginesBenchmark // @Param({"10", "25"}) @Param({"10"}) 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 7598a0c96..48701d0ee 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 @@ -44,15 +44,15 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; -import static org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCallerIntegrationTest.NA12878_CHR20_BAM; -import static org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCallerIntegrationTest.REF; +import static org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerIntegrationTest.NA12878_CHR20_BAM; +import static org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerIntegrationTest.REF; public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends WalkerTest { 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 1b2a27ba1..ad1f0506f 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variant.GATKVCFIndexType; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 f3e48209d..4c2f1ec65 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; /** * Created by IntelliJ IDEA. @@ -53,16 +53,16 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; */ import htsjdk.samtools.reference.ReferenceSequenceFile; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.*; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeClass; 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 cc32d3daf..84fe08671 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.tribble.readers.LineIterator; import htsjdk.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFCodec; import org.testng.Assert; 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 27b429353..5c5109cf9 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.haplotypeBAMWriter.HaplotypeBAMWriter; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.haplotypeBAMWriter.HaplotypeBAMWriter; import org.testng.annotations.Test; import java.util.Arrays; 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 b801f05a9..e227861c9 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 9b08e8214..cd80f0a50 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; 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 116c987a6..400d51544 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 7742c6f58..a16a7c83d 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 @@ -44,23 +44,23 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; import htsjdk.samtools.SAMFileHeader; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingAssembler; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; 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 e9c7ae3d8..643fe59a5 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; /** * Created by IntelliJ IDEA. @@ -52,12 +52,12 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; * Date: 3/14/12 */ -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.pairhmm.PairHMM; -import org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate; -import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.pairhmm.PairHMM; +import org.broadinstitute.gatk.utils.recalibration.covariates.RepeatCovariate; +import org.broadinstitute.gatk.utils.recalibration.covariates.RepeatLengthCovariate; import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeSuite; 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 e201b24fc..c1a7319cf 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.Test; 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 80190e837..effa6aba0 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 @@ -44,19 +44,19 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.pairhmm.ActiveRegionTestDataSet; -import org.broadinstitute.sting.utils.pairhmm.FastLoglessPairHMM; -import org.broadinstitute.sting.utils.pairhmm.FlexibleHMM; -import org.broadinstitute.sting.utils.pairhmm.PairHMM; -import org.broadinstitute.sting.utils.sam.ClippedGATKSAMRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet; +import org.broadinstitute.gatk.utils.pairhmm.FastLoglessPairHMM; +import org.broadinstitute.gatk.utils.pairhmm.FlexibleHMM; +import org.broadinstitute.gatk.utils.pairhmm.PairHMM; +import org.broadinstitute.gatk.utils.sam.ClippedGATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.Reporter; 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 069d1882e..c807457e5 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 @@ -44,20 +44,20 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.samtools.SAMFileHeader; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.*; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeClass; 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 ea1d120b6..ddcfed884 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 44512824a..70fe08745 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; 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 859892e33..c8bf2791b 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; 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 da1474db1..6e2db6528 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 cae39d26a..7f1aa255c 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 bdc8ab36d..fa12faaa1 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.annotations.Test; import org.testng.Assert; 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 01a6b5dbb..cc288a0e1 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.collections.PrimitivePair; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.collections.PrimitivePair; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 e756737a2..52d514411 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 @@ -43,12 +43,12 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Kmer; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 643c21188..53d4cd5ba 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; import htsjdk.samtools.TextCigarCodec; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.CigarUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.CigarUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 a4c0464a5..ccea3da9b 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 c1d822eec..ab9574de1 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 876918816..e9e17559f 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; import htsjdk.samtools.Cigar; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; 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 aeb617b18..df1e058b5 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 @@ -43,9 +43,9 @@ * 7.6 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. * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.jgrapht.EdgeFactory; import org.testng.Assert; import org.testng.Reporter; 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 84b2ee449..b66f5461b 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 eab9dfc27..fc51f26ee 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 eb0432769..53b82667d 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.graphs; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.Pair; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 bbafba5de..1ac94d20d 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.readthreading; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; import htsjdk.samtools.TextCigarCodec; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.KBestHaplotype; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.KBestHaplotypeFinder; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.SeqGraph; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.KBestHaplotype; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.KBestHaplotypeFinder; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.SeqGraph; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 769026f2b..4e90c71cf 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.readthreading; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.*; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.Test; 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 c95f4002e..a54e919fa 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.readthreading; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Kmer; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.*; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 fe381513e..6429e7ff3 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.haplotypecaller.readthreading; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.Test; 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 842fa873e..d7174705f 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; 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 c5bfd4731..7c6367635 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.util.Arrays; 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 bc402cd02..1cf7ca39c 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.ArrayList; 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 22a6407c4..4776dff16 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 @@ -44,14 +44,14 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.SAMFileHeader; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; 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 56c1ffb66..b13e14fbd 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 @@ -44,17 +44,17 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.SAMFileHeader; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.UnvalidatingGenomeLoc; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.annotations.BeforeClass; 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 58dd9be13..ef19a7c4a 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; 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 d294562ec..ba74666f5 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 cbcce3343..f28b9c2ad 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.indels; +package org.broadinstitute.gatk.tools.walkers.indels; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.ArrayList; 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 41f473cfb..26d661721 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; import htsjdk.tribble.readers.LineIterator; import htsjdk.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import htsjdk.variant.vcf.VCFCodec; import org.testng.Assert; import org.testng.annotations.Test; 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 8c8817fe6..acb2c6e53 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.phasing; +package org.broadinstitute.gatk.tools.walkers.phasing; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 62f6bcfbd..c1a6a190c 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.rnaseq; +package org.broadinstitute.gatk.tools.walkers.rnaseq; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; 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 87af68fc4..19deb4f19 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.rnaseq; +package org.broadinstitute.gatk.tools.walkers.rnaseq; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 9e70df34a..57efd535c 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.rnaseq; +package org.broadinstitute.gatk.tools.walkers.rnaseq; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.clipping.ReadClipperTestUtils; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.clipping.ReadClipperTestUtils; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; 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 2d0550dfb..7d719ad5b 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.simulatereads; +package org.broadinstitute.gatk.tools.walkers.simulatereads; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmpliconsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmpliconsIntegrationTest.java index d5e264e3f..2e9ddd18e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmpliconsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmpliconsIntegrationTest.java @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.validation; +package org.broadinstitute.gatk.tools.walkers.validation; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 a3d9121d0..f6ee4a51d 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.validation; +package org.broadinstitute.gatk.tools.walkers.validation; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 9b5290dee..6f0183372 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.varianteval; +package org.broadinstitute.gatk.tools.walkers.varianteval; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 e759b44f8..03184110c 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 @@ -44,20 +44,20 @@ * 7.7 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.sting.gatk.walkers.varianteval; +package org.broadinstitute.gatk.tools.walkers.varianteval; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; -import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier; -import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator; +import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.VariantStratifier; +import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.StratificationManager; +import org.broadinstitute.gatk.tools.walkers.varianteval.util.EvaluationContext; +import org.broadinstitute.gatk.utils.Utils; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; 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 aabcd374d..4aaab5101 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 @@ -44,15 +44,15 @@ * 7.7 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.sting.gatk.walkers.varianteval.stratifications.manager; +package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.Pair; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; 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 81b793f4f..f64ecb348 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import junit.framework.Assert; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import htsjdk.variant.vcf.VCFConstants; import org.testng.annotations.Test; 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 9a1422608..f07961265 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import org.apache.commons.lang.ArrayUtils; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.junit.Assert; import org.testng.annotations.Test; 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 c2f61064a..329430047 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.text.XReadLines; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.annotations.Test; import org.testng.Assert; @@ -89,7 +89,7 @@ public final class VariantGaussianMixtureModelUnitTest extends BaseTest { } } } catch (FileNotFoundException e) { - throw new StingException("foo", e); + throw new GATKException("foo", e); } return vd; 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 7d19eafb7..35c482c48 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantrecalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFCodec; 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 d7cd4e88f..499c09c73 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 cbbf612c4..6da657655 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.Test; 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 91952ec43..baa5f827e 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.io.File; 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 f2771e56b..094282cac 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; import htsjdk.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.gatk.utils.SampleUtils; import htsjdk.variant.vcf.VCFCodec; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; 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 old mode 100755 new mode 100644 index 51b65425b..d49e39fba --- 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFCodec; import htsjdk.variant.vcf.VCFHeader; 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 0348657c9..706f8014f 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 546b2078c..8c214ce5f 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 e2f17a65f..dd3f878fd 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 f62b9c290..9cbeccfba 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 @@ -44,21 +44,21 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMReadGroupRecord; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; 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 c17c9ca55..78bbaa769 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.util.Arrays; 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 bb02a7990..1d77e2b1f 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; /** * Created by IntelliJ IDEA. @@ -52,9 +52,9 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; * Date: 12/8/13 */ -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFConstants; import org.testng.Assert; 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 2fe50ff68..a928e6037 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.util.Arrays; 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 703c044d4..0be8499db 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.util.Arrays; 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 68eb1cc41..646313f5c 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 c34ed38a2..4a6b26381 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.io.File; 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 13ba2f58a..1fc57ea4f 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.util.Arrays; 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 7b1b9b7d2..0c22a9ef7 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; 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 164645171..4c1a1322a 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import org.testng.annotations.DataProvider; 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 3032bd4e2..2b8bb1d5f 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.util.*; 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 17523a5be..b4917aaf4 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.gatk.walkers.variantutils; +package org.broadinstitute.gatk.tools.walkers.variantutils; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.util.List; 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 41ac6d6ca..784820418 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 @@ -44,13 +44,13 @@ * 7.7 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.sting.utils; +package org.broadinstitute.gatk.utils; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; 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 426462ed2..cdcd63427 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 @@ -43,7 +43,7 @@ * 7.6 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. * 7.7 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.sting.utils; +package org.broadinstitute.gatk.utils; import java.util.Random; 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 ae9ead827..64c023496 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 @@ -43,9 +43,9 @@ * 7.6 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. * 7.7 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.sting.utils.collections; +package org.broadinstitute.gatk.utils.collections; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 5987dcdf3..173897b0b 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 @@ -44,10 +44,10 @@ * 7.7 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.sting.utils.genotyper; +package org.broadinstitute.gatk.utils.genotyper; import org.testng.Assert; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.annotations.Test; 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 f7ce58b4c..bcaa8e29b 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.utils.genotyper; +package org.broadinstitute.gatk.utils.genotyper; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.annotations.Test; 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 2ae037d90..9eeeaf866 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 @@ -44,26 +44,26 @@ * 7.7 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.sting.utils.genotyper; +package org.broadinstitute.gatk.utils.genotyper; import htsjdk.samtools.*; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import htsjdk.variant.variantcontext.Allele; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.Utils; import java.util.Map; import java.util.List; import org.testng.Assert; import org.testng.annotations.Test; import htsjdk.samtools.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import java.io.File; import java.io.FileNotFoundException; import java.util.*; 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 690ad8570..3228e87d6 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 @@ -44,12 +44,12 @@ * 7.7 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.sting.utils.gvcf; +package org.broadinstitute.gatk.utils.gvcf; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.ReferenceConfidenceModel; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceModel; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.vcf.VCFConstants; 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 d26ce77c1..36d3aa09e 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.utils.gvcf; +package org.broadinstitute.gatk.utils.gvcf; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparatorUnitTest.java index 26384c190..2c5701c7c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparatorUnitTest.java @@ -44,10 +44,10 @@ * 7.7 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.sting.utils.haplotype; +package org.broadinstitute.gatk.utils.haplotype; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculatorUnitTest.java index 3c3452bbf..d18a12b36 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculatorUnitTest.java @@ -44,9 +44,9 @@ * 7.7 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.sting.utils.haplotype; +package org.broadinstitute.gatk.utils.haplotype; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparatorUnitTest.java index 64a62bc02..55aa2027f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparatorUnitTest.java @@ -44,10 +44,10 @@ * 7.7 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.sting.utils.haplotype; +package org.broadinstitute.gatk.utils.haplotype; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java index 6d8fdd6e9..ddc46d7cd 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java @@ -44,10 +44,10 @@ * 7.7 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.sting.utils.haplotype; +package org.broadinstitute.gatk.utils.haplotype; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/LDMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/LDMergerUnitTest.java index 120e2242b..e09af1ec1 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/LDMergerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/LDMergerUnitTest.java @@ -44,12 +44,12 @@ * 7.7 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.sting.utils.haplotype; +package org.broadinstitute.gatk.utils.haplotype; import htsjdk.samtools.TextCigarCodec; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.*; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; 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 40d436667..52efb030c 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 @@ -44,16 +44,16 @@ * 7.7 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.sting.utils.haplotypeBAMWriter; +package org.broadinstitute.gatk.utils.haplotypeBAMWriter; import htsjdk.samtools.*; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java index 489eff0bc..8466115ca 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java @@ -44,9 +44,9 @@ * 7.7 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.sting.utils.nanoScheduler; +package org.broadinstitute.gatk.utils.nanoScheduler; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/ActiveRegionTestDataSet.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/ActiveRegionTestDataSet.java index 714d11b46..091d11fbe 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/ActiveRegionTestDataSet.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/ActiveRegionTestDataSet.java @@ -44,22 +44,22 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import org.apache.commons.math.distribution.ExponentialDistribution; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.AssemblyResult; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.AssemblyResultSet; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Civar; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResult; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResultSet; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.*; import java.util.regex.Matcher; 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 14ab552e5..46ffef319 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMMUnitTest.java index 18817c9de..bed81399b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMMUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMMUnitTest.java @@ -44,11 +44,11 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; -import org.broadinstitute.sting.gatk.walkers.haplotypecaller.ActiveRegionTestDataSetUnitTest; -import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.ActiveRegionTestDataSetUnitTest; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.Test; 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 151097aad..6f46ceb5c 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 @@ -44,7 +44,7 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; 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 8c54326db..5c68772a2 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 @@ -43,10 +43,10 @@ * 7.6 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. * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.QualityUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java index 69100bcdd..383ecf1e7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java @@ -43,9 +43,9 @@ * 7.6 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. * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.io.File; 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 9160e2f66..befdf2bdc 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 @@ -44,15 +44,15 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.TextCigarCodec; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; import java.util.*; 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 9cb4583ff..5439d5172 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 @@ -44,11 +44,11 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; import htsjdk.samtools.SAMUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.text.XReadLines; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.text.XReadLines; import java.io.*; import java.util.LinkedHashMap; 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 4a224e0be..beb552d2e 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 @@ -44,17 +44,17 @@ * 7.7 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.sting.utils.pairhmm; +package org.broadinstitute.gatk.utils.pairhmm; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ContextCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ContextCovariateUnitTest.java index 7e2581c51..3e90639d6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ContextCovariateUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ContextCovariateUnitTest.java @@ -44,15 +44,15 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.recalibration.covariates.ContextCovariate; -import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; -import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; -import org.broadinstitute.sting.utils.clipping.ReadClipper; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.recalibration.covariates.ContextCovariate; +import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.utils.clipping.ClippingRepresentation; +import org.broadinstitute.gatk.utils.clipping.ReadClipper; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/CycleCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/CycleCovariateUnitTest.java index 4f8a70cc9..82807f713 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/CycleCovariateUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/CycleCovariateUnitTest.java @@ -44,14 +44,14 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.recalibration.covariates.CycleCovariate; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.recalibration.covariates.CycleCovariate; +import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizerUnitTest.java index 696cf846f..be427730b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizerUnitTest.java @@ -44,15 +44,15 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariatesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariatesUnitTest.java index eea8aa8f3..19766a361 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariatesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariatesUnitTest.java @@ -44,14 +44,14 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.recalibration.covariates.*; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadGroupCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadGroupCovariateUnitTest.java index a8366ce5c..fb14aee09 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadGroupCovariateUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadGroupCovariateUnitTest.java @@ -44,13 +44,13 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.recalibration.covariates.ReadGroupCovariate; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.recalibration.covariates.ReadGroupCovariate; +import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumUnitTest.java index 5b7b95be9..1e7c582f1 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumUnitTest.java @@ -44,15 +44,15 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalUtilsUnitTest.java index eae34c2fb..4c5d8b655 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalUtilsUnitTest.java @@ -44,11 +44,11 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.collections.NestedIntegerArray; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReportUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReportUnitTest.java index d3c3ffe97..f9c04d815 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReportUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReportUnitTest.java @@ -44,15 +44,15 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.recalibration.covariates.*; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.collections.NestedIntegerArray; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; +import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTablesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTablesUnitTest.java index 0a88f27fe..9acb52040 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTablesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTablesUnitTest.java @@ -44,11 +44,11 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.collections.NestedIntegerArray; -import org.broadinstitute.sting.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; +import org.broadinstitute.gatk.utils.recalibration.covariates.*; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTestUtils.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTestUtils.java index b465e37eb..fb346a28f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTestUtils.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTestUtils.java @@ -44,10 +44,10 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.recalibration.covariates.*; /** * Created with IntelliJ IDEA. diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RepeatCovariatesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RepeatCovariatesUnitTest.java index 74cb2a1eb..8c7348593 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RepeatCovariatesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RepeatCovariatesUnitTest.java @@ -44,16 +44,16 @@ * 7.7 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.sting.utils.recalibration; +package org.broadinstitute.gatk.utils.recalibration; import com.google.java.contract.Requires; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.recalibration.covariates.*; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.collections.Pair; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java index 43c929bc9..ec3b464cb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java @@ -44,12 +44,12 @@ * 7.7 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.sting.utils.smithwaterman; +package org.broadinstitute.gatk.utils.smithwaterman; import htsjdk.samtools.TextCigarCodec; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; 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 c8fc458e8..ee3d3a60b 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 @@ -44,9 +44,9 @@ * 7.7 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.sting.utils.smithwaterman; +package org.broadinstitute.gatk.utils.smithwaterman; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/pom.xml b/protected/pom.xml index 43c74d647..351bdedd7 100644 --- a/protected/pom.xml +++ b/protected/pom.xml @@ -3,22 +3,40 @@ 4.0.0 - org.broadinstitute.sting - sting-root + org.broadinstitute.gatk + gatk-root 3.2-SNAPSHOT - ../public/sting-root + ../public/gatk-root - sting-protected + gatk-aggregator-protected pom - Sting Protected + GATK Aggregator Protected - gatk-protected + gatk-tools-protected + gatk-package-distribution + - ${project.basedir}/.. + ${project.basedir}/.. + + + + queue + + + !disable.queue + + + + gatk-queue-extensions-distribution + gatk-queue-package-distribution + + + + diff --git a/public/VectorPairHMM/pom.xml b/public/VectorPairHMM/pom.xml index 2b69e5173..5be5a939f 100644 --- a/public/VectorPairHMM/pom.xml +++ b/public/VectorPairHMM/pom.xml @@ -3,26 +3,26 @@ 4.0.0 - org.broadinstitute.sting - sting-root + org.broadinstitute.gatk + gatk-root 3.2-SNAPSHOT - ../../public/sting-root + ../../public/gatk-root VectorPairHMM pom Vectorized PairHMM native libraries - Builds a GNU/Linux x86_64 library of VectorPairHMM using icc (Intel C++ compiler). During install, copies it into sting-utils. Neither tested nor expected to work on any other platform. + Builds a GNU/Linux x86_64 library of VectorPairHMM using icc (Intel C++ compiler). During install, copies it into gatk-utils. Neither tested nor expected to work on any other platform. UTF-8 ${sourceEncoding} ${sourceEncoding} - ${project.basedir}/../.. - ${sting.basedir}/public/sting-utils - - ${sting-utils.basedir}/src/main/resources/org/broadinstitute/sting/utils/pairhmm + ${project.basedir}/../.. + ${gatk.basedir}/public/gatk-utils + + ${gatk-utils.basedir}/src/main/resources/org/broadinstitute/gatk/utils/pairhmm @@ -76,7 +76,7 @@ - + org.apache.maven.plugins maven-resources-plugin @@ -102,7 +102,7 @@ - + com.google.code.sortpom maven-sortpom-plugin diff --git a/public/VectorPairHMM/src/main/c++/Sandbox.java b/public/VectorPairHMM/src/main/c++/Sandbox.java index 698c1b48c..605c5f5e8 100644 --- a/public/VectorPairHMM/src/main/c++/Sandbox.java +++ b/public/VectorPairHMM/src/main/c++/Sandbox.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.vectorpairhmm; +package org.broadinstitute.gatk.utils.vectorpairhmm; import java.util.List; import java.util.LinkedList; diff --git a/public/c/bwa/Makefile b/public/c/bwa/Makefile index 6399a0e6d..bf171cc78 100644 --- a/public/c/bwa/Makefile +++ b/public/c/bwa/Makefile @@ -2,7 +2,7 @@ CXX=g++ CXXFLAGS=-g -Wall -O2 -m64 -fPIC .cpp.o: - $(CXX) -c $(CXXFLAGS) -I$(BWA_HOME) -I$(JAVA_INCLUDE) $< -o $@ + $(CXX) -c $(CXXFLAGS) -I$(BWA_HOME) -I$(JAVA_INCLUDE) -I$(JAVA_PLATFORM_INCLUDE) $< -o $@ all: init lib @@ -10,11 +10,12 @@ init: @echo Please make sure the following platforms are set correctly on your machine. @echo BWA_HOME=$(BWA_HOME) @echo JAVA_INCLUDE=$(JAVA_INCLUDE) + @echo JAVA_PLATFORM_INCLUDE=$(JAVA_PLATFORM_INCLUDE) @echo TARGET_LIB=$(TARGET_LIB) @echo EXTRA_LIBS=$(EXTRA_LIBS) @echo LIBTOOL_COMMAND=$(LIBTOOL_COMMAND) -lib: org_broadinstitute_sting_alignment_bwa_c_BWACAligner.o bwa_gateway.o +lib: org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.o bwa_gateway.o $(LIBTOOL_COMMAND) $? -o $(TARGET_LIB) -L$(BWA_HOME) -lbwacore $(EXTRA_LIBS) clean: diff --git a/public/c/bwa/README.md b/public/c/bwa/README.md new file mode 100644 index 000000000..ba2d9e14d --- /dev/null +++ b/public/c/bwa/README.md @@ -0,0 +1,68 @@ +BWA C Aligner JNI Library +========================= + + +Basic Instructions +------------------ + +- Download BWA svn revision 47 +- Run autoconf and build bwa to create libbwacore.a +- Build mac or linux specific libbwa +- Update the libary path to point to the directory with libbwa + + +Obtaining compatible libbwacore +------------------------------- + +libbwa only works with a very specify range of versions from bwa's svn archive. r25-r47 are known to compile a +libbwacore.a compatible with building libbwa.so or libbwa.dylib. + +From the bwa directory, download bwa revision 47 from svn by running the command: + + svn co http://svn.code.sf.net/p/bio-bwa/code/trunk/bwa@47 bwasvn47 + + +Compiling libbwacore.a +---------------------- + +Once bwa has been downloaded from svn to the directory bwasvn47, using autoconf and make, one can compile libbwacore.a. + +- Install autoconf on Mac using MacPorts + `port install autoconf` + +- Or add autoconf on Linux via the dotkit + `reuse .autoconf-2.69` + +- Change directory to bwasvn47 + `cd bwasvn47` + +- Change permissions to make autogen.sh script executable + `chmod +x autogen.sh` + +- Run configure + `./configure` + +- Build + `make` + +- Return to the bwa directory + `cd ..` + + +Compiling libbwa.so / libbwa.dylib +---------------------------------- + +After successfully compiling libbwacore.a from the bwa svn source, the GATK specific libbwa.so / libbwa.dylib may be +compiled using libbwacore. There are two shell scripts that include libbwacore.a by using paths pointing to bwasvn47. + +- On Mac run `./build_mac.sh` +- On Linux run `./build_linux.sh` + + +Running the GATK with libbwa.so / libbwa.dylib +---------------------------------------------- + +The GATK loads libbwa.so or libbwa.dylib from a directory specified appended to the java.library.path. There are two +ways to specify this directory containing libbwa. Either add the directory to the LD_LIBRARY_PATH environment variable +`export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:`, or set java.library.path java variable on the command line +`-Djava.library.path=`. diff --git a/public/c/bwa/build_linux.sh b/public/c/bwa/build_linux.sh index 8683bb377..e20377992 100755 --- a/public/c/bwa/build_linux.sh +++ b/public/c/bwa/build_linux.sh @@ -1,6 +1,7 @@ #!/bin/sh -export BWA_HOME="/humgen/gsa-scr1/hanna/src/bio-bwa/bwa" -export JAVA_INCLUDE="/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/include -I/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/include/linux" +export BWA_HOME="${PWD}/bwasvn47" +export JAVA_INCLUDE="${JAVA_HOME}/include" +export JAVA_PLATFORM_INCLUDE="${JAVA_HOME}/include/linux" export TARGET_LIB="libbwa.so" export EXTRA_LIBS="-lc -lz -lstdc++ -lpthread" export LIBTOOL_COMMAND="g++ -shared -Wl,-soname,libbwa.so" diff --git a/public/c/bwa/build_mac.sh b/public/c/bwa/build_mac.sh old mode 100644 new mode 100755 index bfed900bb..6879e1442 --- a/public/c/bwa/build_mac.sh +++ b/public/c/bwa/build_mac.sh @@ -1,7 +1,8 @@ #!/bin/sh -export BWA_HOME="/Users/mhanna/src/bwa" -export JAVA_INCLUDE="/System/Library/Frameworks/JavaVM.framework/Headers" +export BWA_HOME="${PWD}/bwasvn47" +export JAVA_INCLUDE="${JAVA_HOME}/include" +export JAVA_PLATFORM_INCLUDE="${JAVA_HOME}/include/darwin" export TARGET_LIB="libbwa.dylib" -export EXTRA_LIBS="-lc -lz -lsupc++" +export EXTRA_LIBS="-lc -lz -lstdc++" export LIBTOOL_COMMAND="libtool -dynamic" make diff --git a/public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.cpp b/public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.cpp index 90d70d4a1..a01e2d8cd 100644 --- a/public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.cpp +++ b/public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.cpp @@ -6,7 +6,7 @@ #include "bwt.h" #include "bwtaln.h" #include "bwa_gateway.h" -#include "org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h" +#include "org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.h" typedef void (BWA::*boolean_setter)(); typedef void (BWA::*int_setter)(int value); @@ -19,7 +19,7 @@ static void set_int_configuration_param(JNIEnv* env, jobject configuration, cons static void set_float_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, float_setter setter); static void throw_config_value_exception(JNIEnv* env, const char* field_name, const char* message); -JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_create(JNIEnv* env, jobject instance, jobject bwtFiles, jobject configuration) +JNIEXPORT jlong JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_create(JNIEnv* env, jobject instance, jobject bwtFiles, jobject configuration) { jstring java_ann = get_configuration_file(env,bwtFiles,"annFile"); if(java_ann == NULL) return 0L; @@ -59,7 +59,7 @@ JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligne reverse_bwt_filename, reverse_sa_filename); - Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_updateConfiguration(env,instance,(jlong)bwa,configuration); + Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_updateConfiguration(env,instance,(jlong)bwa,configuration); if(env->ExceptionCheck()) return 0L; env->ReleaseStringUTFChars(java_ann,ann_filename); @@ -80,13 +80,13 @@ JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligne return (jlong)bwa; } -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_destroy(JNIEnv* env, jobject instance, jlong java_bwa) +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_destroy(JNIEnv* env, jobject instance, jlong java_bwa) { BWA* bwa = (BWA*)java_bwa; delete bwa; } -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_updateConfiguration(JNIEnv *env, jobject instance, jlong java_bwa, jobject configuration) { +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_updateConfiguration(JNIEnv *env, jobject instance, jlong java_bwa, jobject configuration) { BWA* bwa = (BWA*)java_bwa; set_float_configuration_param(env, configuration, "maximumEditDistance", bwa, &BWA::set_max_edit_distance); if(env->ExceptionCheck()) return; @@ -108,7 +108,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner if(env->ExceptionCheck()) return; } -JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getPaths(JNIEnv *env, jobject instance, jlong java_bwa, jbyteArray java_bases) +JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_getPaths(JNIEnv *env, jobject instance, jlong java_bwa, jbyteArray java_bases) { BWA* bwa = (BWA*)java_bwa; @@ -124,13 +124,13 @@ JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWA unsigned best_path_count, second_best_path_count; bwa->find_paths((const char*)read_bases,read_length,paths,num_paths,best_path_count,second_best_path_count); - jobjectArray java_paths = env->NewObjectArray(num_paths, env->FindClass("org/broadinstitute/sting/alignment/bwa/c/BWAPath"), NULL); + jobjectArray java_paths = env->NewObjectArray(num_paths, env->FindClass("org/broadinstitute/gatk/engine/alignment/bwa/c/BWAPath"), NULL); if(java_paths == NULL) return NULL; for(unsigned path_idx = 0; path_idx < (unsigned)num_paths; path_idx++) { bwt_aln1_t& path = *(paths + path_idx); - jclass java_path_class = env->FindClass("org/broadinstitute/sting/alignment/bwa/c/BWAPath"); + jclass java_path_class = env->FindClass("org/broadinstitute/gatk/engine/alignment/bwa/c/BWAPath"); if(java_path_class == NULL) return NULL; jmethodID java_path_constructor = env->GetMethodID(java_path_class, "", "(IIIZJJIII)V"); @@ -164,7 +164,7 @@ JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWA return env->ExceptionCheck() ? NULL : java_paths; } -JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_convertPathsToAlignments(JNIEnv *env, jobject instance, jlong java_bwa, jbyteArray java_bases, jobjectArray java_paths) +JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_convertPathsToAlignments(JNIEnv *env, jobject instance, jlong java_bwa, jbyteArray java_bases, jobjectArray java_paths) { BWA* bwa = (BWA*)java_bwa; @@ -235,7 +235,7 @@ JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWA unsigned num_alignments = 0; bwa->generate_alignments_from_paths((const char*)read_bases,read_length,paths,num_paths,best_count,second_best_count,alignments,num_alignments); - jobjectArray java_alignments = env->NewObjectArray(num_alignments, env->FindClass("org/broadinstitute/sting/alignment/Alignment"), NULL); + jobjectArray java_alignments = env->NewObjectArray(num_alignments, env->FindClass("org/broadinstitute/gatk/engine/alignment/Alignment"), NULL); if(java_alignments == NULL) return NULL; for(unsigned alignment_idx = 0; alignment_idx < (unsigned)num_alignments; alignment_idx++) { @@ -254,7 +254,7 @@ JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWA return env->ExceptionCheck() ? NULL : java_alignments; } -JNIEXPORT jobject JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getBestAlignment(JNIEnv *env, jobject instance, jlong java_bwa, jbyteArray java_bases) { +JNIEXPORT jobject JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_getBestAlignment(JNIEnv *env, jobject instance, jlong java_bwa, jbyteArray java_bases) { BWA* bwa = (BWA*)java_bwa; const jsize read_length = env->GetArrayLength(java_bases); @@ -305,7 +305,7 @@ static jobject convert_to_java_alignment(JNIEnv *env, const jbyte* read_bases, c } delete[] alignment.cigar; - jclass java_alignment_class = env->FindClass("org/broadinstitute/sting/alignment/Alignment"); + jclass java_alignment_class = env->FindClass("org/broadinstitute/gatk/engine/alignment/Alignment"); if(java_alignment_class == NULL) return NULL; jmethodID java_alignment_constructor = env->GetMethodID(java_alignment_class, "", "(IIZI[C[IILjava/lang/String;IIIII)V"); @@ -466,8 +466,8 @@ static void throw_config_value_exception(JNIEnv* env, const char* field_name, co { char* buffer = new char[strlen(field_name)+1+strlen(message)+1]; sprintf(buffer,"%s %s",field_name,message); - jclass sting_exception_class = env->FindClass("org/broadinstitute/sting/utils/StingException"); - if(sting_exception_class == NULL) return; - env->ThrowNew(sting_exception_class, buffer); + jclass gatk_exception_class = env->FindClass("org/broadinstitute/gatk/utils/exceptions/GATKException"); + if(gatk_exception_class == NULL) return; + env->ThrowNew(gatk_exception_class, buffer); delete[] buffer; } diff --git a/public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.h b/public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.h index 0c44e430a..6334472dc 100644 --- a/public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.h +++ b/public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.h @@ -1,58 +1,58 @@ /* DO NOT EDIT THIS FILE - it is machine generated */ #include -/* Header for class org_broadinstitute_sting_alignment_bwa_c_BWACAligner */ +/* Header for class org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner */ -#ifndef _Included_org_broadinstitute_sting_alignment_bwa_c_BWACAligner -#define _Included_org_broadinstitute_sting_alignment_bwa_c_BWACAligner +#ifndef _Included_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner +#define _Included_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner #ifdef __cplusplus extern "C" { #endif /* - * Class: org_broadinstitute_sting_alignment_bwa_c_BWACAligner + * Class: org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner * Method: create - * Signature: (Lorg/broadinstitute/sting/alignment/bwa/BWTFiles;Lorg/broadinstitute/sting/alignment/bwa/BWAConfiguration;)J + * Signature: (Lorg/broadinstitute/gatk/engine/alignment/bwa/BWTFiles;Lorg/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration;)J */ -JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_create +JNIEXPORT jlong JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_create (JNIEnv *, jobject, jobject, jobject); /* - * Class: org_broadinstitute_sting_alignment_bwa_c_BWACAligner + * Class: org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner * Method: updateConfiguration - * Signature: (JLorg/broadinstitute/sting/alignment/bwa/BWAConfiguration;)V + * Signature: (JLorg/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration;)V */ -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_updateConfiguration +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_updateConfiguration (JNIEnv *, jobject, jlong, jobject); /* - * Class: org_broadinstitute_sting_alignment_bwa_c_BWACAligner + * Class: org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner * Method: destroy * Signature: (J)V */ -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_destroy +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_destroy (JNIEnv *, jobject, jlong); /* - * Class: org_broadinstitute_sting_alignment_bwa_c_BWACAligner + * Class: org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner * Method: getPaths - * Signature: (J[B)[Lorg/broadinstitute/sting/alignment/bwa/c/BWAPath; + * Signature: (J[B)[Lorg/broadinstitute/gatk/engine/alignment/bwa/c/BWAPath; */ -JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getPaths +JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_getPaths (JNIEnv *, jobject, jlong, jbyteArray); /* - * Class: org_broadinstitute_sting_alignment_bwa_c_BWACAligner + * Class: org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner * Method: convertPathsToAlignments - * Signature: (J[B[Lorg/broadinstitute/sting/alignment/bwa/c/BWAPath;)[Lorg/broadinstitute/sting/alignment/Alignment; + * Signature: (J[B[Lorg/broadinstitute/gatk/engine/alignment/bwa/c/BWAPath;)[Lorg/broadinstitute/gatk/engine/alignment/Alignment; */ -JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_convertPathsToAlignments +JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_convertPathsToAlignments (JNIEnv *, jobject, jlong, jbyteArray, jobjectArray); /* - * Class: org_broadinstitute_sting_alignment_bwa_c_BWACAligner + * Class: org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner * Method: getBestAlignment - * Signature: (J[B)Lorg/broadinstitute/sting/alignment/Alignment; + * Signature: (J[B)Lorg/broadinstitute/gatk/engine/alignment/Alignment; */ -JNIEXPORT jobject JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getBestAlignment +JNIEXPORT jobject JNICALL Java_org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner_getBestAlignment (JNIEnv *, jobject, jlong, jbyteArray); #ifdef __cplusplus diff --git a/public/doc/GATK_Coding_Standards.tex b/public/doc/GATK_Coding_Standards.tex index 29642d1c2..42b6830a1 100644 --- a/public/doc/GATK_Coding_Standards.tex +++ b/public/doc/GATK_Coding_Standards.tex @@ -52,8 +52,8 @@ To this add the product name (e.g., basecaller), and subdivide packages accordin \lstset{tabsize=4} \begin{lstlisting} -package org.broadinstitute.sting.basecalller.basecallerEngine; // Good -package org.broadinstitute.sting.baseCallingStuff; // Bad +package org.broadinstitute.gatk.tools.walkers.basecalller.basecallerEngine; // Good +package org.broadinstitute.gatk.tools.walkers.baseCallingStuff; // Bad package myBaseCaller; // Unacceptable \end{lstlisting} diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml index 87375c843..c4c8a691c 100644 --- a/public/external-example/pom.xml +++ b/public/external-example/pom.xml @@ -6,50 +6,50 @@ external-example jar 1.0-SNAPSHOT - GATK External Example + External Example - 3.2-SNAPSHOT + 3.2-SNAPSHOT - ../.. + ../.. UTF-8 UTF-8 yyyy/MM/dd HH:mm:ss - true - ${sting.committests.skipped} - ${sting.committests.skipped} + true + ${gatk.committests.skipped} + ${gatk.committests.skipped} - package + package - sting.public.repo.local - Sting Public Local Repository - file:${sting.basedir}/public/repo + gatk.public.repo.local + GATK Public Local Repository + file:${gatk.basedir}/public/repo - org.broadinstitute.sting - gatk-framework - ${sting.version} + org.broadinstitute.gatk + gatk-tools-public + ${gatk.version} - org.broadinstitute.sting - gatk-framework - ${sting.version} + org.broadinstitute.gatk + gatk-tools-public + ${gatk.version} test-jar test @@ -80,9 +80,9 @@ - org.broadinstitute.sting - gatk-framework - ${sting.version} + org.broadinstitute.gatk + gatk-engine + ${gatk.version} example-resources tar.bz2 ${project.build.outputDirectory} @@ -106,19 +106,19 @@ prepare-package - org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet + org.broadinstitute.gatk.utils.help.ResourceBundleExtractorDoclet ${project.build.outputDirectory} - org.broadinstitute.sting - - gatk-framework - ${sting.version} + org.broadinstitute.gatk + + gatk-tools-public + ${gatk.version} 2g false true - -build-timestamp "${maven.build.timestamp}" -absolute-version "${project.version}" -out ${project.build.outputDirectory}/StingText.properties + -build-timestamp "${maven.build.timestamp}" -absolute-version "${project.version}" -out ${project.build.outputDirectory}/GATKText.properties @@ -131,7 +131,7 @@ 2.1 - ${sting.shade.phase} + ${gatk.shade.phase} shade @@ -155,18 +155,18 @@ - org.broadinstitute.sting:gsalib:tar.gz:* - org.broadinstitute.sting:*:tar.bz2:example-resources + org.broadinstitute.gatk:gsalib:tar.gz:* + org.broadinstitute.gatk:*:tar.bz2:example-resources - org.broadinstitute.sting.gatk.CommandLineGATK + org.broadinstitute.gatk.engine.CommandLineGATK - + - StingText.properties + GATKText.properties @@ -200,7 +200,7 @@ test - ${sting.unittests.skipped} + ${gatk.unittests.skipped} **/*UnitTest.class @@ -232,7 +232,7 @@ - ${sting.integrationtests.skipped} + ${gatk.integrationtests.skipped} **/*IntegrationTest.class @@ -248,12 +248,12 @@ packagetests-enabled - sting.packagetests.enabled + gatk.packagetests.enabled true - none + none 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 d65c47c99..1834c4a4a 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 @@ -25,11 +25,11 @@ package org.mycompany.app; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.LocusWalker; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.LocusWalker; import java.io.PrintStream; 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 777079426..ee625a46d 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 @@ -25,7 +25,7 @@ package org.mycompany.app; -import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; import java.io.File; 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 e3e0c81ea..56335f1f0 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 @@ -25,7 +25,7 @@ package org.mycompany.app; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-engine/src/main/assembly/example-resources.xml b/public/gatk-engine/src/main/assembly/example-resources.xml index b285cc05f..5a5fc6623 100644 --- a/public/gatk-engine/src/main/assembly/example-resources.xml +++ b/public/gatk-engine/src/main/assembly/example-resources.xml @@ -6,7 +6,7 @@ false - ${project.build.sourceDirectory}/org/broadinstitute/sting/gatk/walkers/qc + ${project.build.sourceDirectory}/org/broadinstitute/gatk/gatk/walkers/qc . Pileup.java @@ -16,7 +16,7 @@ - ${project.build.sourceDirectory}/org/broadinstitute/sting/gatk/walkers/readutils + ${project.build.sourceDirectory}/org/broadinstitute/gatk/gatk/walkers/readutils . PrintReads.java 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 371add094..0f00bd668 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk; +package org.broadinstitute.gatk.engine; import htsjdk.samtools.filter.SamRecordFilter; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.HashMap; import java.util.Map; @@ -68,7 +68,7 @@ public class ReadMetrics implements Cloneable { newMetrics = (ReadMetrics)super.clone(); } catch(CloneNotSupportedException ex) { - throw new ReviewedStingException("Unable to clone runtime metrics",ex); + throw new ReviewedGATKException("Unable to clone runtime metrics",ex); } newMetrics.nRecords = nRecords; newMetrics.nReads = nReads; 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 9ab6056b4..bd34a1792 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 @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk; \ No newline at end of file +package org.broadinstitute.gatk.engine; \ No newline at end of file diff --git a/public/gatk-queue-extensions-generator/pom.xml b/public/gatk-queue-extensions-generator/pom.xml index 4d77bf1fe..2a4310486 100644 --- a/public/gatk-queue-extensions-generator/pom.xml +++ b/public/gatk-queue-extensions-generator/pom.xml @@ -3,25 +3,25 @@ 4.0.0 - org.broadinstitute.sting - sting-aggregator + org.broadinstitute.gatk + gatk-aggregator 3.2-SNAPSHOT ../.. - gatk-queue-extgen + gatk-queue-extensions-generator jar - Queue GATK ExtGen - Queue GATK Extensions Generator + GATK Queue Extensions Generator + GATK Queue Extensions Generator - ${project.basedir}/../.. + ${project.basedir}/../.. ${project.groupId} - gatk-framework + gatk-tools-public ${project.version} 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 a1ad05e24..c9966c6d0 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk; +package org.broadinstitute.gatk.queue.extensions.gatk; import htsjdk.samtools.BAMIndex; import htsjdk.samtools.SAMFileWriter; import htsjdk.tribble.Tribble; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterArgumentTypeDescriptor; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.File; @@ -161,7 +161,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField { // one can set the specific gatherer to use by adding @Gather before any output argument. // For example (used to be part of UG): - // @Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer") + // @Gather(className = "org.broadinstitute.gatk.queue.extensions.gatk.CatVariantsGatherer") // @Output(doc="File to which variants should be written",required=true) // protected VariantContextWriter writer = null; if (gatherer != null) @@ -171,7 +171,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField { else if (VariantContextWriter.class.isAssignableFrom(argumentDefinition.argumentType)) gatherClass = "CatVariantsGatherer"; // used to be "VcfGatherFunction"; else - gatherClass = "org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction"; + gatherClass = "org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction"; fields.add(new OutputArgumentField(argumentDefinition, gatherClass)); @@ -479,8 +479,8 @@ public abstract class ArgumentDefinitionField extends ArgumentField { } @Override protected String getFreezeFields() { return String.format( - ("if (%2$s != null && !org.broadinstitute.sting.utils.io.IOUtils.isSpecialFile(%2$s))%n" + - " if (!org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor.isCompressed(%2$s.getPath))%n" + + ("if (%2$s != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(%2$s))%n" + + " if (!org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor.isCompressed(%2$s.getPath))%n" + " %1$s = new File(%2$s.getPath + \"%3$s\")%n"), auxFieldName, originalFieldName, Tribble.STANDARD_INDEX_EXTENSION); } @@ -492,7 +492,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField { } @Override protected String getFreezeFields() { return String.format( - ("if (%2$s != null && !org.broadinstitute.sting.utils.io.IOUtils.isSpecialFile(%2$s))%n" + + ("if (%2$s != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(%2$s))%n" + " if (!%3$s)%n" + " %1$s = new File(%2$s.getPath.stripSuffix(\".bam\") + \"%4$s\")%n"), auxFieldName, originalFieldName, SAMFileWriterArgumentTypeDescriptor.DISABLE_INDEXING_FULLNAME, BAMIndex.BAMIndexSuffix); @@ -505,7 +505,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField { } @Override protected String getFreezeFields() { return String.format( - ("if (%2$s != null && !org.broadinstitute.sting.utils.io.IOUtils.isSpecialFile(%2$s))%n" + + ("if (%2$s != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(%2$s))%n" + " if (%3$s)%n" + " %1$s = new File(%2$s.getPath + \"%4$s\")%n"), auxFieldName, originalFieldName, SAMFileWriterArgumentTypeDescriptor.ENABLE_MD5_FULLNAME, ".md5"); 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 45b4e529c..9c93efd5d 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 @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk; +package org.broadinstitute.gatk.queue.extensions.gatk; import htsjdk.samtools.SAMFileReader; import htsjdk.samtools.SAMFileWriter; import org.apache.commons.lang.StringEscapeUtils; import org.apache.commons.lang.StringUtils; -import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper; +import org.broadinstitute.gatk.engine.filters.PlatformUnitFilterHelper; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.File; 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 ced0809f7..d125e3dc0 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 @@ -23,29 +23,29 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk; +package org.broadinstitute.gatk.queue.extensions.gatk; import org.apache.commons.io.FileUtils; import org.apache.commons.lang.StringUtils; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor; -import org.broadinstitute.sting.commandline.CommandLineProgram; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.commandline.ParsingEngine; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.WalkerManager; -import org.broadinstitute.sting.gatk.filters.FilterManager; -import org.broadinstitute.sting.gatk.filters.ReadFilter; -import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor; -import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; -import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor; -import org.broadinstitute.sting.gatk.walkers.PartitionBy; -import org.broadinstitute.sting.gatk.walkers.PartitionType; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.classloader.JVMUtils; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.utils.commandline.ParsingEngine; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.WalkerManager; +import org.broadinstitute.gatk.engine.filters.FilterManager; +import org.broadinstitute.gatk.engine.filters.ReadFilter; +import org.broadinstitute.gatk.engine.io.stubs.OutputStreamArgumentTypeDescriptor; +import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterArgumentTypeDescriptor; +import org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor; +import org.broadinstitute.gatk.engine.walkers.PartitionBy; +import org.broadinstitute.gatk.engine.walkers.PartitionType; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.classloader.JVMUtils; +import org.broadinstitute.gatk.utils.classloader.PluginManager; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.File; import java.io.IOException; @@ -125,7 +125,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram { protected int execute() { try { if (!outputDirectory.isDirectory() && !outputDirectory.mkdirs()) - throw new ReviewedStingException("Unable to create output directory: " + outputDirectory); + throw new ReviewedGATKException("Unable to create output directory: " + outputDirectory); SortedSet> dependents = new TreeSet>(classComparator); @@ -141,7 +141,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram { String clpClassName = clpManager.getName(clp); String clpConstructor = String.format("analysisName = \"%s\"%njavaMainClass = \"%s\"%n", clpClassName, clp.getName()); - writeClass("org.broadinstitute.sting.queue.function.JavaCommandLineFunction", clpClassName, + writeClass("org.broadinstitute.gatk.queue.function.JavaCommandLineFunction", clpClassName, false, clpConstructor, ArgumentDefinitionField.getArgumentFields(parser,clp), dependents); if (clp == CommandLineGATK.class) { @@ -166,13 +166,13 @@ public class GATKExtensionsGenerator extends CommandLineProgram { writeClass(GATK_EXTENSIONS_PACKAGE_NAME + "." + clpClassName, walkerName, isScatter, constructor, argumentFields, dependents); } catch (Exception e) { - throw new ReviewedStingException("Error generating wrappers for walker " + walkerType, e); + throw new ReviewedGATKException("Error generating wrappers for walker " + walkerType, e); } } } } } catch (Exception e) { - throw new ReviewedStingException("Error generating wrappers for " + clp, e); + throw new ReviewedGATKException("Error generating wrappers for " + clp, e); } } @@ -194,11 +194,10 @@ public class GATKExtensionsGenerator extends CommandLineProgram { * The list of packages to search through. */ private static final List gatkPackages = Arrays.asList( - "org.broadinstitute.sting.tools", - "org.broadinstitute.sting.gatk", - "org.broadinstitute.sting.pipeline", - "org.broadinstitute.sting.tools", - "org.broadinstitute.sting.gatk.datasources.reads.utilities"); + "org.broadinstitute.gatk.engine", + "org.broadinstitute.gatk.utils.pipeline", + "org.broadinstitute.gatk.tools", + "org.broadinstitute.gatk.engine.datasources.reads.utilities"); /** * Returns true if the class is part of the GATK. @@ -253,7 +252,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram { * @throws IOException If the file cannot be written. */ private void writeFilter(String className, List argumentFields, Set> dependents) throws IOException { - String content = getContent(TRAIT_TEMPLATE, "org.broadinstitute.sting.queue.function.CommandLineFunction", + String content = getContent(TRAIT_TEMPLATE, "org.broadinstitute.gatk.queue.function.CommandLineFunction", className, "", false, String.format(" + required(\"--read_filter\", \"%s\")", className), argumentFields, dependents); writeFile(GATK_EXTENSIONS_PACKAGE_NAME + "." + className, content); } @@ -366,11 +365,11 @@ public class GATKExtensionsGenerator extends CommandLineProgram { } if (isScatter) { - importSet.add("import org.broadinstitute.sting.queue.function.scattergather.ScatterGatherableFunction"); + importSet.add("import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction"); baseClass += " with ScatterGatherableFunction"; } if (isGather) - importSet.add("import org.broadinstitute.sting.commandline.Gather"); + importSet.add("import org.broadinstitute.gatk.utils.commandline.Gather"); // Sort the imports so that the are always in the same order. List sortedImports = new ArrayList(importSet); 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 51b08f324..b23f1aafa 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk; +package org.broadinstitute.gatk.queue.extensions.gatk; import htsjdk.samtools.filter.SamRecordFilter; -import org.broadinstitute.sting.commandline.ParsingEngine; -import org.broadinstitute.sting.gatk.WalkerManager; -import org.broadinstitute.sting.gatk.walkers.Walker; +import org.broadinstitute.gatk.utils.commandline.ParsingEngine; +import org.broadinstitute.gatk.engine.WalkerManager; +import org.broadinstitute.gatk.engine.walkers.Walker; import java.util.ArrayList; import java.util.List; diff --git a/public/gatk-queue-extensions-public/src/main/assembly/example-resources.xml b/public/gatk-queue-extensions-public/src/main/assembly/example-resources.xml index 7d4ec43ef..f3cd6f962 100644 --- a/public/gatk-queue-extensions-public/src/main/assembly/example-resources.xml +++ b/public/gatk-queue-extensions-public/src/main/assembly/example-resources.xml @@ -6,7 +6,7 @@ false - src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples + src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples . ExampleCountReads.scala 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 9bb031c38..a674d0f11 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 @@ -23,17 +23,17 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.CNV +package org.broadinstitute.gatk.queue.qscripts.CNV -import org.broadinstitute.sting.queue.extensions.gatk._ -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.util.VCF_BAM_utilities -import org.broadinstitute.sting.queue.util.DoC._ -import org.broadinstitute.sting.commandline.Hidden +import org.broadinstitute.gatk.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.util.VCF_BAM_utilities +import org.broadinstitute.gatk.queue.extensions.gatk.DoC._ +import org.broadinstitute.gatk.utils.commandline.Hidden import java.io.{PrintStream, PrintWriter} -import org.broadinstitute.sting.utils.text.XReadLines +import org.broadinstitute.gatk.utils.text.XReadLines import collection.JavaConversions._ -import org.broadinstitute.sting.gatk.walkers.coverage.CoverageUtils +import org.broadinstitute.gatk.tools.walkers.coverage.CoverageUtils class xhmmCNVpipeline extends QScript { qscript => 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 d0c917a9e..d89e6058a 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 @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts +package org.broadinstitute.gatk.queue.qscripts -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.extensions.gatk._ -import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException -import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction -import org.broadinstitute.sting.queue.function.JavaCommandLineFunction +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.extensions.samtools.SamtoolsIndexFunction +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException +import org.broadinstitute.gatk.queue.extensions.picard.PicardBamFunction +import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction class GATKResourcesBundle extends QScript { // todo -- update to released version when things stabilize 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 a7b73cd20..e988a42a5 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.examples +package org.broadinstitute.gatk.queue.qscripts.examples -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ /** * An introductory pipeline with integration tests testing the MD5 of the @Output. 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 1bf3728b9..55711c026 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.examples +package org.broadinstitute.gatk.queue.qscripts.examples -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ /** * An introductory pipeline for Queue. 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 5839426e0..e38ba3ef7 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.examples +package org.broadinstitute.gatk.queue.qscripts.examples -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ /** * A pipeline for Queue that runs a custom walker on the classpath. 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 18f2895b9..440b6f288 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.examples +package org.broadinstitute.gatk.queue.qscripts.examples -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ /** * Script used for testing output to /dev/null, deleting .bai files, etc. 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 bfd472db7..f736406d1 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.examples +package org.broadinstitute.gatk.queue.qscripts.examples -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ /** * Script used for testing inclusion of a read filter 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 21a8db85f..71e009469 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.examples +package org.broadinstitute.gatk.queue.qscripts.examples -import org.broadinstitute.sting.queue.function.RetryMemoryLimit -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.function.RetryMemoryLimit +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ class ExampleRetryMemoryLimit extends QScript { @Input(doc="The reference file for the bam files.", shortName="R") diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala index 0d08307d4..70a1e5e4b 100644 --- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala +++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.examples +package org.broadinstitute.gatk.queue.qscripts.examples -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ /** * An example building on the intro ExampleCountReads.scala. 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 fb7b96b02..c095169b7 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.examples +package org.broadinstitute.gatk.queue.qscripts.examples -import org.broadinstitute.sting.queue.QScript +import org.broadinstitute.gatk.queue.QScript class HelloWorld extends QScript { def script() { 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 b1adfc1a6..ab687c020 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 @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.lib +package org.broadinstitute.gatk.queue.qscripts.lib -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.library.ipf.vcf.VCFExtractIntervals +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.library.ipf.vcf.VCFExtractIntervals import scala.collection.JavaConversions._ -import org.broadinstitute.sting.utils.text.XReadLines +import org.broadinstitute.gatk.utils.text.XReadLines import java.io.PrintStream -import org.broadinstitute.sting.queue.extensions.gatk.SelectVariants +import org.broadinstitute.gatk.queue.extensions.gatk.SelectVariants /** * Created by IntelliJ IDEA. 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 25ff8fddd..d7a104a6a 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 @@ -1,4 +1,29 @@ -package org.broadinstitute.sting.queue.qscripts.lib +/* +* 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. +*/ + +package org.broadinstitute.gatk.queue.qscripts.lib import org.broadinstitute.sting.commandline.Hidden import org.broadinstitute.sting.queue.extensions.gatk.{RodBind, VariantsToTable} 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 920050767..962d495d3 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 @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.qscripts.lib +package org.broadinstitute.gatk.queue.qscripts.lib -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.commandline.Input -import org.broadinstitute.sting.queue.library.ipf.vcf.VCFExtractIntervals -import org.broadinstitute.sting.utils.text.XReadLines +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.utils.commandline.Input +import org.broadinstitute.gatk.queue.library.ipf.vcf.VCFExtractIntervals +import org.broadinstitute.gatk.utils.text.XReadLines import collection.JavaConversions._ import java.io._ -import org.broadinstitute.sting.queue.extensions.gatk.{SelectVariants, VariantsToPed} +import org.broadinstitute.gatk.queue.extensions.gatk.{SelectVariants, VariantsToPed} /** * Created by IntelliJ IDEA. 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 172daf171..92bafd810 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 @@ -23,17 +23,17 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.cancer +package org.broadinstitute.gatk.queue.extensions.cancer import java.io.File -import org.broadinstitute.sting.commandline.Argument -import org.broadinstitute.sting.commandline.Gather -import org.broadinstitute.sting.commandline.Input -import org.broadinstitute.sting.commandline.Output -import org.broadinstitute.sting.queue.function.scattergather.ScatterGatherableFunction -import org.broadinstitute.sting.queue.extensions.gatk.{TaggedFile, VcfGatherFunction, LocusScatterFunction} +import org.broadinstitute.gatk.utils.commandline.Argument +import org.broadinstitute.gatk.utils.commandline.Gather +import org.broadinstitute.gatk.utils.commandline.Input +import org.broadinstitute.gatk.utils.commandline.Output +import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction +import org.broadinstitute.gatk.queue.extensions.gatk.{TaggedFile, VcfGatherFunction, LocusScatterFunction} -class MuTect extends org.broadinstitute.sting.queue.extensions.gatk.CommandLineGATK with ScatterGatherableFunction { +class MuTect extends org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK with ScatterGatherableFunction { analysisName = "MuTect" analysis_type = "MuTect" scatterClass = classOf[LocusScatterFunction] @@ -256,7 +256,7 @@ class MuTect extends org.broadinstitute.sting.queue.extensions.gatk.CommandLineG /** Call-stats output */ @Output(fullName="out", shortName="o", doc="Call-stats output", required=false, exclusiveOf="", validation="") - @Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction]) + @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction]) var out: File = _ /** @@ -319,7 +319,7 @@ class MuTect extends org.broadinstitute.sting.queue.extensions.gatk.CommandLineG /** write out coverage in WIGGLE format to this file */ @Output(fullName="coverage_file", shortName="cov", doc="write out coverage in WIGGLE format to this file", required=false, exclusiveOf="", validation="") - @Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction]) + @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction]) var coverage_file: File = _ /** @@ -336,7 +336,7 @@ class MuTect extends org.broadinstitute.sting.queue.extensions.gatk.CommandLineG /** write out 20x of Q20 coverage in WIGGLE format to this file */ @Output(fullName="coverage_20_q20_file", shortName="cov_q20", doc="write out 20x of Q20 coverage in WIGGLE format to this file", required=false, exclusiveOf="", validation="") - @Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction]) + @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction]) var coverage_20_q20_file: File = _ /** @@ -353,7 +353,7 @@ class MuTect extends org.broadinstitute.sting.queue.extensions.gatk.CommandLineG /** write out power in WIGGLE format to this file */ @Output(fullName="power_file", shortName="pow", doc="write out power in WIGGLE format to this file", required=false, exclusiveOf="", validation="") - @Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction]) + @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction]) var power_file: File = _ /** @@ -370,7 +370,7 @@ class MuTect extends org.broadinstitute.sting.queue.extensions.gatk.CommandLineG /** write out tumor read depth in WIGGLE format to this file */ @Output(fullName="tumor_depth_file", shortName="tdf", doc="write out tumor read depth in WIGGLE format to this file", required=false, exclusiveOf="", validation="") - @Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction]) + @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction]) var tumor_depth_file: File = _ /** @@ -387,7 +387,7 @@ class MuTect extends org.broadinstitute.sting.queue.extensions.gatk.CommandLineG /** write out normal read depth in WIGGLE format to this file */ @Output(fullName="normal_depth_file", shortName="ndf", doc="write out normal read depth in WIGGLE format to this file", required=false, exclusiveOf="", validation="") - @Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction]) + @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction]) var normal_depth_file: File = _ /** @@ -420,8 +420,8 @@ class MuTect extends org.broadinstitute.sting.queue.extensions.gatk.CommandLineG override def freezeFieldValues() { super.freezeFieldValues() - if (vcf != null && !org.broadinstitute.sting.utils.io.IOUtils.isSpecialFile(vcf)) - if (!org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor.isCompressed(vcf.getPath)) + if (vcf != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(vcf)) + if (!org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor.isCompressed(vcf.getPath)) vcfIndex = new File(vcf.getPath + ".idx") dbsnpIndexes ++= dbsnp.filter(orig => orig != null).map(orig => new File(orig.getPath + ".idx")) cosmicIndexes ++= cosmic.filter(orig => orig != null).map(orig => new File(orig.getPath + ".idx")) 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 899551d0f..f852e9d9e 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 @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk -import org.broadinstitute.sting.queue.function.scattergather.GatherFunction -import org.broadinstitute.sting.queue.extensions.picard.MergeSamFiles -import org.broadinstitute.sting.queue.function.RetryMemoryLimit -import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor -import org.broadinstitute.sting.queue.util.ClassFieldCache +import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction +import org.broadinstitute.gatk.queue.extensions.picard.MergeSamFiles +import org.broadinstitute.gatk.queue.function.RetryMemoryLimit +import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterArgumentTypeDescriptor +import org.broadinstitute.gatk.queue.util.ClassFieldCache import java.io.File /** 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 940d98860..fd91e5352 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk -import org.broadinstitute.sting.queue.function.RetryMemoryLimit -import org.broadinstitute.sting.queue.function.scattergather.GatherFunction +import org.broadinstitute.gatk.queue.function.RetryMemoryLimit +import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction /** @@ -34,7 +34,7 @@ import org.broadinstitute.sting.queue.function.scattergather.GatherFunction * Currently this is the default gather for VCFs. * One can set a specific gatherer to use by adding @Gather before any output argument. * For example (used to be part of UG): - * @Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer") + * @Gather(className = "org.broadinstitute.gatk.queue.extensions.gatk.CatVariantsGatherer") * @Output(doc="File to which variants should be written",required=true) * protected VariantContextWriter writer = null; */ 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 b07c74b56..7eff64518 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk import collection.JavaConversions._ -import org.broadinstitute.sting.utils.interval.IntervalUtils -import org.broadinstitute.sting.queue.function.InProcessFunction +import org.broadinstitute.gatk.utils.interval.IntervalUtils +import org.broadinstitute.gatk.queue.function.InProcessFunction /** * Splits intervals by contig instead of evenly. 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 64a69b03c..f4ad99390 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk import java.io.File -import org.broadinstitute.sting.queue.function.InProcessFunction -import org.broadinstitute.sting.queue.function.scattergather.{ScatterFunction, CloneFunction} -import org.broadinstitute.sting.commandline.Output +import org.broadinstitute.gatk.queue.function.InProcessFunction +import org.broadinstitute.gatk.queue.function.scattergather.{ScatterFunction, CloneFunction} +import org.broadinstitute.gatk.utils.commandline.Output import util.Random /** 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 46f59baab..041f14076 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 @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.extensions.gatk import java.io.File -import org.broadinstitute.sting.queue.extensions.gatk.{IntervalScatterFunction, CommandLineGATK} -import org.broadinstitute.sting.queue.function.scattergather.ScatterGatherableFunction -import org.broadinstitute.sting.gatk.downsampling.DownsampleType -import org.broadinstitute.sting.commandline.{Input, Gather, Output} -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.gatk.walkers.coverage.CoverageUtils +import org.broadinstitute.gatk.queue.util.VCF_BAM_utilities +import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction +import org.broadinstitute.gatk.engine.downsampling.DownsampleType +import org.broadinstitute.gatk.utils.commandline.{Input, Gather, Output} +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.tools.walkers.coverage.CoverageUtils package object DoC { class DoC(val bams: List[File], val DoC_output: File, val countType: CoverageUtils.CountPileupType, val MAX_DEPTH: Int, val minMappingQuality: Int, val minBaseQuality: Int, val scatterCountInput: Int, val START_BIN: Int, val NUM_BINS: Int, val minCoverageCalcs: Seq[Int]) extends CommandLineGATK with ScatterGatherableFunction { @@ -52,7 +52,7 @@ package object DoC { // HACK for DoC to work properly within Queue: @Output - @Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction]) + @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction]) var intervalSampleOut: File = new File(DoC_output.getPath + DOC_OUTPUT_SUFFIX) override def commandLine = super.commandLine + @@ -72,7 +72,7 @@ package object DoC { class DoCwithDepthOutputAtEachBase(bams: List[File], DoC_output: File, countType: CoverageUtils.CountPileupType, MAX_DEPTH: Int, minMappingQuality: Int, minBaseQuality: Int, scatterCountInput: Int, START_BIN: Int, NUM_BINS: Int, minCoverageCalcs: Seq[Int]) extends DoC(bams, DoC_output, countType: CoverageUtils.CountPileupType, MAX_DEPTH: Int, minMappingQuality, minBaseQuality, scatterCountInput, START_BIN, NUM_BINS, minCoverageCalcs) { // HACK for DoC to work properly within Queue: @Output - @Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction]) + @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction]) var outPrefix = DoC_output override def commandLine = super.commandLine.replaceAll(" --omitDepthOutputAtEachBase", "") 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 c4c193110..0e568b61f 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 @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk import java.io.File import collection.JavaConversions._ -import org.broadinstitute.sting.utils.interval.{IntervalSetRule, IntervalMergingRule, IntervalUtils} -import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource +import org.broadinstitute.gatk.utils.interval.{IntervalSetRule, IntervalMergingRule, IntervalUtils} +import org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource import htsjdk.samtools.SAMFileHeader -import org.broadinstitute.sting.utils.GenomeLoc -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.GenomeLoc +import org.broadinstitute.gatk.utils.commandline._ import htsjdk.tribble.Feature case class GATKIntervals(reference: File, intervals: Seq[File], intervalsString: Seq[String], 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 1b4e8dbdb..01075c393 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 @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk -import org.broadinstitute.sting.utils.interval.IntervalUtils +import org.broadinstitute.gatk.utils.interval.IntervalUtils import java.io.File -import org.broadinstitute.sting.utils.io.IOUtils -import org.broadinstitute.sting.queue.function.scattergather.{CloneFunction, ScatterFunction} -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.io.IOUtils +import org.broadinstitute.gatk.queue.function.scattergather.{CloneFunction, ScatterFunction} +import org.broadinstitute.gatk.utils.commandline._ trait GATKScatterFunction extends ScatterFunction { /* The runtime field to set for specifying intervals. */ 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 713a2aa44..99454d459 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk import collection.JavaConversions._ -import org.broadinstitute.sting.utils.interval.IntervalUtils -import org.broadinstitute.sting.queue.function.InProcessFunction +import org.broadinstitute.gatk.utils.interval.IntervalUtils +import org.broadinstitute.gatk.queue.function.InProcessFunction /** * An interval scatter function. 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 b4370cf83..5d71d3585 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk import collection.JavaConversions._ -import org.broadinstitute.sting.utils.interval.IntervalUtils -import org.broadinstitute.sting.queue.function.InProcessFunction +import org.broadinstitute.gatk.utils.interval.IntervalUtils +import org.broadinstitute.gatk.queue.function.InProcessFunction /** * A scatter function that divides down to the locus level. 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 472be89e3..01e9eed2d 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk /* * Copyright (c) 2011, The Broad Institute 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 8a58c7aa7..e1612091f 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk import java.io.File -import org.broadinstitute.sting.utils.io.FileExtension -import org.broadinstitute.sting.queue.util.ShellUtils +import org.broadinstitute.gatk.utils.io.FileExtension +import org.broadinstitute.gatk.queue.util.ShellUtils /** * Used to provide tagged -I input_file arguments to the GATK. 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 73be41e89..fe778fcfe 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk -import org.broadinstitute.sting.queue.function.scattergather.GatherFunction -import org.broadinstitute.sting.queue.function.{RetryMemoryLimit, QFunction} -import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor -import org.broadinstitute.sting.queue.util.ClassFieldCache +import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction +import org.broadinstitute.gatk.queue.function.{RetryMemoryLimit, QFunction} +import org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor +import org.broadinstitute.gatk.queue.util.ClassFieldCache /** * Merges a vcf text file. 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 24d83058c..290eff973 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk -import org.broadinstitute.sting.queue.function.InProcessFunction -import org.broadinstitute.sting.commandline.{Output, Argument, Input} +import org.broadinstitute.gatk.queue.function.InProcessFunction +import org.broadinstitute.gatk.utils.commandline.{Output, Argument, Input} import java.io.File -import org.broadinstitute.sting.utils.interval.IntervalUtils +import org.broadinstitute.gatk.utils.interval.IntervalUtils class WriteFlankingIntervalsFunction extends InProcessFunction { @Input(doc="The reference sequence") 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 0ca404f28..6b70d2f58 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import java.io.File @@ -35,7 +35,7 @@ import java.io.File * Date: 6/22/11 * Time: 10:35 AM */ -class AddOrReplaceReadGroups extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { +class AddOrReplaceReadGroups extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "AddOrReplaceReadGroups" javaMainClass = "picard.sam.AddOrReplaceReadGroups" 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 cbad1206b..51c3b00a6 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline.{Argument, Output, Input} +import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input} import java.io.File import picard.analysis.MetricAccumulationLevel @@ -36,7 +36,7 @@ import picard.analysis.MetricAccumulationLevel * Time: 5:59 PM * To change this template use File | Settings | File Templates. */ -class CalculateHsMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction { +class CalculateHsMetrics extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardMetricsFunction { analysisName = "CalculateHsMetrics" javaMainClass = "picard.analysis.directed.CalculateHsMetrics" 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 620be56a7..f0d2300c4 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline.{Argument, Output, Input} +import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input} import java.io.File /** @@ -35,7 +35,7 @@ import java.io.File * Time: 10:37 AM * To change this template use File | Settings | File Templates. */ -class CollectGcBiasMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction { +class CollectGcBiasMetrics extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardMetricsFunction { analysisName = "CollectGcBiasMetrics" javaMainClass = "picard.analysis.CollectGcBiasMetrics" 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 18079808c..15073668a 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline.{Argument, Output, Input} +import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input} import java.io.File /** @@ -35,7 +35,7 @@ import java.io.File * Time: 10:37 AM * To change this template use File | Settings | File Templates. */ -class CollectMultipleMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction{ +class CollectMultipleMetrics extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardMetricsFunction{ analysisName = "CollectMultipleMetrics" javaMainClass = "picard.analysis.CollectMultipleMetrics" 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 11e2aa349..44e10af86 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard /* * Copyright (c) 2012 The Broad Institute @@ -50,11 +50,11 @@ package org.broadinstitute.sting.queue.extensions.picard * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import java.io.File -class FastqToSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction /*with PicardBamFunction*/ { +class FastqToSam extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction /*with PicardBamFunction*/ { analysisName = "FastqToSam" javaMainClass = "picard.sam.FastqToSam" 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 68d0c9ef3..66460b688 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import java.io.File @@ -35,7 +35,7 @@ import java.io.File * Date: 6/22/11 * Time: 10:35 AM */ -class MarkDuplicates extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { +class MarkDuplicates extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "MarkDuplicates" javaMainClass = "picard.sam.MarkDuplicates" 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 1333d4a19..1b25a8e6c 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import java.io.File @@ -35,7 +35,7 @@ import java.io.File * Date: 6/22/11 * Time: 10:35 AM */ -class MergeSamFiles extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { +class MergeSamFiles extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "MergeSamFiles" javaMainClass = "picard.sam.MergeSamFiles" 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 08ac5352e..a2db658bc 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard import java.io.File -import org.broadinstitute.sting.queue.function.JavaCommandLineFunction +import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction import htsjdk.samtools.SAMFileReader.ValidationStringency import htsjdk.samtools.SAMFileHeader.SortOrder 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 b48715292..eaeaa1837 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard import java.io.File -import org.broadinstitute.sting.queue.function.JavaCommandLineFunction +import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction import htsjdk.samtools.SAMFileReader.ValidationStringency import htsjdk.samtools.SAMFileHeader.SortOrder 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 ff17cfda6..1813694a3 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import java.io.File /* @@ -34,7 +34,7 @@ import java.io.File * Date: 6/22/11 * Time: 10:35 AM */ -class ReorderSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { +class ReorderSam extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "ReorderSam" javaMainClass = "picard.sam.ReorderSam" 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 c099faf4c..2012b543e 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import java.io.File @@ -35,7 +35,7 @@ import java.io.File * Date: 6/22/11 * Time: 10:35 AM */ -class RevertSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { +class RevertSam extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "RevertSam" javaMainClass = "picard.sam.RevertSam" 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 adc0afb2f..e5624fcd6 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import java.io.File @@ -35,7 +35,7 @@ import java.io.File * Date: 6/22/11 * Time: 10:35 AM */ -class SamToFastq extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { +class SamToFastq extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "SamToFastq" javaMainClass = "picard.sam.SamToFastq" 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 d34b421f4..847ed9238 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import java.io.File @@ -35,7 +35,7 @@ import java.io.File * Date: 6/22/11 * Time: 10:35 AM */ -class SortSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { +class SortSam extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "SortSam" javaMainClass = "picard.sam.SortSam" 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 5690b488d..e9ad0970f 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.picard +package org.broadinstitute.gatk.queue.extensions.picard -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import picard.sam.ValidateSamFile.Mode @@ -37,7 +37,7 @@ import java.io.File * Date: 6/22/11 * Time: 10:35 AM */ -class ValidateSamFile extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { +class ValidateSamFile extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "ValidateSamFile" javaMainClass = "picard.sam.ValidateSamFile" 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 016b35631..a7e603074 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.samtools +package org.broadinstitute.gatk.queue.extensions.samtools -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.commandline.Argument +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.utils.commandline.Argument /** * samtools command line function 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 01763110d..cb55c06fb 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.samtools +package org.broadinstitute.gatk.queue.extensions.samtools import java.io.File -import org.broadinstitute.sting.commandline.{Output, Input} +import org.broadinstitute.gatk.utils.commandline.{Output, Input} /** * Indexes a BAM file using samtools. 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 7916896ba..4d7c0c6fd 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.samtools +package org.broadinstitute.gatk.queue.extensions.samtools import java.io.File -import org.broadinstitute.sting.commandline.{Argument, Output, Input} +import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input} /** * Merges BAM files using samtools. 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 529615c24..ae316bcc2 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.snpeff +package org.broadinstitute.gatk.queue.extensions.snpeff -import org.broadinstitute.sting.queue.function.JavaCommandLineFunction +import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction import java.io.File -import org.broadinstitute.sting.commandline.{Argument, Output, Input} +import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input} /** * Basic snpEff support. 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 74be13948..f2ec8a929 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 @@ -23,18 +23,18 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.extensions.gatk +package org.broadinstitute.gatk.queue.extensions.gatk import java.io.File import org.testng.Assert import org.testng.annotations.{DataProvider, Test} -import org.broadinstitute.sting.BaseTest -import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile -import org.broadinstitute.sting.utils.{GenomeLocSortedSet, GenomeLocParser} +import org.broadinstitute.gatk.utils.BaseTest +import org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile +import org.broadinstitute.gatk.utils.{GenomeLocSortedSet, GenomeLocParser} import collection.JavaConversions._ -import org.broadinstitute.sting.utils.interval.IntervalUtils -import org.broadinstitute.sting.utils.exceptions.UserException +import org.broadinstitute.gatk.utils.interval.IntervalUtils +import org.broadinstitute.gatk.utils.exceptions.UserException class GATKIntervalsUnitTest { private final lazy val hg18Reference = new File(BaseTest.hg18Reference) 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 b1149054a..d9abf68bc 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.pipeline.examples +package org.broadinstitute.gatk.queue.pipeline.examples import org.testng.annotations.Test -import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec} -import org.broadinstitute.sting.BaseTest +import org.broadinstitute.gatk.queue.pipeline.{QueueTest, QueueTestSpec} +import org.broadinstitute.gatk.utils.BaseTest class ExampleCountLociQueueTest { @Test(timeOut=36000000) @@ -36,7 +36,7 @@ class ExampleCountLociQueueTest { val spec = new QueueTestSpec spec.name = "countloci" spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM.bam", " -o " + testOut).mkString 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 e023a9dda..7ee48d5fb 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.pipeline.examples +package org.broadinstitute.gatk.queue.pipeline.examples import org.testng.annotations.Test -import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec} -import org.broadinstitute.sting.BaseTest +import org.broadinstitute.gatk.queue.pipeline.{QueueTest, QueueTestSpec} +import org.broadinstitute.gatk.utils.BaseTest class ExampleCountReadsQueueTest { @Test(timeOut=36000000) @@ -35,7 +35,7 @@ class ExampleCountReadsQueueTest { val spec = new QueueTestSpec spec.name = "countreads" spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM.bam").mkString QueueTest.executeTest(spec) 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 667187bd2..68df21f6b 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.pipeline.examples +package org.broadinstitute.gatk.queue.pipeline.examples /* * Copyright (c) 2011, The Broad Institute @@ -50,8 +50,8 @@ package org.broadinstitute.sting.queue.pipeline.examples */ import org.testng.annotations.Test -import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec} -import org.broadinstitute.sting.BaseTest +import org.broadinstitute.gatk.queue.pipeline.{QueueTest, QueueTestSpec} +import org.broadinstitute.gatk.utils.BaseTest class ExamplePrintReadsQueueTest { @Test(timeOut=36000000) @@ -59,7 +59,7 @@ class ExamplePrintReadsQueueTest { val spec = new QueueTestSpec spec.name = "devnulloutput" spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExamplePrintReads.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM.bam", " -out /dev/null").mkString @@ -72,7 +72,7 @@ class ExamplePrintReadsQueueTest { val spec = new QueueTestSpec spec.name = "cleanupbai" spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExamplePrintReads.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM.bam", " -out exampleOut.bam").mkString 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 82fd57ee3..73d62b76f 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.pipeline.examples +package org.broadinstitute.gatk.queue.pipeline.examples /* * Copyright (c) 2012, The Broad Institute @@ -74,8 +74,8 @@ package org.broadinstitute.sting.queue.pipeline.examples */ import org.testng.annotations.Test -import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec} -import org.broadinstitute.sting.BaseTest +import org.broadinstitute.gatk.queue.pipeline.{QueueTest, QueueTestSpec} +import org.broadinstitute.gatk.utils.BaseTest class ExampleReadFilterQueueTest { @Test(timeOut=36000000) @@ -83,7 +83,7 @@ class ExampleReadFilterQueueTest { val spec = new QueueTestSpec spec.name = "examplereadfilter" spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM.bam").mkString QueueTest.executeTest(spec) 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 3e314708c..6a6258eef 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.pipeline.examples +package org.broadinstitute.gatk.queue.pipeline.examples import org.testng.annotations.Test -import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec} -import org.broadinstitute.sting.BaseTest +import org.broadinstitute.gatk.queue.pipeline.{QueueTest, QueueTestSpec} +import org.broadinstitute.gatk.utils.BaseTest class ExampleRetryMemoryLimitQueueTest { @@ -37,7 +37,7 @@ class ExampleRetryMemoryLimitQueueTest { val spec = new QueueTestSpec spec.name = "RetryMemoryLimit" spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM.bam", " -retry 1").mkString diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala index 20f97ea61..57408bdee 100644 --- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala +++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.pipeline.examples +package org.broadinstitute.gatk.queue.pipeline.examples import org.testng.annotations.{DataProvider, Test} -import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec} -import org.broadinstitute.sting.BaseTest +import org.broadinstitute.gatk.queue.pipeline.{QueueTest, QueueTestSpec} +import org.broadinstitute.gatk.utils.BaseTest class ExampleUnifiedGenotyperQueueTest { @Test(timeOut=36000000) @@ -35,7 +35,7 @@ class ExampleUnifiedGenotyperQueueTest { val spec = new QueueTestSpec spec.name = "unifiedgenotyper" spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM.bam", " -filter QD", @@ -57,7 +57,7 @@ class ExampleUnifiedGenotyperQueueTest { val spec = new QueueTestSpec spec.name = "unifiedgenotyper_with_" + intervalsName spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", " -I " + BaseTest.validationDataLocation + "OV-0930.normal.chunk.bam", " -R " + BaseTest.hg18Reference, " -L " + intervalsPath).mkString @@ -70,7 +70,7 @@ class ExampleUnifiedGenotyperQueueTest { val spec = new QueueTestSpec spec.name = "unifiedgenotyper_no_gc_opt" spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM.bam", " -noGCOpt").mkString @@ -86,7 +86,7 @@ class ExampleUnifiedGenotyperQueueTest { val spec = new QueueTestSpec spec.name = "unifiedgenotyper_" + reqParam spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM.bam", " -resMemReqParam " + reqParam).mkString @@ -99,7 +99,7 @@ class ExampleUnifiedGenotyperQueueTest { val spec = new QueueTestSpec spec.name = "unifiedgenotyper_with_log_directory" spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", + " -S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -I " + BaseTest.publicTestDir + "exampleBAM.bam", " -logDir exampleUGLogDir").mkString 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 5d3923250..5423ba124 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 @@ -23,17 +23,17 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.pipeline.examples +package org.broadinstitute.gatk.queue.pipeline.examples import org.testng.annotations.Test -import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec} +import org.broadinstitute.gatk.queue.pipeline.{QueueTest, QueueTestSpec} class HelloWorldQueueTest { @Test(timeOut=36000000) def testHelloWorld() { val spec = new QueueTestSpec spec.name = "HelloWorld" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" spec.jobRunners = QueueTest.allJobRunners QueueTest.executeTest(spec) } @@ -42,7 +42,7 @@ class HelloWorldQueueTest { def testHelloWorldWithRunName() { val spec = new QueueTestSpec spec.name = "HelloWorldWithRunName" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -runName HelloWorld" spec.jobRunners = QueueTest.allJobRunners QueueTest.executeTest(spec) @@ -52,7 +52,7 @@ class HelloWorldQueueTest { def testHelloWorldWithMemoryLimit() { val spec = new QueueTestSpec spec.name = "HelloWorldMemoryLimit" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -memLimit 1.25" spec.jobRunners = QueueTest.allJobRunners QueueTest.executeTest(spec) @@ -62,7 +62,7 @@ class HelloWorldQueueTest { def testHelloWorldWithPriority() { val spec = new QueueTestSpec spec.name = "HelloWorldWithPriority" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -jobPriority 100" spec.jobRunners = QueueTest.allJobRunners QueueTest.executeTest(spec) @@ -72,7 +72,7 @@ class HelloWorldQueueTest { def testHelloWorldWithLsfResource() { val spec = new QueueTestSpec spec.name = "HelloWorldWithLsfResource" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -jobResReq rusage[iodine_io=1] -jobResReq select[swp>0] -jobResReq order[swp]" spec.jobRunners = Seq("Lsf706") QueueTest.executeTest(spec) @@ -82,7 +82,7 @@ class HelloWorldQueueTest { def testHelloWorldWithLsfResourceAndMemoryLimit() { val spec = new QueueTestSpec spec.name = "HelloWorldWithLsfResourceAndMemoryLimit" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -memLimit 1.25 -jobResReq rusage[iodine_io=1] -jobResReq select[swp>0] -jobResReq order[swp]" spec.jobRunners = Seq("Lsf706") QueueTest.executeTest(spec) @@ -92,7 +92,7 @@ class HelloWorldQueueTest { def testHelloWorldWithLsfEnvironment() { val spec = new QueueTestSpec spec.name = "HelloWorldWithLsfEnvironment" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -jobEnv tv" spec.jobRunners = Seq("Lsf706") QueueTest.executeTest(spec) @@ -102,7 +102,7 @@ class HelloWorldQueueTest { def testHelloWorldWithGridEngineResource() { val spec = new QueueTestSpec spec.name = "HelloWorldWithGridEngineResource" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -jobResReq s_core=1000M" spec.jobRunners = Seq("GridEngine") QueueTest.executeTest(spec) @@ -112,7 +112,7 @@ class HelloWorldQueueTest { def testHelloWorldWithGridEngineResourceAndMemoryLimit() { val spec = new QueueTestSpec spec.name = "HelloWorldWithGridEngineResourceAndMemoryLimit" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -memLimit 1.25 -jobResReq s_core=1000M" spec.jobRunners = Seq("GridEngine") QueueTest.executeTest(spec) @@ -122,7 +122,7 @@ class HelloWorldQueueTest { def testHelloWorldWithGridEngineEnvironment() { val spec = new QueueTestSpec spec.name = "HelloWorldWithGridEngineEnvironment" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -jobEnv \"make 1\"" spec.jobRunners = Seq("GridEngine") QueueTest.executeTest(spec) @@ -133,7 +133,7 @@ class HelloWorldQueueTest { def testHelloWorldWithWalltime() { val spec = new QueueTestSpec spec.name = "HelloWorldWithWalltime" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -wallTime 100" spec.jobRunners = QueueTest.allJobRunners QueueTest.executeTest(spec) @@ -143,7 +143,7 @@ class HelloWorldQueueTest { def testHelloWorldWithLogDirectory() { val spec = new QueueTestSpec spec.name = "HelloWorldWithLogDirectory" - spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" + + spec.args = "-S public/scala/qscript/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala" + " -logDir pipelineLogDir" spec.jobRunners = QueueTest.allJobRunners spec.expectedFilePaths = Seq("pipelineLogDir/HelloWorld-1.out") diff --git a/public/gatk-queue/pom.xml b/public/gatk-queue/pom.xml index 10bf533b0..81c5a9053 100644 --- a/public/gatk-queue/pom.xml +++ b/public/gatk-queue/pom.xml @@ -3,27 +3,25 @@ 4.0.0 - org.broadinstitute.sting - sting-aggregator + org.broadinstitute.gatk + gatk-aggregator 3.2-SNAPSHOT ../.. - queue-framework + gatk-queue jar - Queue Framework + GATK Queue - ${project.basedir}/../.. - ${project.build.directory}/generated-sources/gatk-extensions - false - queue-package + ${project.basedir}/../.. + gatk-queue-package-distribution ${project.groupId} - gatk-framework + gatk-tools-public ${project.version} @@ -46,103 +44,18 @@ javax.mail mail - ${project.groupId} - gatk-queue-extgen - ${project.version} - runtime - - - - - ${project.groupId} - gatk-framework + gatk-tools-public ${project.version} test-jar test - - - org.testng - testng - test - - - - org.codehaus.mojo - exec-maven-plugin - - - generate-gatk-extensions - - exec - - generate-sources - - ${sting.generate-gatk-extensions.skipped} - java - - -classpath - - org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator - -l - WARN - -outDir - ${gatk.extensions.sources} - - - - - - - org.codehaus.mojo - build-helper-maven-plugin - - - add-gatk-extensions - - add-source - - generate-sources - - - ${gatk.extensions.sources} - - - - - - - org.apache.maven.plugins - maven-assembly-plugin - - - example-resources - ${sting.generate-resources.phase} - - - org.scala-tools maven-scala-plugin @@ -207,36 +120,12 @@ - protected + private-testdata - ${basedir}/../../protected/gatk-protected/pom.xml + ${basedir}/../../private/pom.xml - - - ${project.groupId} - gatk-protected - ${project.version} - true - - - - - private - - - ${basedir}/../../private/gatk-private/pom.xml - - - - - ${project.groupId} - gatk-private - ${project.version} - true - - 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 3e75755b2..e5e9dcb08 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue; +package org.broadinstitute.gatk.queue; /** - * Generates the Queue version in the StingText.properties by working around http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4492654 + * Generates the Queue version in the GATKText.properties by working around http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4492654 */ public class QueueVersion { } 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 27b97c6a3..755b69683 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 @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue; +package org.broadinstitute.gatk.queue; 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 88e57182e..297e10bb3 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 @@ -23,19 +23,19 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue +package org.broadinstitute.gatk.queue import java.io.File -import org.broadinstitute.sting.commandline._ -import org.broadinstitute.sting.queue.util._ -import org.broadinstitute.sting.queue.engine.{QStatusMessenger, QGraphSettings, QGraph} +import org.broadinstitute.gatk.utils.commandline._ +import org.broadinstitute.gatk.queue.util._ +import org.broadinstitute.gatk.queue.engine.{QStatusMessenger, QGraphSettings, QGraph} import collection.JavaConversions._ -import org.broadinstitute.sting.utils.classloader.PluginManager -import org.broadinstitute.sting.utils.exceptions.UserException -import org.broadinstitute.sting.utils.io.IOUtils -import org.broadinstitute.sting.utils.help.ApplicationDetails +import org.broadinstitute.gatk.utils.classloader.PluginManager +import org.broadinstitute.gatk.utils.exceptions.UserException +import org.broadinstitute.gatk.utils.io.IOUtils +import org.broadinstitute.gatk.utils.help.ApplicationDetails import java.util.{ResourceBundle, Arrays} -import org.broadinstitute.sting.utils.text.TextFormattingUtils +import org.broadinstitute.gatk.utils.text.TextFormattingUtils import org.apache.commons.io.FilenameUtils /** @@ -266,10 +266,10 @@ class QCommandLine extends CommandLineProgram with Logging { } private def getQueueVersion : String = { - val stingResources : ResourceBundle = TextFormattingUtils.loadResourceBundle("StingText") + val stingResources : ResourceBundle = TextFormattingUtils.loadResourceBundle("GATKText") - if ( stingResources.containsKey("org.broadinstitute.sting.queue.QueueVersion.version") ) { - stingResources.getString("org.broadinstitute.sting.queue.QueueVersion.version") + if ( stingResources.containsKey("org.broadinstitute.gatk.queue.QueueVersion.version") ) { + stingResources.getString("org.broadinstitute.gatk.queue.QueueVersion.version") } else { "" @@ -277,7 +277,7 @@ class QCommandLine extends CommandLineProgram with Logging { } private def getBuildTimestamp : String = { - val stingResources : ResourceBundle = TextFormattingUtils.loadResourceBundle("StingText") + val stingResources : ResourceBundle = TextFormattingUtils.loadResourceBundle("GATKText") if ( stingResources.containsKey("build.timestamp") ) { stingResources.getString("build.timestamp") 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 dcec18130..6df8b3c36 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue +package org.broadinstitute.gatk.queue import engine.QStatusMessenger import util.RemoteFileConverter 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 dafb61b5d..1ae41e950 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue +package org.broadinstitute.gatk.queue -import org.broadinstitute.sting.utils.exceptions.StingException +import org.broadinstitute.gatk.utils.exceptions.GATKException class QException(private val message: String, private val throwable: Throwable = null) - extends StingException(message, throwable) + extends GATKException(message, throwable) 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 afd1bbc19..f01044539 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 @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue +package org.broadinstitute.gatk.queue import engine.JobRunInfo -import org.broadinstitute.sting.queue.function.QFunction +import org.broadinstitute.gatk.queue.function.QFunction import annotation.target.field import util._ -import org.broadinstitute.sting.commandline.ArgumentSource +import org.broadinstitute.gatk.utils.commandline.ArgumentSource /** * Defines a Queue pipeline as a collection of CommandLineFunctions. @@ -38,21 +38,21 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon // Type aliases so users don't have to import type File = java.io.File - type CommandLineFunction = org.broadinstitute.sting.queue.function.CommandLineFunction - type InProcessFunction = org.broadinstitute.sting.queue.function.InProcessFunction - type ScatterGatherableFunction = org.broadinstitute.sting.queue.function.scattergather.ScatterGatherableFunction - type SimpleTextGatherFunction = org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction + type CommandLineFunction = org.broadinstitute.gatk.queue.function.CommandLineFunction + type InProcessFunction = org.broadinstitute.gatk.queue.function.InProcessFunction + type ScatterGatherableFunction = org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction + type SimpleTextGatherFunction = org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction // Make sure annotations can be used in class constructors but target the fields // ex: class MyClass(@Input var myVar: File) {} // This was implicitly enabled in 2.8.0-RC2 and then updated to this new syntax: // http://lampsvn.epfl.ch/trac/scala/ticket/3596 // http://lampsvn.epfl.ch/trac/scala/ticket/3421 - type Input = org.broadinstitute.sting.commandline.Input @field - type Output = org.broadinstitute.sting.commandline.Output @field - type Argument = org.broadinstitute.sting.commandline.Argument @field - type ArgumentCollection = org.broadinstitute.sting.commandline.ArgumentCollection @field - type Gather = org.broadinstitute.sting.commandline.Gather @field + type Input = org.broadinstitute.gatk.utils.commandline.Input @field + type Output = org.broadinstitute.gatk.utils.commandline.Output @field + type Argument = org.broadinstitute.gatk.utils.commandline.Argument @field + type ArgumentCollection = org.broadinstitute.gatk.utils.commandline.ArgumentCollection @field + type Gather = org.broadinstitute.gatk.utils.commandline.Gather @field /** * Default settings for QFunctions 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 80dd53302..8df12c25f 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 @@ -23,20 +23,20 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue +package org.broadinstitute.gatk.queue import scala.tools.nsc.{Global, Settings} import scala.tools.nsc.io.PlainFile -import org.broadinstitute.sting.queue.util.Logging +import org.broadinstitute.gatk.queue.util.Logging import collection.JavaConversions._ import java.io.File import scala.tools.nsc.reporters.AbstractReporter import java.lang.String import org.apache.log4j.Level -import org.broadinstitute.sting.queue.util.TextFormatUtils._ -import org.broadinstitute.sting.utils.classloader.JVMUtils +import org.broadinstitute.gatk.queue.util.TextFormatUtils._ +import org.broadinstitute.gatk.utils.classloader.JVMUtils import scala.reflect.internal.util.{FakePos, NoPosition, Position, StringOps} -import org.broadinstitute.sting.utils.exceptions.UserException +import org.broadinstitute.gatk.utils.exceptions.UserException /** * Plugin manager for QScripts which loads QScripts into the current class loader. 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 197d45e0a..86457fb49 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue +package org.broadinstitute.gatk.queue import java.io.File -import org.broadinstitute.sting.commandline.{ClassType, Argument} +import org.broadinstitute.gatk.utils.commandline.{ClassType, Argument} /** * Default settings settable on the command line and passed to CommandLineFunctions. 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 be812344d..a3b004ce6 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine -import org.broadinstitute.sting.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.function.CommandLineFunction /** * Creates and stops CommandLineJobRunners 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 ecc87c651..e5c2594b5 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine -import org.broadinstitute.sting.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.function.CommandLineFunction import java.io.File -import org.broadinstitute.sting.queue.util.Logging -import org.broadinstitute.sting.utils.io.IOUtils +import org.broadinstitute.gatk.queue.util.Logging +import org.broadinstitute.gatk.utils.io.IOUtils /** * Runs a command line function. 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 cefd0a0e3..3931c5f0c 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine -import org.broadinstitute.sting.utils.classloader.PluginManager +import org.broadinstitute.gatk.utils.classloader.PluginManager class CommandLinePluginManager extends PluginManager[CommandLineJobManager[CommandLineJobRunner]]( 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 8cf61c3d5..1b02f5dde 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine -import org.broadinstitute.sting.queue.function.QFunction +import org.broadinstitute.gatk.queue.function.QFunction import java.io.{StringWriter, PrintWriter} -import org.broadinstitute.sting.queue.util.Logging -import org.broadinstitute.sting.utils.io.IOUtils +import org.broadinstitute.gatk.queue.util.Logging +import org.broadinstitute.gatk.utils.io.IOUtils import org.apache.commons.io.FileUtils import org.apache.commons.lang.StringUtils 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 2f89c013f..aa7d06955 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine -import org.broadinstitute.sting.queue.function.InProcessFunction +import org.broadinstitute.gatk.queue.function.InProcessFunction class InProcessJobManager extends JobManager[InProcessFunction, InProcessRunner] { def runnerType = classOf[InProcessRunner] 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 941ebd156..bb8896d48 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine -import org.broadinstitute.sting.queue.function.InProcessFunction +import org.broadinstitute.gatk.queue.function.InProcessFunction import java.util.Date -import org.broadinstitute.sting.utils.Utils +import org.broadinstitute.gatk.utils.Utils import org.apache.commons.io.{IOUtils, FileUtils} import java.io.PrintStream 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 d6f313459..e8fb1f08d 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine -import org.broadinstitute.sting.queue.function.QFunction +import org.broadinstitute.gatk.queue.function.QFunction /** * Creates and stops JobRunners 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 348e93504..20a536e91 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine import java.text.SimpleDateFormat 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 f9d44a9ca..d7e4868e7 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine -import org.broadinstitute.sting.queue.function.QFunction +import org.broadinstitute.gatk.queue.function.QFunction /** * Base interface for job runners. 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 48102b6ea..af5160216 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine /** * Utility class to map a set of inputs to set of outputs. 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 4403cfe7c..d3f2f4ba6 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine /** * An edge in the QGraph 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 aab0059b1..7d09bf561 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine import org.jgrapht.traverse.TopologicalOrderIterator import org.jgrapht.graph.SimpleDirectedGraph @@ -32,14 +32,14 @@ import org.jgrapht.alg.CycleDetector import org.jgrapht.EdgeFactory import org.jgrapht.ext.DOTExporter import org.jgrapht.event.{TraversalListenerAdapter, EdgeTraversalEvent} -import org.broadinstitute.sting.queue.QException -import org.broadinstitute.sting.queue.function.{InProcessFunction, CommandLineFunction, QFunction} +import org.broadinstitute.gatk.queue.QException +import org.broadinstitute.gatk.queue.function.{InProcessFunction, CommandLineFunction, QFunction} import org.apache.commons.lang.StringUtils -import org.broadinstitute.sting.queue.util._ +import org.broadinstitute.gatk.queue.util._ import collection.immutable.{TreeSet, TreeMap} -import org.broadinstitute.sting.queue.function.scattergather.{ScatterFunction, CloneFunction, GatherFunction, ScatterGatherableFunction} +import org.broadinstitute.gatk.queue.function.scattergather.{ScatterFunction, CloneFunction, GatherFunction, ScatterGatherableFunction} import java.util.Date -import org.broadinstitute.sting.utils.Utils +import org.broadinstitute.gatk.utils.Utils import org.apache.commons.io.{FilenameUtils, FileUtils, IOUtils} import java.io.{OutputStreamWriter, File} @@ -136,7 +136,7 @@ class QGraph extends Logging { def run() { runningLock.synchronized { if (running) { - org.broadinstitute.sting.utils.io.IOUtils.checkTempDir(settings.qSettings.tempDirectory) + org.broadinstitute.gatk.utils.io.IOUtils.checkTempDir(settings.qSettings.tempDirectory) fillGraph() val isReady = numMissingValues == 0 @@ -1149,10 +1149,10 @@ class QGraph extends Logging { else settings.qSettings.runName + ".jobreport.txt" - val reportFile = org.broadinstitute.sting.utils.io.IOUtils.absolute(settings.qSettings.runDirectory, jobStringName) + val reportFile = org.broadinstitute.gatk.utils.io.IOUtils.absolute(settings.qSettings.runDirectory, jobStringName) val pdfFile = if ( settings.run ) - Some(org.broadinstitute.sting.utils.io.IOUtils.absolute(settings.qSettings.runDirectory, FilenameUtils.removeExtension(jobStringName) + ".pdf")) + Some(org.broadinstitute.gatk.utils.io.IOUtils.absolute(settings.qSettings.runDirectory, FilenameUtils.removeExtension(jobStringName) + ".pdf")) else None 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 f2929378e..49dace949 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine import java.io.File -import org.broadinstitute.sting.queue.QSettings -import org.broadinstitute.sting.queue.util.{EmailSettings, SystemUtils} -import org.broadinstitute.sting.commandline.{Advanced, ArgumentCollection, Argument} +import org.broadinstitute.gatk.queue.QSettings +import org.broadinstitute.gatk.queue.util.{EmailSettings, SystemUtils} +import org.broadinstitute.gatk.utils.commandline.{Advanced, ArgumentCollection, Argument} /** * Command line options for a QGraph. 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 7230c46fb..5751a723d 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine import java.io.File 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 dd17221e5..14e40821b 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine -import org.broadinstitute.sting.queue.util.RemoteFile +import org.broadinstitute.gatk.queue.util.RemoteFile /** * Plugin to sends QStatus messages 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 77e1170f8..93c9fde91 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine +package org.broadinstitute.gatk.queue.engine object RunnerStatus extends Enumeration { val PENDING = Value("pending") 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 8485fce1a..02cf34e85 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine.drmaa +package org.broadinstitute.gatk.queue.engine.drmaa -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.engine.CommandLineJobManager -import org.broadinstitute.sting.jna.drmaa.v1_0.JnaSessionFactory +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.engine.CommandLineJobManager +import org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSessionFactory import org.ggf.drmaa.Session /** 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 b405c91a2..aa19bfa26 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine.drmaa +package org.broadinstitute.gatk.queue.engine.drmaa -import org.broadinstitute.sting.queue.QException -import org.broadinstitute.sting.queue.util.{Logging,Retry} -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.engine.{RunnerStatus, CommandLineJobRunner} +import org.broadinstitute.gatk.queue.QException +import org.broadinstitute.gatk.queue.util.{Logging,Retry} +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.engine.{RunnerStatus, CommandLineJobRunner} import org.ggf.drmaa._ import java.util.{Date, Collections} 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 7418b602c..eb60cb324 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine.gridengine +package org.broadinstitute.gatk.queue.engine.gridengine -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.engine.drmaa.DrmaaJobManager +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobManager class GridEngineJobManager extends DrmaaJobManager { override def create(function: CommandLineFunction) = new GridEngineJobRunner(session, function) 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 7f55050de..7ca585e01 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine.gridengine +package org.broadinstitute.gatk.queue.engine.gridengine -import org.broadinstitute.sting.queue.util.Logging -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.engine.drmaa.DrmaaJobRunner +import org.broadinstitute.gatk.queue.util.Logging +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner import org.ggf.drmaa.Session /** 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 4cf4de955..dbe25366a 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine.lsf +package org.broadinstitute.gatk.queue.engine.lsf -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.engine.CommandLineJobManager +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.engine.CommandLineJobManager /** * Creates and stops Lsf706JobRunners 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 e9f141880..eeb82a333 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 @@ -23,16 +23,16 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine.lsf +package org.broadinstitute.gatk.queue.engine.lsf -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.util._ -import org.broadinstitute.sting.queue.QException -import org.broadinstitute.sting.jna.lsf.v7_0_6.{LibLsf, LibBat} -import org.broadinstitute.sting.utils.Utils -import org.broadinstitute.sting.jna.clibrary.LibC -import org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.{submitReply, submit} -import org.broadinstitute.sting.queue.engine.{RunnerStatus, CommandLineJobRunner} +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.util._ +import org.broadinstitute.gatk.queue.QException +import org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.{LibLsf, LibBat} +import org.broadinstitute.gatk.utils.Utils +import org.broadinstitute.gatk.utils.jna.clibrary.LibC +import org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.{submitReply, submit} +import org.broadinstitute.gatk.queue.engine.{RunnerStatus, CommandLineJobRunner} import java.util.regex.Pattern import java.lang.StringBuffer import java.util.Date 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 ac0185c61..fb68231d2 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine.pbsengine +package org.broadinstitute.gatk.queue.engine.pbsengine -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.engine.drmaa.DrmaaJobManager +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobManager class PbsEngineJobManager extends DrmaaJobManager { override def create(function: CommandLineFunction) = new PbsEngineJobRunner(session, function) 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 c2b2f8465..092152f3b 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine.pbsengine +package org.broadinstitute.gatk.queue.engine.pbsengine -import org.broadinstitute.sting.queue.util.Logging -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.engine.drmaa.DrmaaJobRunner +import org.broadinstitute.gatk.queue.util.Logging +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner import org.ggf.drmaa.Session /** 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 2720682a0..5645590e2 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine.shell +package org.broadinstitute.gatk.queue.engine.shell -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.engine.CommandLineJobManager +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.engine.CommandLineJobManager class ShellJobManager extends CommandLineJobManager[ShellJobRunner] { def runnerType = classOf[ShellJobRunner] 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 e3528f54f..327be225e 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 @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.engine.shell +package org.broadinstitute.gatk.queue.engine.shell -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.engine.{RunnerStatus, CommandLineJobRunner} +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.engine.{RunnerStatus, CommandLineJobRunner} import java.util.Date -import org.broadinstitute.sting.utils.Utils -import org.broadinstitute.sting.utils.runtime.{ProcessSettings, OutputStreamSettings, ProcessController} +import org.broadinstitute.gatk.utils.Utils +import org.broadinstitute.gatk.utils.runtime.{ProcessSettings, OutputStreamSettings, ProcessController} /** * Runs jobs one at a time locally 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 9bacca51a..e1cb7d037 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function +package org.broadinstitute.gatk.queue.function -import org.broadinstitute.sting.queue.util._ -import org.broadinstitute.sting.commandline.Argument +import org.broadinstitute.gatk.queue.util._ +import org.broadinstitute.gatk.utils.commandline.Argument /** * A command line that will be run in a pipeline. 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 9e39e3b20..5525eeb91 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function +package org.broadinstitute.gatk.queue.function import java.io.PrintStream 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 669c74fc4..80027a02d 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function +package org.broadinstitute.gatk.queue.function -import org.broadinstitute.sting.commandline.Argument -import org.broadinstitute.sting.utils.io.IOUtils +import org.broadinstitute.gatk.utils.commandline.Argument +import org.broadinstitute.gatk.utils.io.IOUtils import java.io.File /** 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 baf828900..c7450b1c0 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function +package org.broadinstitute.gatk.queue.function -import org.broadinstitute.sting.commandline.{Input, Output} +import org.broadinstitute.gatk.utils.commandline.{Input, Output} import java.io.{PrintWriter, File} import org.apache.commons.io.IOUtils 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 9208c04f7..f7e26718e 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 @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function +package org.broadinstitute.gatk.queue.function import java.io.File import java.lang.annotation.Annotation -import org.broadinstitute.sting.commandline._ -import org.broadinstitute.sting.queue.{QException, QSettings} +import org.broadinstitute.gatk.utils.commandline._ +import org.broadinstitute.gatk.queue.{QException, QSettings} import java.lang.IllegalStateException -import org.broadinstitute.sting.queue.util._ -import org.broadinstitute.sting.utils.io.IOUtils +import org.broadinstitute.gatk.queue.util._ +import org.broadinstitute.gatk.utils.io.IOUtils import scala.language.reflectiveCalls /** 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 982b4393a..9202c2aa2 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function +package org.broadinstitute.gatk.queue.function -import org.broadinstitute.sting.commandline.Argument +import org.broadinstitute.gatk.utils.commandline.Argument object RetryMemoryLimit { private val defaultRetryMemoryFunction: (Double => Double) = ( 2 * _ ) 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 5dae0adc2..ccc9dcfbe 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function.scattergather +package org.broadinstitute.gatk.queue.function.scattergather -import org.broadinstitute.sting.commandline.ArgumentSource -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.queue.util.ClassFieldCache +import org.broadinstitute.gatk.utils.commandline.ArgumentSource +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.util.ClassFieldCache /** * Shadow clones another command line function. 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 411b36d8d..b97cee157 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function.scattergather +package org.broadinstitute.gatk.queue.function.scattergather -import org.broadinstitute.sting.queue.function.InProcessFunction -import org.broadinstitute.sting.queue.QException -import org.broadinstitute.sting.commandline.Input +import org.broadinstitute.gatk.queue.function.InProcessFunction +import org.broadinstitute.gatk.queue.QException +import org.broadinstitute.gatk.utils.commandline.Input import org.apache.commons.io.FileUtils import java.io.File import collection.JavaConversions._ @@ -45,7 +45,7 @@ class ConcatenateLogsFunction extends InProcessFunction { override def shortDescription = analysisName + ": " + jobOutputFile.getName def run() { - val missing = org.broadinstitute.sting.utils.io.IOUtils.waitFor(logs, 120) + val missing = org.broadinstitute.gatk.utils.io.IOUtils.waitFor(logs, 120) if (!missing.isEmpty) throw new QException("Unable to find log: " + missing.mkString(", ")) logs.foreach(log => { 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 8157db8d8..704426524 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 @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function.scattergather +package org.broadinstitute.gatk.queue.function.scattergather import java.io.File -import org.broadinstitute.sting.commandline.{Input, Output} -import org.broadinstitute.sting.queue.function.QFunction -import org.broadinstitute.sting.queue.QException -import org.broadinstitute.sting.utils.io.IOUtils +import org.broadinstitute.gatk.utils.commandline.{Input, Output} +import org.broadinstitute.gatk.queue.function.QFunction +import org.broadinstitute.gatk.queue.QException +import org.broadinstitute.gatk.utils.io.IOUtils import collection.JavaConversions._ /** 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 7b7dea38a..4fcc19f90 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function.scattergather +package org.broadinstitute.gatk.queue.function.scattergather -import org.broadinstitute.sting.commandline.Gatherer -import org.broadinstitute.sting.queue.function.InProcessFunction +import org.broadinstitute.gatk.utils.commandline.Gatherer +import org.broadinstitute.gatk.queue.function.InProcessFunction import collection.JavaConversions._ /** 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 be69dfcd3..29f8c41c1 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function.scattergather +package org.broadinstitute.gatk.queue.function.scattergather import java.io.File -import org.broadinstitute.sting.commandline.Input -import org.broadinstitute.sting.queue.function.QFunction +import org.broadinstitute.gatk.utils.commandline.Input +import org.broadinstitute.gatk.queue.function.QFunction /** * Base class for Scatter functions. 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 67138eb75..50ad3cf9a 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 @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function.scattergather +package org.broadinstitute.gatk.queue.function.scattergather import java.io.File -import org.broadinstitute.sting.queue.util._ -import org.broadinstitute.sting.commandline.{Gatherer, Gather, ArgumentSource} -import org.broadinstitute.sting.queue.function.{QFunction, CommandLineFunction} -import org.broadinstitute.sting.queue.QException -import org.broadinstitute.sting.utils.io.IOUtils +import org.broadinstitute.gatk.queue.util._ +import org.broadinstitute.gatk.utils.commandline.{Gatherer, Gather, ArgumentSource} +import org.broadinstitute.gatk.queue.function.{QFunction, CommandLineFunction} +import org.broadinstitute.gatk.queue.QException +import org.broadinstitute.gatk.utils.io.IOUtils import collection.immutable.ListMap /** 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 b100f6834..2c6aa58d2 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function.scattergather +package org.broadinstitute.gatk.queue.function.scattergather -import org.broadinstitute.sting.queue.function.InProcessFunction -import org.broadinstitute.sting.queue.QException +import org.broadinstitute.gatk.queue.function.InProcessFunction +import org.broadinstitute.gatk.queue.QException import java.io.PrintWriter import org.apache.commons.io.{LineIterator, IOUtils, FileUtils} 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 733b66e05..e3b936f0b 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.library.clf.vcf +package org.broadinstitute.gatk.queue.library.clf.vcf import java.io.File -import org.broadinstitute.sting.commandline.{Argument, Output, Input} -import org.broadinstitute.sting.queue.function.CommandLineFunction +import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input} +import org.broadinstitute.gatk.queue.function.CommandLineFunction class VCFExtractIntervals(inVCF: File, outList: File, passOnly: Boolean ) extends CommandLineFunction { def this(vcf: File, list: File ) = this(vcf,list,false) 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 261346104..799061abc 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 @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.library.clf.vcf +package org.broadinstitute.gatk.queue.library.clf.vcf import java.io.File import collection.JavaConversions._ -import org.broadinstitute.sting.commandline._ -import org.broadinstitute.sting.queue.function.CommandLineFunction -import org.broadinstitute.sting.utils.text.XReadLines +import org.broadinstitute.gatk.utils.commandline._ +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.utils.text.XReadLines class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extends CommandLineFunction { @Input(doc="input VCF from which to extract samples") var inputVCF : File = inVCF 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 4b648204a..0ee38e99b 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.library.ipf +package org.broadinstitute.gatk.queue.library.ipf import collection.JavaConversions._ -import org.broadinstitute.sting.queue.function.InProcessFunction -import org.broadinstitute.sting.commandline._ -import org.broadinstitute.sting.utils.text.XReadLines +import org.broadinstitute.gatk.queue.function.InProcessFunction +import org.broadinstitute.gatk.utils.commandline._ +import org.broadinstitute.gatk.utils.text.XReadLines import java.io.{PrintStream, PrintWriter, File} import collection.immutable.HashMap 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 10b73829f..8abcf5bc0 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.library.ipf.vcf +package org.broadinstitute.gatk.queue.library.ipf.vcf import collection.JavaConversions._ -import org.broadinstitute.sting.queue.function.InProcessFunction -import org.broadinstitute.sting.commandline._ -import org.broadinstitute.sting.utils.text.XReadLines +import org.broadinstitute.gatk.queue.function.InProcessFunction +import org.broadinstitute.gatk.utils.commandline._ +import org.broadinstitute.gatk.utils.text.XReadLines import java.io.{PrintStream, PrintWriter, File} class VCFExtractIntervals(inVCF: File, outList: File, useFilterSites: Boolean) extends InProcessFunction { 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 ddff95f21..99571e9f2 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.library.ipf.vcf +package org.broadinstitute.gatk.queue.library.ipf.vcf -import org.broadinstitute.sting.queue.function.InProcessFunction -import org.broadinstitute.sting.utils.text.XReadLines +import org.broadinstitute.gatk.queue.function.InProcessFunction +import org.broadinstitute.gatk.utils.text.XReadLines import collection.JavaConversions._ -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import java.io.{PrintWriter, PrintStream, File} class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extends InProcessFunction { 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 3ea88bd13..5bd25bf55 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 @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.library.ipf.vcf +package org.broadinstitute.gatk.queue.library.ipf.vcf import collection.JavaConversions._ -import org.broadinstitute.sting.queue.function.InProcessFunction -import org.broadinstitute.sting.commandline._ -import org.broadinstitute.sting.utils.text.XReadLines +import org.broadinstitute.gatk.queue.function.InProcessFunction +import org.broadinstitute.gatk.utils.commandline._ +import org.broadinstitute.gatk.utils.text.XReadLines import java.io.{PrintStream, PrintWriter, File} 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 6c17ff47e..b3093c8f2 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 @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.library.ipf.vcf +package org.broadinstitute.gatk.queue.library.ipf.vcf import collection.JavaConversions._ -import org.broadinstitute.sting.queue.function.InProcessFunction -import org.broadinstitute.sting.commandline._ -import org.broadinstitute.sting.utils.text.XReadLines +import org.broadinstitute.gatk.queue.function.InProcessFunction +import org.broadinstitute.gatk.utils.commandline._ +import org.broadinstitute.gatk.utils.text.XReadLines import java.io.{PrintStream, PrintWriter, File} import htsjdk.samtools.{SAMSequenceRecord, SAMSequenceDictionary} -import org.broadinstitute.sting.utils.{GenomeLocParser, GenomeLoc} +import org.broadinstitute.gatk.utils.{GenomeLocParser, GenomeLoc} class VCFSimpleMerge extends InProcessFunction { @Input(doc="VCFs to be merged") var vcfs: List[File] = Nil 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 771a9a050..82b8ca572 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util -import org.broadinstitute.sting.commandline._ +import org.broadinstitute.gatk.utils.commandline._ import scala.Some -import org.broadinstitute.sting.queue.QException +import org.broadinstitute.gatk.queue.QException import collection.JavaConversions._ import java.io.File 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 ec1eb5774..5c0be04a0 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util /** * Utilities that try to deeply apply operations to collections, specifically Traversable and Option. 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 96a5973be..e38183af6 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import org.apache.commons.mail.{MultiPartEmail, EmailAttachment} import java.io.{IOException, FileReader, File} 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 359d272ba..d31541060 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import java.io.File -import org.broadinstitute.sting.commandline.Argument +import org.broadinstitute.gatk.utils.commandline.Argument /** * Email server settings. 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 0e691d937..3a83a2f50 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import org.apache.log4j._ import java.lang.{Throwable, String} 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 cb7b95b76..edaf80229 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import scala.language.implicitConversions 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 29177759b..be5a17f43 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 @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util -import org.broadinstitute.sting.queue.function.QFunction -import org.broadinstitute.sting.gatk.report.GATKReportTable -import org.broadinstitute.sting.queue.engine.JobRunInfo +import org.broadinstitute.gatk.queue.function.QFunction +import org.broadinstitute.gatk.engine.report.GATKReportTable +import org.broadinstitute.gatk.queue.engine.JobRunInfo /** * A mixin to add Job info to the class 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 480984941..b3b0b33c8 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 @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import java.io.{PrintStream, File} -import org.broadinstitute.sting.utils.io.{Resource} -import org.broadinstitute.sting.queue.engine.{JobRunInfo, QGraph} -import org.broadinstitute.sting.queue.function.QFunction -import org.broadinstitute.sting.utils.R.{RScriptLibrary, RScriptExecutor} -import org.broadinstitute.sting.gatk.report.{GATKReportTable, GATKReport} -import org.broadinstitute.sting.utils.exceptions.UserException +import org.broadinstitute.gatk.utils.io.{Resource} +import org.broadinstitute.gatk.queue.engine.{JobRunInfo, QGraph} +import org.broadinstitute.gatk.queue.function.QFunction +import org.broadinstitute.gatk.utils.R.{RScriptLibrary, RScriptExecutor} +import org.broadinstitute.gatk.engine.report.{GATKReportTable, GATKReport} +import org.broadinstitute.gatk.utils.exceptions.UserException import org.apache.commons.io.{FileUtils, IOUtils} /** 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 cad16a6df..3fbce2292 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import java.io.File import io.Source._ 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 9594e7b2a..d172e976a 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 @@ -23,16 +23,16 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util -import org.broadinstitute.sting.queue.QException +import org.broadinstitute.gatk.queue.QException import java.lang.annotation.Annotation import java.lang.reflect.{ParameterizedType, Field} -import org.broadinstitute.sting.commandline.ClassType -import org.broadinstitute.sting.utils.classloader.JVMUtils +import org.broadinstitute.gatk.utils.commandline.ClassType +import org.broadinstitute.gatk.utils.classloader.JVMUtils /** - * A collection of scala extensions to the Sting JVMUtils. + * A collection of scala extensions to the GATK JVMUtils. */ object ReflectionUtils { @@ -158,7 +158,7 @@ object ReflectionUtils { * @return The array of classes that are in the collection type, or None if the type cannot be found. */ private def getGenericTypes(field: Field): Option[Array[Class[_]]] = { - // TODO: Refactor: based on java code in org.broadinstitute.sting.commandline.ArgumentTypeDescriptor + // TODO: Refactor: based on java code in org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor // If this is a parameterized collection, find the contained type. If blow up if only one type exists. if (hasAnnotation(field, classOf[ClassType])) { Some(Array(getAnnotation(field, classOf[ClassType]).value)) 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 23a99b586..141081385 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 @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import java.io.File -import org.broadinstitute.sting.utils.io.FileExtension +import org.broadinstitute.gatk.utils.io.FileExtension import java.util.Date import java.net.URL 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 b487d3bbb..b38b27a5a 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import java.io.File 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 5b9e42a1e..8d1c1cfca 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util -import org.broadinstitute.sting.queue.util.TextFormatUtils._ +import org.broadinstitute.gatk.queue.util.TextFormatUtils._ /** * Utilities for retrying a function and waiting a number of minutes. 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 9d900cb44..ffd69cc7f 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 @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util -import org.broadinstitute.sting.queue.QException +import org.broadinstitute.gatk.queue.QException /** * Thrown after giving up on retrying. 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 735c3ca36..80ab0683b 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 @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import collection.JavaConversions._ -import org.broadinstitute.sting.queue.QException +import org.broadinstitute.gatk.queue.QException import java.lang.Class -import org.broadinstitute.sting.commandline.{ArgumentMatches, ArgumentSource, ArgumentTypeDescriptor, ParsingEngine} -import org.broadinstitute.sting.utils.exceptions.UserException +import org.broadinstitute.gatk.utils.commandline.{ArgumentMatches, ArgumentSource, ArgumentTypeDescriptor, ParsingEngine} +import org.broadinstitute.gatk.utils.exceptions.UserException import java.lang.reflect.Type /** 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 3907ef909..02d767a6d 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import java.lang.IllegalArgumentException 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 ff99cb346..ee21380ee 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import java.io.{Serializable, File} import scala.language.implicitConversions 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 ca6aeb77b..35b047a93 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import java.net.InetAddress import java.io.File 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 c3760ad62..c776dd531 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util object TextFormatUtils { /** 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 f500be0fb..9de4b288f 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import java.io.File import org.apache.commons.io.FilenameUtils 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 2e94063e5..351fb71e0 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.function +package org.broadinstitute.gatk.queue.function import org.testng.Assert import org.testng.annotations.{DataProvider, Test} 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 9c32a40be..c5bd554c1 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 @@ -23,19 +23,19 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.pipeline +package org.broadinstitute.gatk.queue.pipeline -import org.broadinstitute.sting.utils.Utils +import org.broadinstitute.gatk.utils.Utils import org.testng.Assert -import org.broadinstitute.sting.commandline.CommandLineProgram +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram import java.util.Date import java.text.SimpleDateFormat -import org.broadinstitute.sting.BaseTest -import org.broadinstitute.sting.MD5DB -import org.broadinstitute.sting.queue.{QScript, QCommandLine} -import org.broadinstitute.sting.queue.util.Logging +import org.broadinstitute.gatk.utils.BaseTest +import org.broadinstitute.gatk.utils.MD5DB +import org.broadinstitute.gatk.queue.{QScript, QCommandLine} +import org.broadinstitute.gatk.queue.util.Logging import java.io.{FilenameFilter, File} -import org.broadinstitute.sting.gatk.report.GATKReport +import org.broadinstitute.gatk.engine.report.GATKReport import org.apache.commons.io.FileUtils import org.apache.commons.io.filefilter.WildcardFileFilter 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 2295d7185..764449cff 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.pipeline +package org.broadinstitute.gatk.queue.pipeline /** * Data validations to evaluate on a GATKReport. 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 e05350bce..4fdcb08da 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.pipeline +package org.broadinstitute.gatk.queue.pipeline class QueueTestSpec(var name: String = null) { 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 ce3bb902d..944cc851a 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import org.testng.annotations.Test import org.testng.Assert 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 5ee02b8bc..160e04036 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import org.testng.annotations.Test import java.io.File 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 2c59c315c..2fd78e363 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.queue.util +package org.broadinstitute.gatk.queue.util import org.testng.annotations.Test import org.testng.Assert diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml index 38078312f..b0adc4cc9 100644 --- a/public/gatk-root/pom.xml +++ b/public/gatk-root/pom.xml @@ -3,18 +3,18 @@ 4.0.0 - org.broadinstitute.sting - sting-root + org.broadinstitute.gatk + gatk-root 3.2-SNAPSHOT pom - Sting Root + GATK Root 3.0.4 @@ -27,20 +27,21 @@ 1.7 1.7 yyyy/MM/dd HH:mm:ss - ${project.basedir}/../.. - true - ${sting.committests.skipped} - ${sting.committests.skipped} - ${sting.committests.skipped} - true - true - false + ${project.basedir}/../.. + true + ${gatk.committests.skipped} + ${gatk.committests.skipped} + ${gatk.committests.skipped} + true + true + false 1g 4g 4 50 10 -Xmx${test.maxmemory} -XX:+UseParallelOldGC -XX:ParallelGCThreads=${java.gc.threads} -XX:GCTimeLimit=${java.gc.timeLimit} -XX:GCHeapFreeLimit=${java.gc.heapFreeLimit} + org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter 1.112.1452 @@ -70,6 +71,10 @@ htsjdk ${htsjdk.version} + org.testng testng @@ -239,6 +244,24 @@ 6.8 test + + org.uncommons + reportng + 1.1.2 + test + + + org.testng + testng + + + + + com.google.inject + guice + 3.0 + test + com.google.caliper caliper @@ -258,6 +281,25 @@ + + + org.testng + testng + test + + + + org.uncommons + reportng + test + + + com.google.inject + guice + test + + + @@ -353,6 +395,10 @@ usedefaultlisteners false + + listener + ${test.listeners} + diff @@ -373,7 +419,7 @@ - ${sting.unittests.skipped} + ${gatk.unittests.skipped} ${project.build.directory}/surefire-reports/unit/${test} **/*UnitTest.class @@ -399,12 +445,16 @@ usedefaultlisteners false + + listener + ${test.listeners} + diff true - ${sting.queuetests.run} + ${gatk.queuetests.run} ${java.io.tmpdir} @@ -418,7 +468,7 @@ - ${sting.integrationtests.skipped} + ${gatk.integrationtests.skipped} ${project.build.directory}/failsafe-reports/integration/${it.test} ${project.build.directory}/failsafe-reports/integration/failsafe-summary-${it.test}.xml @@ -435,9 +485,9 @@ - ${sting.queuetests.skipped} - ${project.build.directory}/failsafe-reports/queuetest/${it.test} - ${project.build.directory}/failsafe-reports/queuetest/failsafe-summary-${it.test}.xml + ${gatk.queuetests.skipped} + ${project.build.directory}/failsafe-reports/queue/${it.test} + ${project.build.directory}/failsafe-reports/queue/failsafe-summary-${it.test}.xml **/*QueueTest.class @@ -451,7 +501,7 @@ - ${sting.largescaletests.skipped} + ${gatk.largescaletests.skipped} ${project.build.directory}/failsafe-reports/largescale/${it.test} ${project.build.directory}/failsafe-reports/largescale/failsafe-summary-${it.test}.xml @@ -467,7 +517,7 @@ - ${sting.knowledgebasetests.skipped} + ${gatk.knowledgebasetests.skipped} ${project.build.directory}/failsafe-reports/knowledgebasetests/${it.test} ${project.build.directory}/failsafe-reports/knowledgebasetests/failsafe-summary-${it.test}.xml @@ -609,9 +659,9 @@ - sting.public.repo.local - Sting Public Local Repository - file:${sting.basedir}/public/repo + gatk.public.repo.local + GATK Public Local Repository + file:${gatk.basedir}/public/repo diff --git a/public/gatk-tools-public/pom.xml b/public/gatk-tools-public/pom.xml index de7e2a477..92d63de48 100644 --- a/public/gatk-tools-public/pom.xml +++ b/public/gatk-tools-public/pom.xml @@ -3,33 +3,28 @@ 4.0.0 - org.broadinstitute.sting - sting-aggregator + org.broadinstitute.gatk + gatk-aggregator 3.2-SNAPSHOT ../.. - gatk-framework + gatk-tools-public jar - GATK Framework + GATK Tools Public - ${project.basedir}/../.. - gatk-package + ${project.basedir}/../.. + gatk-package-distribution ${project.groupId} - sting-utils + gatk-engine ${project.version} - - org.testng - testng - test - com.google.caliper caliper @@ -39,16 +34,6 @@ - - org.apache.maven.plugins - maven-assembly-plugin - - - example-resources - ${sting.generate-resources.phase} - - - org.apache.maven.plugins maven-resources-plugin @@ -95,10 +80,10 @@ - private + private-testdata - ${basedir}/../../private/gatk-private/pom.xml + ${basedir}/../../private/pom.xml diff --git a/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java b/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java index b68cd499e..c2a5e8042 100644 --- a/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java +++ b/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java @@ -26,7 +26,7 @@ package htsjdk.samtools; import htsjdk.samtools.util.PeekableIterator; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.ArrayList; import java.util.Arrays; @@ -151,7 +151,7 @@ public class GATKBAMFileSpan extends BAMFileSpan { List chunks = getChunks(); for ( int i = 1; i < chunks.size(); i++ ) { if ( chunks.get(i).getChunkStart() < chunks.get(i-1).getChunkEnd() ) { - throw new ReviewedStingException(String.format("Chunk list is unsorted; chunk %s is before chunk %s", chunks.get(i-1), chunks.get(i))); + throw new ReviewedGATKException(String.format("Chunk list is unsorted; chunk %s is before chunk %s", chunks.get(i-1), chunks.get(i))); } } diff --git a/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKChunk.java b/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKChunk.java index 6d695f43c..aed7aecde 100644 --- a/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKChunk.java +++ b/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKChunk.java @@ -33,7 +33,7 @@ package htsjdk.samtools; public class GATKChunk extends Chunk { /** * The average ratio of compressed block size / uncompressed block size, computed empirically - * using the output of org.broadinstitute.sting.gatk.datasources.reads.utilities.PrintBGZFBounds. + * using the output of org.broadinstitute.gatk.engine.datasources.reads.utilities.PrintBGZFBounds. */ private static final double AVERAGE_BAM_COMPRESSION_RATIO = 0.39; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java index 86ecaffe0..b8221bb16 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java @@ -23,24 +23,24 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk; +package org.broadinstitute.gatk.engine; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor; -import org.broadinstitute.sting.commandline.CommandLineProgram; -import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; -import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; -import org.broadinstitute.sting.gatk.filters.ReadFilter; -import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor; -import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; -import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor; -import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; -import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.crypt.CryptUtils; -import org.broadinstitute.sting.utils.crypt.GATKKey; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.text.ListFileUtils; +import org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; +import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; +import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; +import org.broadinstitute.gatk.engine.filters.ReadFilter; +import org.broadinstitute.gatk.engine.io.stubs.OutputStreamArgumentTypeDescriptor; +import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterArgumentTypeDescriptor; +import org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor; +import org.broadinstitute.gatk.engine.phonehome.GATKRunReport; +import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.crypt.CryptUtils; +import org.broadinstitute.gatk.utils.crypt.GATKKey; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.text.ListFileUtils; import java.security.PublicKey; import java.util.ArrayList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java index 237366ae7..f88c413bb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java @@ -23,21 +23,21 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk; +package org.broadinstitute.gatk.engine; import picard.PicardException; import htsjdk.samtools.SAMException; import htsjdk.tribble.TribbleException; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.commandline.CommandLineProgram; -import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; -import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; -import org.broadinstitute.sting.gatk.walkers.Attribution; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.*; -import org.broadinstitute.sting.utils.text.TextFormattingUtils; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; +import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; +import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager; +import org.broadinstitute.gatk.engine.walkers.Attribution; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.*; +import org.broadinstitute.gatk.utils.text.TextFormattingUtils; import java.util.*; @@ -113,7 +113,7 @@ public class CommandLineGATK extends CommandLineExecutable { // lazy loaded, so they aren't caught elsewhere and made into User Exceptions exitSystemWithUserError(e); } catch(PicardException e) { - // TODO: Should Picard exceptions be, in general, UserExceptions or ReviewedStingExceptions? + // TODO: Should Picard exceptions be, in general, UserExceptions or ReviewedGATKExceptions? exitSystemWithError(e); } catch (SAMException e) { checkForMaskedUserErrors(e); @@ -179,12 +179,12 @@ public class CommandLineGATK extends CommandLineExecutable { } public static String getVersionNumber() { - ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText"); - return headerInfo.containsKey("org.broadinstitute.sting.gatk.version") ? headerInfo.getString("org.broadinstitute.sting.gatk.version") : ""; + ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText"); + return headerInfo.containsKey("org.broadinstitute.gatk.tools.version") ? headerInfo.getString("org.broadinstitute.gatk.tools.version") : ""; } public static String getBuildTime() { - ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText"); + ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText"); return headerInfo.containsKey("build.timestamp") ? headerInfo.getString("build.timestamp") : ""; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java index 86ee1ec29..8e5ae61fb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk; +package org.broadinstitute.gatk.engine; import com.google.java.contract.Ensures; import htsjdk.samtools.reference.IndexedFastaSequenceFile; @@ -32,38 +32,38 @@ import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; -import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; -import org.broadinstitute.sting.gatk.datasources.reads.*; -import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod; -import org.broadinstitute.sting.gatk.executive.MicroScheduler; -import org.broadinstitute.sting.gatk.filters.FilterManager; -import org.broadinstitute.sting.gatk.filters.ReadFilter; -import org.broadinstitute.sting.gatk.filters.ReadGroupBlackListFilter; -import org.broadinstitute.sting.gatk.io.OutputTracker; -import org.broadinstitute.sting.gatk.io.stubs.Stub; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; -import org.broadinstitute.sting.gatk.iterators.ReadTransformersMode; -import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; -import org.broadinstitute.sting.gatk.refdata.tracks.IndexDictionaryUtils; -import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder; -import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; -import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.gatk.samples.SampleDB; -import org.broadinstitute.sting.gatk.samples.SampleDBBuilder; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.sting.utils.progressmeter.ProgressMeter; -import org.broadinstitute.sting.utils.recalibration.BQSRArgumentSet; -import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; +import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.engine.datasources.reads.*; +import org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.engine.executive.MicroScheduler; +import org.broadinstitute.gatk.engine.filters.FilterManager; +import org.broadinstitute.gatk.engine.filters.ReadFilter; +import org.broadinstitute.gatk.engine.filters.ReadGroupBlackListFilter; +import org.broadinstitute.gatk.engine.io.OutputTracker; +import org.broadinstitute.gatk.engine.io.stubs.Stub; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.iterators.ReadTransformersMode; +import org.broadinstitute.gatk.engine.phonehome.GATKRunReport; +import org.broadinstitute.gatk.engine.refdata.tracks.IndexDictionaryUtils; +import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; +import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; +import org.broadinstitute.gatk.engine.samples.SampleDB; +import org.broadinstitute.gatk.engine.samples.SampleDBBuilder; +import org.broadinstitute.gatk.utils.*; +import org.broadinstitute.gatk.utils.classloader.PluginManager; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.interval.IntervalUtils; +import org.broadinstitute.gatk.utils.progressmeter.ProgressMeter; +import org.broadinstitute.gatk.utils.recalibration.BQSRArgumentSet; +import org.broadinstitute.gatk.utils.text.XReadLines; +import org.broadinstitute.gatk.utils.threading.ThreadEfficiencyMonitor; import htsjdk.variant.vcf.VCFConstants; import java.io.File; @@ -71,8 +71,8 @@ import java.io.FileNotFoundException; import java.util.*; import java.util.concurrent.TimeUnit; -import static org.broadinstitute.sting.utils.DeprecatedToolChecks.getWalkerDeprecationInfo; -import static org.broadinstitute.sting.utils.DeprecatedToolChecks.isDeprecatedWalker; +import static org.broadinstitute.gatk.utils.DeprecatedToolChecks.getWalkerDeprecationInfo; +import static org.broadinstitute.gatk.utils.DeprecatedToolChecks.isDeprecatedWalker; /** * A GenomeAnalysisEngine that runs a specified walker. @@ -261,12 +261,12 @@ public class GenomeAnalysisEngine { // validate our parameters if (args == null) { - throw new ReviewedStingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null."); + throw new ReviewedGATKException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null."); } // validate our parameters if (this.walker == null) - throw new ReviewedStingException("The walker passed to GenomeAnalysisEngine can not be null."); + throw new ReviewedGATKException("The walker passed to GenomeAnalysisEngine can not be null."); if (args.nonDeterministicRandomSeed) resetRandomGenerator(System.currentTimeMillis()); @@ -424,7 +424,7 @@ public class GenomeAnalysisEngine { protected void setReadTransformers(final List readTransformers) { if ( readTransformers == null ) - throw new ReviewedStingException("read transformers cannot be null"); + throw new ReviewedGATKException("read transformers cannot be null"); // sort them in priority order Collections.sort(readTransformers, new ReadTransformer.ReadTransformerComparator()); @@ -632,7 +632,7 @@ public class GenomeAnalysisEngine { return readsDataSource.createShardIteratorOverIntervals(intervals, new ReadShardBalancer()); } else - throw new ReviewedStingException("Unable to determine walker type for walker " + walker.getClass().getName()); + throw new ReviewedGATKException("Unable to determine walker type for walker " + walker.getClass().getName()); } else { // TODO -- Determine what the ideal shard size should be here. Matt suggested that a multiple of 16K might work well diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java index b4f12b796..86d19269a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk; +package org.broadinstitute.gatk.engine; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileReader; -import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; -import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; -import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod; -import org.broadinstitute.sting.gatk.filters.ReadFilter; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; +import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.engine.filters.ReadFilter; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import java.util.Collection; import java.util.List; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java index 6dfb2c2a5..fb9d48903 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java @@ -23,20 +23,20 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk; +package org.broadinstitute.gatk.engine; -import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.downsampling.DownsampleType; -import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod; -import org.broadinstitute.sting.gatk.filters.FilterManager; -import org.broadinstitute.sting.gatk.filters.ReadFilter; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet; -import org.broadinstitute.sting.utils.text.TextFormattingUtils; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.commandline.Hidden; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.engine.filters.FilterManager; +import org.broadinstitute.gatk.engine.filters.ReadFilter; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.utils.classloader.PluginManager; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.help.ResourceBundleExtractorDoclet; +import org.broadinstitute.gatk.utils.text.TextFormattingUtils; import java.lang.annotation.Annotation; import java.util.*; @@ -53,7 +53,7 @@ public class WalkerManager extends PluginManager { public WalkerManager() { super(Walker.class,"walker",""); - helpText = TextFormattingUtils.loadResourceBundle("StingText"); + helpText = TextFormattingUtils.loadResourceBundle("GATKText"); } /** @@ -161,7 +161,7 @@ public class WalkerManager extends PluginManager { public static DataSource getWalkerDataSource(Class walkerClass) { By byDataSource = walkerClass.getAnnotation(By.class); if( byDataSource == null ) - throw new ReviewedStingException("Unable to find By annotation for walker class " + walkerClass.getName()); + throw new ReviewedGATKException("Unable to find By annotation for walker class " + walkerClass.getName()); return byDataSource.value(); } @@ -368,7 +368,7 @@ public class WalkerManager extends PluginManager { private static Requires getWalkerRequirements(Class walkerClass) { Requires requiresDataSource = walkerClass.getAnnotation(Requires.class); if( requiresDataSource == null ) - throw new ReviewedStingException( "Unable to find data types required by walker class " + walkerClass.getName()); + throw new ReviewedGATKException( "Unable to find data types required by walker class " + walkerClass.getName()); return requiresDataSource; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java index b171b5f49..e9622c931 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment; +package org.broadinstitute.gatk.engine.alignment; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java index 1db842045..02bc06fa0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment; +package org.broadinstitute.gatk.engine.alignment; import htsjdk.samtools.*; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; /** * Represents an alignment of a read to a site in the reference genome. @@ -214,7 +214,7 @@ public class Alignment { read = (SAMRecord)unmappedRead.clone(); } catch(CloneNotSupportedException ex) { - throw new ReviewedStingException("Unable to create aligned read from template."); + throw new ReviewedGATKException("Unable to create aligned read from template."); } if(newSAMHeader != null) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/CheckAlignment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/CheckAlignment.java index d313f35ce..5996418ac 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/CheckAlignment.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/CheckAlignment.java @@ -23,21 +23,21 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment; +package org.broadinstitute.gatk.engine.alignment; -import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; -import org.broadinstitute.sting.alignment.bwa.BWTFiles; -import org.broadinstitute.sting.alignment.bwa.c.BWACAligner; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.alignment.bwa.BWAConfiguration; +import org.broadinstitute.gatk.engine.alignment.bwa.BWTFiles; +import org.broadinstitute.gatk.engine.alignment.bwa.c.BWACAligner; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.ReadWalker; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Iterator; @@ -130,7 +130,7 @@ public class CheckAlignment extends ReadWalker { logger.error(String.format(" Mapping quality: %s%n", alignmentsByScore[i].getMappingQuality())); } } - throw new ReviewedStingException(String.format("Read %s mismatches!", read.getReadName())); + throw new ReviewedGATKException(String.format("Read %s mismatches!", read.getReadName())); } return 1; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java index 47948bf2f..2668b8ce7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa; +package org.broadinstitute.gatk.engine.alignment.bwa; -import org.broadinstitute.sting.alignment.Aligner; +import org.broadinstitute.gatk.engine.alignment.Aligner; /** * Align reads using BWA. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java index 757749e7d..b533a0d33 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa; +package org.broadinstitute.gatk.engine.alignment.bwa; /** * Configuration for the BWA/C aligner. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java index 58ee44645..16cc4adac 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa; +package org.broadinstitute.gatk.engine.alignment.bwa; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import htsjdk.samtools.util.StringUtil; -import org.broadinstitute.sting.alignment.reference.bwt.*; -import org.broadinstitute.sting.alignment.reference.packing.PackUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.alignment.reference.bwt.*; +import org.broadinstitute.gatk.engine.alignment.reference.packing.PackUtils; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.File; import java.io.IOException; @@ -94,7 +94,7 @@ public class BWTFiles { */ public BWTFiles(String prefix) { if(prefix == null) - throw new ReviewedStingException("Prefix must not be null."); + throw new ReviewedGATKException("Prefix must not be null."); annFile = new File(prefix + ".ann"); ambFile = new File(prefix + ".amb"); pacFile = new File(prefix + ".pac"); @@ -153,7 +153,7 @@ public class BWTFiles { success &= reverseSAFile.delete(); if(!success) - throw new ReviewedStingException("Unable to clean up autogenerated representation"); + throw new ReviewedGATKException("Unable to clean up autogenerated representation"); } } @@ -201,7 +201,7 @@ public class BWTFiles { writeEncodedReferenceSequence(reverseReferenceSequence,rpacFile,rbwtFile,rsaFile); } catch(IOException ex) { - throw new ReviewedStingException("Unable to write autogenerated reference sequence to temporary files"); + throw new ReviewedGATKException("Unable to write autogenerated reference sequence to temporary files"); } // Make sure that, at the very least, all temporary files are deleted on exit. @@ -247,13 +247,13 @@ public class BWTFiles { * Convert the given reference sequence into a form suitable for building into * on-the-fly sequences. * @param referenceSequence The reference sequence to normalize. - * @throws org.broadinstitute.sting.utils.exceptions.ReviewedStingException if normalized sequence cannot be generated. + * @throws org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException if normalized sequence cannot be generated. */ private static void normalizeReferenceSequence(byte[] referenceSequence) { StringUtil.toUpperCase(referenceSequence); for(byte base: referenceSequence) { if(base != 'A' && base != 'C' && base != 'G' && base != 'T') - throw new ReviewedStingException(String.format("Base type %c is not supported when building references on-the-fly",(char)base)); + throw new ReviewedGATKException(String.format("Base type %c is not supported when building references on-the-fly",(char)base)); } } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWACAligner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWACAligner.java index d09e7f038..892dbebcc 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWACAligner.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWACAligner.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa.c; +package org.broadinstitute.gatk.engine.alignment.bwa.c; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.alignment.Alignment; -import org.broadinstitute.sting.alignment.bwa.BWAAligner; -import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; -import org.broadinstitute.sting.alignment.bwa.BWTFiles; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.alignment.Alignment; +import org.broadinstitute.gatk.engine.alignment.bwa.BWAAligner; +import org.broadinstitute.gatk.engine.alignment.bwa.BWAConfiguration; +import org.broadinstitute.gatk.engine.alignment.bwa.BWTFiles; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.Arrays; import java.util.Iterator; @@ -55,15 +55,15 @@ public class BWACAligner extends BWAAligner { public BWACAligner(BWTFiles bwtFiles, BWAConfiguration configuration) { super(bwtFiles,configuration); if(thunkPointer != 0) - throw new ReviewedStingException("BWA/C attempting to reinitialize."); + throw new ReviewedGATKException("BWA/C attempting to reinitialize."); - if(!bwtFiles.annFile.exists()) throw new ReviewedStingException("ANN file is missing; please rerun 'bwa aln' to regenerate it."); - if(!bwtFiles.ambFile.exists()) throw new ReviewedStingException("AMB file is missing; please rerun 'bwa aln' to regenerate it."); - if(!bwtFiles.pacFile.exists()) throw new ReviewedStingException("PAC file is missing; please rerun 'bwa aln' to regenerate it."); - if(!bwtFiles.forwardBWTFile.exists()) throw new ReviewedStingException("Forward BWT file is missing; please rerun 'bwa aln' to regenerate it."); - if(!bwtFiles.forwardSAFile.exists()) throw new ReviewedStingException("Forward SA file is missing; please rerun 'bwa aln' to regenerate it."); - if(!bwtFiles.reverseBWTFile.exists()) throw new ReviewedStingException("Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it."); - if(!bwtFiles.reverseSAFile.exists()) throw new ReviewedStingException("Reverse SA file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.annFile.exists()) throw new ReviewedGATKException("ANN file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.ambFile.exists()) throw new ReviewedGATKException("AMB file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.pacFile.exists()) throw new ReviewedGATKException("PAC file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.forwardBWTFile.exists()) throw new ReviewedGATKException("Forward BWT file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.forwardSAFile.exists()) throw new ReviewedGATKException("Forward SA file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.reverseBWTFile.exists()) throw new ReviewedGATKException("Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.reverseSAFile.exists()) throw new ReviewedGATKException("Reverse SA file is missing; please rerun 'bwa aln' to regenerate it."); thunkPointer = create(bwtFiles,configuration); } @@ -86,7 +86,7 @@ public class BWACAligner extends BWAAligner { @Override public void updateConfiguration(BWAConfiguration configuration) { if(thunkPointer == 0) - throw new ReviewedStingException("BWA/C: attempting to update configuration of uninitialized aligner."); + throw new ReviewedGATKException("BWA/C: attempting to update configuration of uninitialized aligner."); updateConfiguration(thunkPointer,configuration); } @@ -96,7 +96,7 @@ public class BWACAligner extends BWAAligner { @Override public void close() { if(thunkPointer == 0) - throw new ReviewedStingException("BWA/C close attempted, but BWA/C is not properly initialized."); + throw new ReviewedGATKException("BWA/C close attempted, but BWA/C is not properly initialized."); destroy(thunkPointer); } @@ -108,7 +108,7 @@ public class BWACAligner extends BWAAligner { @Override public Alignment getBestAlignment(final byte[] bases) { if(thunkPointer == 0) - throw new ReviewedStingException("BWA/C getBestAlignment attempted, but BWA/C is not properly initialized."); + throw new ReviewedGATKException("BWA/C getBestAlignment attempted, but BWA/C is not properly initialized."); return getBestAlignment(thunkPointer,bases); } @@ -219,7 +219,7 @@ public class BWACAligner extends BWAAligner { */ public BWAPath[] getPaths(byte[] bases) { if(thunkPointer == 0) - throw new ReviewedStingException("BWA/C getPaths attempted, but BWA/C is not properly initialized."); + throw new ReviewedGATKException("BWA/C getPaths attempted, but BWA/C is not properly initialized."); return getPaths(thunkPointer,bases); } @@ -252,7 +252,7 @@ public class BWACAligner extends BWAAligner { */ protected Alignment[] convertPathsToAlignments(byte[] bases, BWAPath[] paths) { if(thunkPointer == 0) - throw new ReviewedStingException("BWA/C convertPathsToAlignments attempted, but BWA/C is not properly initialized."); + throw new ReviewedGATKException("BWA/C convertPathsToAlignments attempted, but BWA/C is not properly initialized."); return convertPathsToAlignments(thunkPointer,bases,paths); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWAPath.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWAPath.java index 438ad2b39..77e0711b5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWAPath.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWAPath.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa.c; +package org.broadinstitute.gatk.engine.alignment.bwa.c; /** * Models a BWA path. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java index 5e2d6e94d..158551ead 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa.java; +package org.broadinstitute.gatk.engine.alignment.bwa.java; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.*; -import org.broadinstitute.sting.alignment.Aligner; -import org.broadinstitute.sting.alignment.Alignment; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.alignment.Aligner; +import org.broadinstitute.gatk.engine.alignment.Alignment; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.File; import java.io.FileNotFoundException; @@ -85,7 +85,7 @@ public class AlignerTestHarness { alignmentCleaned = (SAMRecord)read.clone(); } catch( CloneNotSupportedException ex ) { - throw new ReviewedStingException("SAMRecord clone not supported", ex); + throw new ReviewedGATKException("SAMRecord clone not supported", ex); } if( alignmentCleaned.getReadNegativeStrandFlag() ) @@ -101,7 +101,7 @@ public class AlignerTestHarness { Iterable alignments = aligner.getAllAlignments(alignmentCleaned.getReadBases()); if(!alignments.iterator().hasNext() ) { - //throw new StingException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count)); + //throw new GATKException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count)); System.out.printf("Unable to align read %s to reference; count = %d%n",read.getReadName(),count); failures++; } @@ -151,7 +151,7 @@ public class AlignerTestHarness { } } - //throw new StingException(String.format("Read %s was placed at incorrect location; count = %d%n",read.getReadName(),count)); + //throw new GATKException(String.format("Read %s was placed at incorrect location; count = %d%n",read.getReadName(),count)); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java index 04022581b..f1148c6c2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa.java; +package org.broadinstitute.gatk.engine.alignment.bwa.java; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.ArrayDeque; import java.util.Deque; @@ -56,7 +56,7 @@ public class AlignmentMatchSequence implements Cloneable { copy = (AlignmentMatchSequence)super.clone(); } catch( CloneNotSupportedException ex ) { - throw new ReviewedStingException("Unable to clone AlignmentMatchSequence."); + throw new ReviewedGATKException("Unable to clone AlignmentMatchSequence."); } copy.entries = new ArrayDeque(); @@ -76,7 +76,7 @@ public class AlignmentMatchSequence implements Cloneable { case MATCH_MISMATCH: operator = CigarOperator.MATCH_OR_MISMATCH; break; case INSERTION: operator = CigarOperator.INSERTION; break; case DELETION: operator = CigarOperator.DELETION; break; - default: throw new ReviewedStingException("convertToCigar: cannot process state: " + entry.getAlignmentState()); + default: throw new ReviewedGATKException("convertToCigar: cannot process state: " + entry.getAlignmentState()); } cigar.add( new CigarElement(entry.count,operator) ); } @@ -152,7 +152,7 @@ public class AlignmentMatchSequence implements Cloneable { return (AlignmentMatchSequenceEntry)super.clone(); } catch( CloneNotSupportedException ex ) { - throw new ReviewedStingException("Unable to clone AlignmentMatchSequenceEntry."); + throw new ReviewedGATKException("Unable to clone AlignmentMatchSequenceEntry."); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java index a76b8ef06..f4ba1bb9e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa.java; +package org.broadinstitute.gatk.engine.alignment.bwa.java; /** * The state of a given base in the alignment. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java index 7b9b4ea04..88ef4a557 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa.java; +package org.broadinstitute.gatk.engine.alignment.bwa.java; import htsjdk.samtools.Cigar; -import org.broadinstitute.sting.alignment.Alignment; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.alignment.Alignment; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; /** * An alignment object to be used incrementally as the BWA aligner @@ -173,7 +173,7 @@ public class BWAAlignment extends Alignment implements Cloneable { newAlignment = (BWAAlignment)super.clone(); } catch( CloneNotSupportedException ex ) { - throw new ReviewedStingException("Unable to clone BWAAlignment."); + throw new ReviewedGATKException("Unable to clone BWAAlignment."); } newAlignment.creationNumber = numCreated++; newAlignment.alignmentMatchSequence = alignmentMatchSequence.clone(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java index 98c447b06..09a5b4584 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java @@ -23,16 +23,16 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa.java; +package org.broadinstitute.gatk.engine.alignment.bwa.java; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.alignment.Alignment; -import org.broadinstitute.sting.alignment.bwa.BWAAligner; -import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; -import org.broadinstitute.sting.alignment.reference.bwt.*; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.engine.alignment.Alignment; +import org.broadinstitute.gatk.engine.alignment.bwa.BWAAligner; +import org.broadinstitute.gatk.engine.alignment.bwa.BWAConfiguration; +import org.broadinstitute.gatk.engine.alignment.reference.bwt.*; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.Utils; import java.io.File; import java.util.ArrayList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java index fbd6102e0..e5e292bd8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.bwa.java; +package org.broadinstitute.gatk.engine.alignment.bwa.java; -import org.broadinstitute.sting.alignment.reference.bwt.BWT; +import org.broadinstitute.gatk.engine.alignment.reference.bwt.BWT; import java.util.ArrayList; import java.util.List; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java index daf959306..5a6d70d21 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment; \ No newline at end of file +package org.broadinstitute.gatk.engine.alignment; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java index 3432c7f61..b090bab0e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java index 1de24410d..123b3ca1f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java index d2e9e503d..7d0c43b4a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; -import org.broadinstitute.sting.alignment.reference.packing.PackUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.alignment.reference.packing.PackUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; /** * Represents the Burrows-Wheeler Transform of a reference sequence. @@ -149,7 +149,7 @@ public class BWT { */ protected byte getBase(long index) { if(index == inverseSA0) - throw new ReviewedStingException(String.format("Base at index %d does not have a text representation",index)); + throw new ReviewedGATKException(String.format("Base at index %d does not have a text representation",index)); SequenceBlock block = getSequenceBlock(index); int position = getSequencePosition(index); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java index 320055ae4..9b28e2a42 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; -import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream; -import org.broadinstitute.sting.alignment.reference.packing.PackUtils; -import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.alignment.reference.packing.BasePackedInputStream; +import org.broadinstitute.gatk.engine.alignment.reference.packing.PackUtils; +import org.broadinstitute.gatk.engine.alignment.reference.packing.UnsignedIntPackedInputStream; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.File; import java.io.FileInputStream; @@ -56,7 +56,7 @@ public class BWTReader { this.inputStream = new FileInputStream(inputFile); } catch( FileNotFoundException ex ) { - throw new ReviewedStingException("Unable to open input file", ex); + throw new ReviewedGATKException("Unable to open input file", ex); } } @@ -94,7 +94,7 @@ public class BWTReader { } } catch( IOException ex ) { - throw new ReviewedStingException("Unable to read BWT from input stream.", ex); + throw new ReviewedGATKException("Unable to read BWT from input stream.", ex); } return new BWT(inverseSA0, new Counts(count,true), sequenceBlocks); @@ -108,7 +108,7 @@ public class BWTReader { inputStream.close(); } catch( IOException ex ) { - throw new ReviewedStingException("Unable to close input file", ex); + throw new ReviewedGATKException("Unable to close input file", ex); } } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java index 9f1e7933a..e60a78bd4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.samtools.reference.ReferenceSequenceFileFactory; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java index e0a9a1699..4f2a15945 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; -import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream; -import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.alignment.reference.packing.BasePackedOutputStream; +import org.broadinstitute.gatk.engine.alignment.reference.packing.UnsignedIntPackedOutputStream; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.*; import java.nio.ByteOrder; @@ -53,7 +53,7 @@ public class BWTWriter { this.outputStream = new BufferedOutputStream(new FileOutputStream(outputFile)); } catch( FileNotFoundException ex ) { - throw new ReviewedStingException("Unable to open output file", ex); + throw new ReviewedGATKException("Unable to open output file", ex); } } @@ -78,7 +78,7 @@ public class BWTWriter { intPackedOutputStream.write(bwt.counts.toArray(false)); } catch( IOException ex ) { - throw new ReviewedStingException("Unable to read BWT from input stream.", ex); + throw new ReviewedGATKException("Unable to read BWT from input stream.", ex); } } @@ -90,7 +90,7 @@ public class BWTWriter { outputStream.close(); } catch( IOException ex ) { - throw new ReviewedStingException("Unable to close input file", ex); + throw new ReviewedGATKException("Unable to close input file", ex); } } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java index d569df44a..d0cd84994 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.*; @@ -112,7 +112,7 @@ public class Bases implements Iterable if( entry.getValue().equals(ascii) ) return entry.getKey(); } - throw new ReviewedStingException(String.format("Base %c is an invalid base to pack", (char)ascii)); + throw new ReviewedGATKException(String.format("Base %c is an invalid base to pack", (char)ascii)); } /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java index 50678b57a..c6684b5ad 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.HashMap; import java.util.Map; @@ -121,7 +121,7 @@ public class Counts implements Cloneable { other = (Counts)super.clone(); } catch(CloneNotSupportedException ex) { - throw new ReviewedStingException("Unable to clone counts object", ex); + throw new ReviewedGATKException("Unable to clone counts object", ex); } other.counts = new HashMap(counts); other.cumulativeCounts = new HashMap(cumulativeCounts); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java index 0f0d3a994..baa5ebefc 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; import htsjdk.samtools.reference.ReferenceSequence; import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.samtools.reference.ReferenceSequenceFileFactory; -import org.broadinstitute.sting.alignment.reference.packing.PackUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.alignment.reference.packing.PackUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.File; import java.io.IOException; @@ -182,7 +182,7 @@ public class CreateBWTFromReference { for( int i = 0; i < bwt.length(); i++ ) { if( bwtSequence[i] != existingBWTSequence[i] ) - throw new ReviewedStingException("BWT mismatch at " + i); + throw new ReviewedGATKException("BWT mismatch at " + i); } File existingSAFile = new File(inputFileName+".sa"); @@ -193,7 +193,7 @@ public class CreateBWTFromReference { if( i % 10000 == 0 ) System.out.printf("Validating suffix array entry %d%n", i); if( suffixArray.get(i) != existingSuffixArray.get(i) ) - throw new ReviewedStingException(String.format("Suffix array mismatch at %d; SA is %d; should be %d",i,existingSuffixArray.get(i),suffixArray.get(i))); + throw new ReviewedGATKException(String.format("Suffix array mismatch at %d; SA is %d; should be %d",i,existingSuffixArray.get(i),suffixArray.get(i))); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java index 2c14ce5aa..555e7ccb4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; /** * Models a block of bases within the BWT. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java index 1d15770d3..d1edfe5cb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; import htsjdk.samtools.util.StringUtil; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.Comparator; import java.util.TreeSet; @@ -77,7 +77,7 @@ public class SuffixArray { this.bwt = bwt; if(sequenceInterval != 1 && bwt == null) - throw new ReviewedStingException("A BWT must be provided if the sequence interval is not 1"); + throw new ReviewedGATKException("A BWT must be provided if the sequence interval is not 1"); } /** @@ -142,7 +142,7 @@ public class SuffixArray { inverseSA0 = i; } if(inverseSA0 < 0) - throw new ReviewedStingException("Unable to find first inverse SA entry in generated suffix array."); + throw new ReviewedGATKException("Unable to find first inverse SA entry in generated suffix array."); return new SuffixArray(inverseSA0,occurrences,suffixArray); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java index 34cb04698..dc8cdc0c1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; -import org.broadinstitute.sting.alignment.reference.packing.PackUtils; -import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.alignment.reference.packing.PackUtils; +import org.broadinstitute.gatk.engine.alignment.reference.packing.UnsignedIntPackedInputStream; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.File; import java.io.FileInputStream; @@ -63,7 +63,7 @@ public class SuffixArrayReader { this.bwt = bwt; } catch( FileNotFoundException ex ) { - throw new ReviewedStingException("Unable to open input file", ex); + throw new ReviewedGATKException("Unable to open input file", ex); } } @@ -89,7 +89,7 @@ public class SuffixArrayReader { uintPackedInputStream.read(suffixArray); } catch( IOException ex ) { - throw new ReviewedStingException("Unable to read BWT from input stream.", ex); + throw new ReviewedGATKException("Unable to read BWT from input stream.", ex); } return new SuffixArray(inverseSA0, new Counts(occurrences,true), suffixArray, suffixArrayInterval, bwt); @@ -104,7 +104,7 @@ public class SuffixArrayReader { inputStream.close(); } catch( IOException ex ) { - throw new ReviewedStingException("Unable to close input file", ex); + throw new ReviewedGATKException("Unable to close input file", ex); } } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java index 164b2eecf..df152b90a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.bwt; +package org.broadinstitute.gatk.engine.alignment.reference.bwt; -import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.alignment.reference.packing.UnsignedIntPackedOutputStream; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.*; import java.nio.ByteOrder; @@ -52,7 +52,7 @@ public class SuffixArrayWriter { this.outputStream = new BufferedOutputStream(new FileOutputStream(outputFile)); } catch( FileNotFoundException ex ) { - throw new ReviewedStingException("Unable to open input file", ex); + throw new ReviewedGATKException("Unable to open input file", ex); } } @@ -73,7 +73,7 @@ public class SuffixArrayWriter { uintPackedOutputStream.write(suffixArray.sequence,1,suffixArray.sequence.length-1); } catch( IOException ex ) { - throw new ReviewedStingException("Unable to read BWT from input stream.", ex); + throw new ReviewedGATKException("Unable to read BWT from input stream.", ex); } } @@ -86,7 +86,7 @@ public class SuffixArrayWriter { outputStream.close(); } catch( IOException ex ) { - throw new ReviewedStingException("Unable to close input file", ex); + throw new ReviewedGATKException("Unable to close input file", ex); } } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java index ef3bef917..727a378d6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.packing; +package org.broadinstitute.gatk.engine.alignment.reference.packing; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.File; import java.io.FileInputStream; @@ -79,7 +79,7 @@ public class BasePackedInputStream { public BasePackedInputStream( Class type, FileInputStream inputStream, ByteOrder byteOrder ) { if( type != Integer.class ) - throw new ReviewedStingException("Only bases packed into 32-bit words are currently supported by this input stream. Type specified: " + type.getName()); + throw new ReviewedGATKException("Only bases packed into 32-bit words are currently supported by this input stream. Type specified: " + type.getName()); this.type = type; this.targetInputStream = inputStream; this.targetInputChannel = inputStream.getChannel(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java index e21216702..b3dbba893 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.packing; +package org.broadinstitute.gatk.engine.alignment.reference.packing; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.*; import java.nio.ByteBuffer; @@ -159,7 +159,7 @@ public class BasePackedOutputStream { else if( type == Byte.class ) buffer.put((byte)packedBases); else - throw new ReviewedStingException("Cannot pack bases into type " + type.getName()); + throw new ReviewedGATKException("Cannot pack bases into type " + type.getName()); targetOutputStream.write(buffer.array()); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java index a6719c2eb..fac3d92ff 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.packing; +package org.broadinstitute.gatk.engine.alignment.reference.packing; import htsjdk.samtools.reference.ReferenceSequence; import htsjdk.samtools.reference.ReferenceSequenceFile; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java index c24c1c803..e60780a64 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.packing; +package org.broadinstitute.gatk.engine.alignment.reference.packing; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.File; import java.io.FileOutputStream; @@ -83,14 +83,14 @@ public class PackUtils { long typeSize = type.getField("MAX_VALUE").getLong(null) - type.getField("MIN_VALUE").getLong(null)+1; long intTypeSize = (long)Integer.MAX_VALUE - (long)Integer.MIN_VALUE + 1; if( typeSize > intTypeSize ) - throw new ReviewedStingException("Cannot determine number of bits available in type: " + type.getName()); + throw new ReviewedGATKException("Cannot determine number of bits available in type: " + type.getName()); return (int)(Math.log(typeSize)/Math.log(2)); } catch( NoSuchFieldException ex ) { - throw new ReviewedStingException("Cannot determine number of bits available in type: " + type.getName(),ex); + throw new ReviewedGATKException("Cannot determine number of bits available in type: " + type.getName(),ex); } catch( IllegalAccessException ex ) { - throw new ReviewedStingException("Cannot determine number of bits available in type: " + type.getName(),ex); + throw new ReviewedGATKException("Cannot determine number of bits available in type: " + type.getName(),ex); } } @@ -110,7 +110,7 @@ public class PackUtils { case 'T': return 3; default: - throw new ReviewedStingException("Unknown base type: " + base); + throw new ReviewedGATKException("Unknown base type: " + base); } } @@ -130,7 +130,7 @@ public class PackUtils { case 3: return 'T'; default: - throw new ReviewedStingException("Unknown pack type: " + pack); + throw new ReviewedGATKException("Unknown pack type: " + pack); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java index 4752c8dd5..060050047 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.packing; +package org.broadinstitute.gatk.engine.alignment.reference.packing; import java.io.File; import java.io.FileInputStream; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java index e8d24c894..44c462b89 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.alignment.reference.packing; +package org.broadinstitute.gatk.engine.alignment.reference.packing; import java.io.File; import java.io.FileOutputStream; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java index 7ff3622f5..05ebffa07 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.arguments; +package org.broadinstitute.gatk.engine.arguments; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.gatk.utils.commandline.Input; +import org.broadinstitute.gatk.utils.commandline.RodBinding; import htsjdk.variant.variantcontext.VariantContext; /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java index 08597adc6..f13936a1e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java @@ -23,19 +23,19 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.arguments; +package org.broadinstitute.gatk.engine.arguments; import htsjdk.samtools.SAMFileReader; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.downsampling.DownsampleType; -import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod; -import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; -import org.broadinstitute.sting.gatk.samples.PedigreeValidationType; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.variant.GATKVCFIndexType; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.engine.phonehome.GATKRunReport; +import org.broadinstitute.gatk.engine.samples.PedigreeValidationType; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.baq.BAQ; +import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import java.io.File; import java.util.ArrayList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java index 10aea1537..331029f52 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.arguments; +package org.broadinstitute.gatk.engine.arguments; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.gatk.utils.commandline.Input; +import org.broadinstitute.gatk.utils.commandline.RodBinding; import htsjdk.variant.variantcontext.VariantContext; /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/ValidationExclusion.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/ValidationExclusion.java index 75a68d978..ccd4fdc44 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/ValidationExclusion.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/ValidationExclusion.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.arguments; +package org.broadinstitute.gatk.engine.arguments; -import org.broadinstitute.sting.commandline.EnumerationArgumentDefault; +import org.broadinstitute.gatk.utils.commandline.EnumerationArgumentDefault; import java.util.ArrayList; import java.util.List; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContext.java index edf7a4c0a..6ac204865 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContext.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContext.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.contexts; +package org.broadinstitute.gatk.engine.contexts; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.HasGenomeLocation; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.List; @@ -66,9 +66,9 @@ public class AlignmentContext implements HasGenomeLocation { } public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, long skippedBases,boolean hasPileupBeenDownsampled ) { - if ( loc == null ) throw new ReviewedStingException("BUG: GenomeLoc in Alignment context is null"); - if ( basePileup == null ) throw new ReviewedStingException("BUG: ReadBackedPileup in Alignment context is null"); - if ( skippedBases < 0 ) throw new ReviewedStingException("BUG: skippedBases is -1 in Alignment context"); + if ( loc == null ) throw new ReviewedGATKException("BUG: GenomeLoc in Alignment context is null"); + if ( basePileup == null ) throw new ReviewedGATKException("BUG: ReadBackedPileup in Alignment context is null"); + if ( skippedBases < 0 ) throw new ReviewedGATKException("BUG: skippedBases is -1 in Alignment context"); this.loc = loc; this.basePileup = basePileup; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContextUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContextUtils.java index 323006635..afeb1e735 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContextUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContextUtils.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.contexts; +package org.broadinstitute.gatk.engine.contexts; import htsjdk.samtools.SAMReadGroupRecord; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.pileup.*; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.pileup.*; import java.util.*; @@ -67,7 +67,7 @@ public class AlignmentContextUtils { case REVERSE: return new AlignmentContext(context.getLocation(),context.getPileup().getNegativeStrandPileup()); default: - throw new ReviewedStingException("Unable to get alignment context for type = " + type); + throw new ReviewedGATKException("Unable to get alignment context for type = " + type); } } @@ -137,7 +137,7 @@ public class AlignmentContextUtils { GenomeLoc loc = contexts.iterator().next().getLocation(); for(AlignmentContext context: contexts) { if(!loc.equals(context.getLocation())) - throw new ReviewedStingException("Illegal attempt to join contexts from different genomic locations"); + throw new ReviewedGATKException("Illegal attempt to join contexts from different genomic locations"); } List pe = new ArrayList(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/ReferenceContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/ReferenceContext.java index 90d6dda48..201ea49fd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/ReferenceContext.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/ReferenceContext.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.contexts; +package org.broadinstitute.gatk.engine.contexts; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; /** * The section of the reference that overlaps with the given diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java index 94fb75a47..680da25bb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources; \ No newline at end of file +package org.broadinstitute.gatk.engine.datasources; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java index ea2708dda..56ecce2ef 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.iterators.GenomeLocusIterator; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Collections; import java.util.List; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java index 644523c04..900612a49 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; /** * User: hanna * Date: May 12, 2009 diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java index ed1f25544..9100905f3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import htsjdk.samtools.util.PeekableIterator; -import org.broadinstitute.sting.gatk.refdata.RODRecordListImpl; -import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.gatk.engine.refdata.RODRecordListImpl; +import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.GenomeLoc; import java.util.Collection; import java.util.LinkedList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java index ea195d7eb..23f4f73e8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java @@ -23,17 +23,17 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.util.PeekableIterator; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.reads.ReadShard; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.datasources.reads.ReadShard; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; import java.util.ArrayList; import java.util.Collection; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java index 7b34e0703..997435d84 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; /** * Created by IntelliJ IDEA. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java index b10a274a5..b53505097 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.reference.ReferenceSequence; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.walkers.Reference; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.Window; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.walkers.Reference; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.engine.walkers.Window; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; /* * Copyright (c) 2009 The Broad Institute * @@ -109,8 +109,8 @@ public class LocusReferenceView extends ReferenceView { if( walker.getClass().isAnnotationPresent(Reference.class) ) { Window window = walker.getClass().getAnnotation(Reference.class).window(); - if( window.start() > 0 ) throw new ReviewedStingException( "Reference window starts after current locus" ); - if( window.stop() < 0 ) throw new ReviewedStingException( "Reference window ends before current locus" ); + if( window.start() > 0 ) throw new ReviewedGATKException( "Reference window starts after current locus" ); + if( window.stop() < 0 ) throw new ReviewedGATKException( "Reference window ends before current locus" ); windowStart = window.start(); windowStop = window.stop(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java index 46a67d05e..7dc589da7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.gatk.ReadProperties; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.utils.locusiterator.LocusIterator; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.gatk.engine.ReadProperties; +import org.broadinstitute.gatk.engine.datasources.reads.Shard; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.utils.locusiterator.LocusIterator; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; import java.util.Collection; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java index 6b3661baa..9bc37e549 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.sting.gatk.downsampling.DownsampleType; -import org.broadinstitute.sting.gatk.ReadProperties; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.utils.locusiterator.LocusIterator; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState; +import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.engine.ReadProperties; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.locusiterator.LocusIterator; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState; import java.util.Arrays; import java.util.Collection; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java index 50f2369cb..2dd42c1cc 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.GenomeLoc; import java.util.ArrayList; import java.util.Collection; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java index e078e678b..f244e504d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.collections.Pair; import java.util.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java index 1774c11b7..1d73501bd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java @@ -23,19 +23,19 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.datasources.reads.ReadShard; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.gatk.engine.datasources.reads.ReadShard; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; import java.util.ArrayList; import java.util.Collection; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java index 980dc720c..14d5827a3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.GenomeLoc; /* * Copyright (c) 2009 The Broad Institute * diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java index 7ef00f038..8acfad0b1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.gatk.engine.datasources.reads.Shard; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.GenomeLocParser; import java.util.Collection; @@ -43,14 +43,14 @@ public class ReadShardDataProvider extends ShardDataProvider { /** * The raw collection of reads. */ - private final StingSAMIterator reads; + private final GATKSAMIterator reads; /** * Create a data provider for the shard given the reads and reference. * @param shard The chunk of data over which traversals happen. * @param reference A getter for a section of the reference. */ - public ReadShardDataProvider(Shard shard, GenomeLocParser genomeLocParser, StingSAMIterator reads, IndexedFastaSequenceFile reference, Collection rods) { + public ReadShardDataProvider(Shard shard, GenomeLocParser genomeLocParser, GATKSAMIterator reads, IndexedFastaSequenceFile reference, Collection rods) { super(shard,genomeLocParser,reference,rods); this.reads = reads; } @@ -67,7 +67,7 @@ public class ReadShardDataProvider extends ShardDataProvider { * Gets an iterator over all the reads bound by this shard. * @return An iterator over all reads in this shard. */ - public StingSAMIterator getReadIterator() { + public GATKSAMIterator getReadIterator() { return reads; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java index 4430ed37f..160dbd585 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; +import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; import java.util.Arrays; import java.util.Collection; @@ -50,7 +50,7 @@ public class ReadView implements View, Iterable { /** * The iterator into the reads supplied by this provider. */ - private StingSAMIterator reads; + private GATKSAMIterator reads; /** * Create a new view of the reads given the current data set. @@ -82,7 +82,7 @@ public class ReadView implements View, Iterable { * Gets an iterator into the reads supplied by this provider. * @return Iterator into the reads that this provider covers. */ - public StingSAMIterator iterator() { + public GATKSAMIterator iterator() { return reads; } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java index 85c20a6c3..9f3db5143 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.GenomeLoc; public interface ReferenceOrderedView extends View { RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc ); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java index 9b3d5d40d..2eade15e2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.reference.ReferenceSequence; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMSequenceRecord; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.Arrays; import java.util.Collection; @@ -118,7 +118,7 @@ public class ReferenceView implements View { int overhang = (int)(genomeLoc.getStop() - stop); if ( overhang > 0 ) { if ( overhang > BUFFER ) // todo -- this is a bit dangerous - throw new ReviewedStingException("Insufficient buffer size for Xs overhanging genome -- expand BUFFER"); + throw new ReviewedGATKException("Insufficient buffer size for Xs overhanging genome -- expand BUFFER"); byte[] all = new byte[subsequence.getBases().length + overhang]; System.arraycopy(subsequence.getBases(), 0, all, 0, subsequence.getBases().length); System.arraycopy(Xs, 0, all, subsequence.getBases().length, overhang); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java index 1b6c14628..21cb3efa6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java @@ -23,17 +23,17 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.collections.RODMergingIterator; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.collections.RODMergingIterator; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; import java.util.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java index 60e2b8497..a36bee579 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.datasources.reads.Shard; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.ArrayList; import java.util.Collection; @@ -156,7 +156,7 @@ public abstract class ShardDataProvider { Collection> conflicts = registeredView.getConflictingViews(); for( Class conflict: conflicts ) { if( conflict.isInstance(view) ) - throw new ReviewedStingException(String.format("Tried to register two conflicting views: %s and %s", + throw new ReviewedGATKException(String.format("Tried to register two conflicting views: %s and %s", registeredView.getClass().getSimpleName(), view.getClass().getSimpleName())); } @@ -166,7 +166,7 @@ public abstract class ShardDataProvider { for( Class conflict: view.getConflictingViews() ) { for( View registeredView: registeredViews ) { if( conflict.isInstance(registeredView) ) - throw new ReviewedStingException(String.format("Tried to register two conflicting views: %s and %s", + throw new ReviewedGATKException(String.format("Tried to register two conflicting views: %s and %s", registeredView.getClass().getSimpleName(), view.getClass().getSimpleName())); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java index 275008cb4..f628bb47c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; +package org.broadinstitute.gatk.engine.datasources.providers; import java.util.Collection; /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java index fb3934444..bc8a60251 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.providers; \ No newline at end of file +package org.broadinstitute.gatk.engine.datasources.providers; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java index febdc788e..efe6336ad 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import java.util.Iterator; import java.util.LinkedList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java index 368dc7622..1e30d6c38 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java @@ -23,12 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.GATKBAMFileSpan; import htsjdk.samtools.GATKChunk; import htsjdk.samtools.util.BlockCompressedFilePointerUtil; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.LinkedList; import java.util.List; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java index 44633af17..a80b0a475 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java @@ -23,17 +23,17 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.Bin; import htsjdk.samtools.GATKBAMFileSpan; import htsjdk.samtools.GATKChunk; import htsjdk.samtools.util.CloseableIterator; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.File; import java.io.IOException; @@ -91,7 +91,7 @@ public class BAMSchedule implements CloseableIterator { */ public BAMSchedule(final SAMDataSource dataSource, final List intervals) { if(intervals.isEmpty()) - throw new ReviewedStingException("Tried to write schedule for empty interval list."); + throw new ReviewedGATKException("Tried to write schedule for empty interval list."); referenceSequence = dataSource.getHeader().getSequence(intervals.get(0).getContig()).getSequenceIndex(); @@ -206,7 +206,7 @@ public class BAMSchedule implements CloseableIterator { * @param e * @return */ - private final StingException makeIOFailureException(final boolean wasWriting, final String message, final Exception e) { + private final GATKException makeIOFailureException(final boolean wasWriting, final String message, final Exception e) { if ( wasWriting ) { if ( e == null ) return new UserException.CouldNotCreateOutputFile(scheduleFile, message); @@ -412,7 +412,7 @@ public class BAMSchedule implements CloseableIterator { // Make sure we read in a complete bin header: if ( binHeaderBytesRead < INT_SIZE_IN_BYTES * 3 ) { - throw new ReviewedStingException(String.format("Unable to read a complete bin header from BAM schedule file %s for BAM file %s. " + + throw new ReviewedGATKException(String.format("Unable to read a complete bin header from BAM schedule file %s for BAM file %s. " + "The BAM schedule file is likely incomplete/corrupt.", scheduleFile.getAbsolutePath(), reader.getSamFilePath())); } @@ -433,7 +433,7 @@ public class BAMSchedule implements CloseableIterator { chunkData.limit(numChunks*LONG_SIZE_IN_BYTES*2); long bytesRead = read(chunkData); if(bytesRead != numChunks*LONG_SIZE_IN_BYTES*2) - throw new ReviewedStingException("Unable to read all chunks from file"); + throw new ReviewedGATKException("Unable to read all chunks from file"); // Prepare for reading. chunkData.flip(); @@ -507,7 +507,7 @@ class BAMScheduleEntry { final int otherSize = other.fileSpans.size(); fileSpans.putAll(other.fileSpans); if(fileSpans.size() != thisSize+otherSize) - throw new ReviewedStingException("Unable to handle overlaps when merging BAM schedule entries."); + throw new ReviewedGATKException("Unable to handle overlaps when merging BAM schedule entries."); } /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java index c92e58bef..1ea8d39aa 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java @@ -23,19 +23,19 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.GATKBAMFileSpan; import htsjdk.samtools.GATKChunk; import htsjdk.samtools.SAMSequenceRecord; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocSortedSet; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.util.*; @@ -286,7 +286,7 @@ public class BAMScheduler implements Iterator { List lociInContig = new LinkedList(); for(GenomeLoc locus: loci) { if (!GenomeLoc.isUnmapped(locus) && dataSource.getHeader().getSequence(locus.getContig()) == null) - throw new ReviewedStingException("BAM file(s) do not have the contig: " + locus.getContig() + ". You are probably using a different reference than the one this file was aligned with"); + throw new ReviewedGATKException("BAM file(s) do not have the contig: " + locus.getContig() + ". You are probably using a different reference than the one this file was aligned with"); if (!GenomeLoc.isUnmapped(locus) && dataSource.getHeader().getSequence(locus.getContig()).getSequenceIndex() == lastReferenceSequenceLoaded) lociInContig.add(locus); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java index 36a6c780d..cc1d9e9a4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.LinkedList; import java.util.Queue; @@ -77,7 +77,7 @@ public class BGZFBlockLoadingDispatcher { inputQueue.wait(); } catch(InterruptedException ex) { - throw new ReviewedStingException("Interrupt occurred waiting for next block reader work item"); + throw new ReviewedGATKException("Interrupt occurred waiting for next block reader work item"); } } return inputQueue.poll(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java index a0366ac2b..11fecb661 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.GATKBAMFileSpan; import htsjdk.samtools.GATKChunk; import htsjdk.samtools.util.BlockCompressedInputStream; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.IOException; import java.io.InputStream; @@ -131,7 +131,7 @@ public class BlockInputStream extends InputStream { validatingInputStream = null; } catch(IOException ex) { - throw new ReviewedStingException("Unable to validate against Picard input stream",ex); + throw new ReviewedGATKException("Unable to validate against Picard input stream",ex); } } @@ -150,7 +150,7 @@ public class BlockInputStream extends InputStream { } // if(validatingInputStream != null && filePointer != validatingInputStream.getFilePointer()) -// throw new ReviewedStingException(String.format("Position of input stream is invalid; expected (block address, block offset) = (%d,%d), got (%d,%d)", +// throw new ReviewedGATKException(String.format("Position of input stream is invalid; expected (block address, block offset) = (%d,%d), got (%d,%d)", // BlockCompressedFilePointerUtil.getBlockAddress(validatingInputStream.getFilePointer()),BlockCompressedFilePointerUtil.getBlockOffset(validatingInputStream.getFilePointer()), // BlockCompressedFilePointerUtil.getBlockAddress(filePointer),BlockCompressedFilePointerUtil.getBlockOffset(filePointer))); @@ -203,7 +203,7 @@ public class BlockInputStream extends InputStream { validatingInputStream.seek(makeFilePointer(accessPlan.getBlockAddress(),0)); } catch(IOException ex) { - throw new ReviewedStingException("Unable to validate against Picard input stream",ex); + throw new ReviewedGATKException("Unable to validate against Picard input stream",ex); } } @@ -271,7 +271,7 @@ public class BlockInputStream extends InputStream { validatingInputStream.seek(currentFilePointer); if(!Arrays.equals(validBytes,currentBytes)) - throw new ReviewedStingException(String.format("Bytes being inserted into BlockInputStream %s are incorrect",this)); + throw new ReviewedGATKException(String.format("Bytes being inserted into BlockInputStream %s are incorrect",this)); } compactBuffer(); @@ -329,7 +329,7 @@ public class BlockInputStream extends InputStream { private void checkForErrors() { synchronized(lock) { if(error != null) { - ReviewedStingException toThrow = new ReviewedStingException(String.format("Thread %s, BlockInputStream %s: Unable to retrieve BAM data from disk",Thread.currentThread().getId(),this),error); + ReviewedGATKException toThrow = new ReviewedGATKException(String.format("Thread %s, BlockInputStream %s: Unable to retrieve BAM data from disk",Thread.currentThread().getId(),this),error); toThrow.setStackTrace(error.getStackTrace()); throw toThrow; } @@ -392,11 +392,11 @@ public class BlockInputStream extends InputStream { // validatingInputStream.read(validBytes,offset,length); // for(int i = offset; i < offset+length; i++) { // if(bytes[i] != validBytes[i]) -// throw new ReviewedStingException(String.format("Thread %s: blockInputStream %s attempting to return wrong set of bytes; mismatch at offset %d",Thread.currentThread().getId(),this,i)); +// throw new ReviewedGATKException(String.format("Thread %s: blockInputStream %s attempting to return wrong set of bytes; mismatch at offset %d",Thread.currentThread().getId(),this,i)); // } // } // catch(IOException ex) { -// throw new ReviewedStingException("Unable to validate against Picard input stream",ex); +// throw new ReviewedGATKException("Unable to validate against Picard input stream",ex); // } // } @@ -414,7 +414,7 @@ public class BlockInputStream extends InputStream { validatingInputStream.close(); } catch(IOException ex) { - throw new ReviewedStingException("Unable to validate against Picard input stream",ex); + throw new ReviewedGATKException("Unable to validate against Picard input stream",ex); } } } @@ -432,7 +432,7 @@ public class BlockInputStream extends InputStream { lock.wait(); } catch(InterruptedException ex) { - throw new ReviewedStingException("Interrupt occurred waiting for buffer to fill",ex); + throw new ReviewedGATKException("Interrupt occurred waiting for buffer to fill",ex); } } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java index 2b3d28bab..09a0cab2a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.BlockCompressedStreamConstants; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.FileInputStream; import java.io.IOException; @@ -117,7 +117,7 @@ class BlockLoader implements Runnable { // value into an int buffer to transfer the bitwise contents into an int. inputBuffer.flip(); if(inputBuffer.remaining() != BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH) - throw new ReviewedStingException("BUG: unable to read a the complete block header in one pass."); + throw new ReviewedGATKException("BUG: unable to read a the complete block header in one pass."); // Verify that the file was read at a valid point. if(unpackUByte8(inputBuffer,0) != BlockCompressedStreamConstants.GZIP_ID1 || @@ -126,7 +126,7 @@ class BlockLoader implements Runnable { unpackUInt16(inputBuffer,10) != BlockCompressedStreamConstants.GZIP_XLEN || unpackUByte8(inputBuffer,12) != BlockCompressedStreamConstants.BGZF_ID1 || unpackUByte8(inputBuffer,13) != BlockCompressedStreamConstants.BGZF_ID2) { - throw new ReviewedStingException("BUG: Started reading compressed block at incorrect position"); + throw new ReviewedGATKException("BUG: Started reading compressed block at incorrect position"); } inputBuffer.position(BlockCompressedStreamConstants.BLOCK_LENGTH_OFFSET); @@ -168,7 +168,7 @@ class BlockLoader implements Runnable { inflater.setInput(compressedContent); int bytesUncompressed = inflater.inflate(uncompressedContent); if(bytesUncompressed != uncompressedBufferSize) - throw new ReviewedStingException("Error decompressing block"); + throw new ReviewedGATKException("Error decompressing block"); return ByteBuffer.wrap(uncompressedContent); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java index 5f42532d7..8d5ab3b03 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.StingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.GATKException; import java.io.FileInputStream; import java.io.IOException; @@ -92,7 +92,7 @@ public class FileHandleCache { lock.wait(); } catch(InterruptedException ex) { - throw new ReviewedStingException("Interrupted while waiting for a file handle"); + throw new ReviewedGATKException("Interrupted while waiting for a file handle"); } inputStream = openInputStream(key); } @@ -158,7 +158,7 @@ public class FileHandleCache { return new FileInputStream(reader.getSamFilePath()); } catch(IOException ex) { - throw new StingException("Unable to open input file"); + throw new GATKException("Unable to open input file"); } } @@ -167,7 +167,7 @@ public class FileHandleCache { inputStream.close(); } catch(IOException ex) { - throw new StingException("Unable to open input file"); + throw new GATKException("Unable to open input file"); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java index 48c7f4fa7..99d9def5a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java @@ -23,19 +23,19 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.GATKBAMFileSpan; import htsjdk.samtools.GATKChunk; import htsjdk.samtools.SAMFileSpan; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; -import org.broadinstitute.sting.utils.interval.IntervalUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; +import org.broadinstitute.gatk.utils.interval.IntervalUtils; import java.util.*; @@ -96,7 +96,7 @@ public class FilePointer { foundMapped = true; } if ( foundMapped && foundUnmapped ) - throw new ReviewedStingException("BUG: File pointers cannot be mixed mapped/unmapped."); + throw new ReviewedGATKException("BUG: File pointers cannot be mixed mapped/unmapped."); return foundUnmapped; } @@ -111,7 +111,7 @@ public class FilePointer { for ( GenomeLoc location : locations ) { if ( previousContigIndex != null && previousContigIndex != location.getContigIndex() ) { - throw new ReviewedStingException("Non-monolithic file pointers must contain intervals from at most one contig"); + throw new ReviewedGATKException("Non-monolithic file pointers must contain intervals from at most one contig"); } previousContigIndex = location.getContigIndex(); @@ -120,10 +120,10 @@ public class FilePointer { private void validateLocation( GenomeLoc location ) { if ( isRegionUnmapped != GenomeLoc.isUnmapped(location) ) { - throw new ReviewedStingException("BUG: File pointers cannot be mixed mapped/unmapped."); + throw new ReviewedGATKException("BUG: File pointers cannot be mixed mapped/unmapped."); } if ( ! isRegionUnmapped && ! isMonolithic && contigIndex != null && contigIndex != location.getContigIndex() ) { - throw new ReviewedStingException("Non-monolithic file pointers must contain intervals from at most one contig"); + throw new ReviewedGATKException("Non-monolithic file pointers must contain intervals from at most one contig"); } } @@ -329,7 +329,7 @@ public class FilePointer { */ private void mergeElementsInto(final FilePointer combined, Iterator>... iterators) { if(iterators.length == 0) - throw new ReviewedStingException("Tried to add zero elements to an existing file pointer."); + throw new ReviewedGATKException("Tried to add zero elements to an existing file pointer."); Map.Entry initialElement = iterators[0].next(); GATKBAMFileSpan fileSpan = (GATKBAMFileSpan)initialElement.getValue(); for(int i = 1; i < iterators.length; i++) @@ -362,7 +362,7 @@ public class FilePointer { for ( FilePointer filePointer : filePointers ) { locations.addAll(filePointer.getLocations()); if (mergeRule != filePointer.getIntervalMergingRule()) - throw new ReviewedStingException("All FilePointers in FilePointer.union() must have use the same IntervalMergeRule"); + throw new ReviewedGATKException("All FilePointers in FilePointer.union() must have use the same IntervalMergeRule"); for ( Map.Entry fileSpanEntry : filePointer.getFileSpans().entrySet() ) { GATKBAMFileSpan fileSpan = (GATKBAMFileSpan)fileSpanEntry.getValue(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java index 7594ea28c..17afd5894 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.Bin; import htsjdk.samtools.GATKBin; @@ -31,8 +31,8 @@ import htsjdk.samtools.GATKChunk; import htsjdk.samtools.LinearIndex; import htsjdk.samtools.seekablestream.SeekableBufferedStream; import htsjdk.samtools.seekablestream.SeekableFileStream; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.File; import java.io.IOException; @@ -98,7 +98,7 @@ public class GATKBAMIndex { seek(0); final byte[] buffer = readBytes(4); if (!Arrays.equals(buffer, BAM_INDEX_MAGIC)) { - throw new ReviewedStingException("Invalid file header in BAM index " + mFile + + throw new ReviewedGATKException("Invalid file header in BAM index " + mFile + ": " + new String(buffer)); } @@ -122,7 +122,7 @@ public class GATKBAMIndex { openIndexFile(); if (referenceSequence >= sequenceCount) - throw new ReviewedStingException("Invalid sequence number " + referenceSequence + " in index file " + mFile); + throw new ReviewedGATKException("Invalid sequence number " + referenceSequence + " in index file " + mFile); skipToSequence(referenceSequence); @@ -193,12 +193,12 @@ public class GATKBAMIndex { public int getLevelForBin(final Bin bin) { GATKBin gatkBin = new GATKBin(bin); if(gatkBin.getBinNumber() >= MAX_BINS) - throw new ReviewedStingException("Tried to get level for invalid bin in index file " + mFile); + throw new ReviewedGATKException("Tried to get level for invalid bin in index file " + mFile); for(int i = getNumIndexLevels()-1; i >= 0; i--) { if(gatkBin.getBinNumber() >= LEVEL_STARTS[i]) return i; } - throw new ReviewedStingException("Unable to find correct bin for bin " + bin + " in index file " + mFile); + throw new ReviewedGATKException("Unable to find correct bin for bin " + bin + " in index file " + mFile); } /** @@ -312,7 +312,7 @@ public class GATKBAMIndex { fileLength=bufferedStream.length(); } catch (IOException exc) { - throw new ReviewedStingException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc); + throw new ReviewedGATKException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc); } } @@ -323,7 +323,7 @@ public class GATKBAMIndex { fileLength = -1; } catch (IOException exc) { - throw new ReviewedStingException("Unable to close index file " + mFile, exc); + throw new ReviewedGATKException("Unable to close index file " + mFile, exc); } } @@ -403,7 +403,7 @@ public class GATKBAMIndex { buffer.put(byteArray, 0, bytesRequested); } catch(IOException ex) { - throw new ReviewedStingException("Index: unable to read bytes from index file " + mFile); + throw new ReviewedGATKException("Index: unable to read bytes from index file " + mFile); } } @@ -435,11 +435,11 @@ public class GATKBAMIndex { long skipped = bufferedStream.skip(count); if( skipped != count ) { //if not managed to skip the requested amount - throw new ReviewedStingException("Index: unable to reposition file channel of index file " + mFile); + throw new ReviewedGATKException("Index: unable to reposition file channel of index file " + mFile); } } catch(IOException ex) { - throw new ReviewedStingException("Index: unable to reposition file channel of index file " + mFile); + throw new ReviewedGATKException("Index: unable to reposition file channel of index file " + mFile); } } @@ -449,7 +449,7 @@ public class GATKBAMIndex { bufferedStream.seek(position); } catch(IOException ex) { - throw new ReviewedStingException("Index: unable to reposition of file channel of index file " + mFile); + throw new ReviewedGATKException("Index: unable to reposition of file channel of index file " + mFile); } } @@ -462,7 +462,7 @@ public class GATKBAMIndex { return bufferedStream.position(); } catch (IOException exc) { - throw new ReviewedStingException("Unable to read position from index file " + mFile, exc); + throw new ReviewedGATKException("Unable to read position from index file " + mFile, exc); } } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java index f87779572..f1d6203d6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java index 373aa51af..c272e0acd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; import java.util.List; import java.util.NoSuchElementException; @@ -93,7 +93,7 @@ class IntervalOverlapFilteringIterator implements CloseableIterator { if(foundMappedIntervals) { if(keepOnlyUnmappedReads) - throw new ReviewedStingException("Tried to apply IntervalOverlapFilteringIterator to a mixed of mapped and unmapped intervals. Please apply this filter to only mapped or only unmapped reads"); + throw new ReviewedGATKException("Tried to apply IntervalOverlapFilteringIterator to a mixed of mapped and unmapped intervals. Please apply this filter to only mapped or only unmapped reads"); this.intervalContigIndices = new int[intervals.size()]; this.intervalStarts = new int[intervals.size()]; this.intervalEnds = new int[intervals.size()]; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java index a873be832..e355c7ee2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.PeekableIterator; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocSortedSet; +import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; import java.util.Iterator; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java index 12a5d7ec6..28d4faf2c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.SAMFileSpan; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.Utils; import java.util.List; import java.util.Map; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java index 1c57ea78f..6fb4d48ed 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import java.util.Iterator; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java index 3fd0aa98f..d4321da3b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java @@ -23,16 +23,16 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.*; import htsjdk.samtools.util.CloseableIterator; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.engine.iterators.GATKSAMIteratorAdapter; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.*; @@ -148,7 +148,7 @@ public class ReadShard extends Shard { @Override public void fill( PeekableIterator readIter ) { if( ! buffersReads() ) - throw new ReviewedStingException("Attempting to fill a non-buffering shard."); + throw new ReviewedGATKException("Attempting to fill a non-buffering shard."); SAMFileHeader.SortOrder sortOrder = getReadProperties().getSortOrder(); SAMRecord read = null; @@ -205,8 +205,8 @@ public class ReadShard extends Shard { * Creates an iterator over reads stored in this shard's read cache. * @return */ - public StingSAMIterator iterator() { - return StingSAMIteratorAdapter.adapt(reads.iterator()); + public GATKSAMIterator iterator() { + return GATKSAMIteratorAdapter.adapt(reads.iterator()); } /** @@ -244,7 +244,7 @@ public class ReadShard extends Shard { for ( final SAMRecord read : reads ) { if ( contig != null && ! read.getReferenceName().equals(contig) ) - throw new ReviewedStingException("ReadShard contains reads spanning contig boundaries, which is no longer allowed. " + throw new ReviewedGATKException("ReadShard contains reads spanning contig boundaries, which is no longer allowed. " + "First contig is " + contig + " next read was " + read.getReferenceName() ); contig = read.getReferenceName(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java index 04f70b894..4a27219e4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.*; @@ -186,11 +186,11 @@ public class ReadShardBalancer extends ShardBalancer { // Make sure that if we see a monolithic FilePointer (representing all regions in all files) that // it is the ONLY FilePointer we ever encounter if ( encounteredMonolithicFilePointer ) { - throw new ReviewedStingException("Bug: encountered additional FilePointers after encountering a monolithic FilePointer"); + throw new ReviewedGATKException("Bug: encountered additional FilePointers after encountering a monolithic FilePointer"); } if ( filePointers.peek().isMonolithic() ) { if ( totalFilePointersConsumed > 0 ) { - throw new ReviewedStingException("Bug: encountered additional FilePointers before encountering a monolithic FilePointer"); + throw new ReviewedGATKException("Bug: encountered additional FilePointers before encountering a monolithic FilePointer"); } encounteredMonolithicFilePointer = true; logger.debug(String.format("Encountered monolithic FilePointer: %s", filePointers.peek())); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java index 4801ab69d..6df0d89ba 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.MergingSamRecordIterator; import htsjdk.samtools.SamFileHeaderMerger; @@ -31,23 +31,23 @@ import htsjdk.samtools.*; import htsjdk.samtools.util.CloseableIterator; import htsjdk.samtools.util.RuntimeIOException; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.ReadMetrics; -import org.broadinstitute.sting.gatk.ReadProperties; -import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; -import org.broadinstitute.sting.gatk.downsampling.*; -import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator; -import org.broadinstitute.sting.gatk.filters.ReadFilter; -import org.broadinstitute.sting.gatk.iterators.*; -import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.SimpleTimer; -import org.broadinstitute.sting.utils.baq.ReadTransformingIterator; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory; +import org.broadinstitute.gatk.engine.ReadMetrics; +import org.broadinstitute.gatk.engine.ReadProperties; +import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.engine.downsampling.*; +import org.broadinstitute.gatk.engine.filters.CountingFilteringIterator; +import org.broadinstitute.gatk.engine.filters.ReadFilter; +import org.broadinstitute.gatk.engine.iterators.*; +import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocSortedSet; +import org.broadinstitute.gatk.utils.SimpleTimer; +import org.broadinstitute.gatk.utils.baq.ReadTransformingIterator; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; +import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory; import java.io.File; import java.lang.reflect.InvocationTargetException; @@ -504,7 +504,7 @@ public class SAMDataSource { this.readMetrics.incrementMetrics(readMetrics); } - public StingSAMIterator seek(Shard shard) { + public GATKSAMIterator seek(Shard shard) { if(shard.buffersReads()) { return shard.iterator(); } @@ -524,7 +524,7 @@ public class SAMDataSource { if(readers.getReader(id) == read.getFileSource().getReader()) return id; } - throw new ReviewedStingException("Unable to find id for reader associated with read " + read.getReadName()); + throw new ReviewedGATKException("Unable to find id for reader associated with read " + read.getReadName()); } /** @@ -550,7 +550,7 @@ public class SAMDataSource { * @param shard The shard specifying the data limits. * @return An iterator over the selected data. */ - protected StingSAMIterator getIterator( Shard shard ) { + protected GATKSAMIterator getIterator( Shard shard ) { return getIterator(resourcePool.getAvailableReaders(), shard, shard instanceof ReadShard); } @@ -561,7 +561,7 @@ public class SAMDataSource { * @param enableVerification True to verify. For compatibility with old sharding strategy. * @return An iterator over the selected data. */ - private StingSAMIterator getIterator(SAMReaders readers, Shard shard, boolean enableVerification) { + private GATKSAMIterator getIterator(SAMReaders readers, Shard shard, boolean enableVerification) { // Set up merging to dynamically merge together multiple BAMs. Map> iteratorMap = new HashMap>(); @@ -571,7 +571,7 @@ public class SAMDataSource { // TODO: null used to be the signal for unmapped, but we've replaced that with a simple index query for the last bin. // TODO: Kill this check once we've proven that the design elements are gone. if(shard.getFileSpans().get(id) == null) - throw new ReviewedStingException("SAMDataSource: received null location for reader " + id + ", but null locations are no longer supported."); + throw new ReviewedGATKException("SAMDataSource: received null location for reader " + id + ", but null locations are no longer supported."); try { if(threadAllocation.getNumIOThreads() > 0) { @@ -603,7 +603,7 @@ public class SAMDataSource { return applyDecoratingIterators(readMetrics, enableVerification, readProperties.useOriginalBaseQualities(), - new ReleasingIterator(readers,StingSAMIteratorAdapter.adapt(mergingIterator)), + new ReleasingIterator(readers,GATKSAMIteratorAdapter.adapt(mergingIterator)), readProperties.getValidationExclusionList().contains(ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION), readProperties.getSupplementalFilters(), readProperties.getReadTransformers(), @@ -667,10 +667,10 @@ public class SAMDataSource { * @param isLocusBasedTraversal true if we're dealing with a read stream from a LocusShard * @return An iterator wrapped with filters reflecting the passed-in parameters. Will not be null. */ - protected StingSAMIterator applyDecoratingIterators(ReadMetrics readMetrics, + protected GATKSAMIterator applyDecoratingIterators(ReadMetrics readMetrics, boolean enableVerification, boolean useOriginalBaseQualities, - StingSAMIterator wrappedIterator, + GATKSAMIterator wrappedIterator, Boolean noValidationOfReadOrder, Collection supplementalFilters, List readTransformers, @@ -686,7 +686,7 @@ public class SAMDataSource { // Read Filters: these are applied BEFORE downsampling, so that we downsample within the set of reads // that actually survive filtering. Otherwise we could get much less coverage than requested. - wrappedIterator = StingSAMIteratorAdapter.adapt(new CountingFilteringIterator(readMetrics,wrappedIterator,supplementalFilters)); + wrappedIterator = GATKSAMIteratorAdapter.adapt(new CountingFilteringIterator(readMetrics,wrappedIterator,supplementalFilters)); // Downsampling: @@ -719,7 +719,7 @@ public class SAMDataSource { return wrappedIterator; } - protected StingSAMIterator applyDownsamplingIterator( StingSAMIterator wrappedIterator ) { + protected GATKSAMIterator applyDownsamplingIterator( GATKSAMIterator wrappedIterator ) { if ( readProperties.getDownsamplingMethod() == null || readProperties.getDownsamplingMethod().type == DownsampleType.NONE ) { return wrappedIterator; @@ -791,7 +791,7 @@ public class SAMDataSource { public synchronized void releaseReaders(SAMReaders readers) { if(!allResources.contains(readers)) - throw new ReviewedStingException("Tried to return readers from the pool that didn't originate in the pool."); + throw new ReviewedGATKException("Tried to return readers from the pool that didn't originate in the pool."); availableResources.add(readers); } @@ -806,12 +806,12 @@ public class SAMDataSource { if(id != null) return id; } - throw new ReviewedStingException("No such reader id is available"); + throw new ReviewedGATKException("No such reader id is available"); } private synchronized void createNewResource() { if(allResources.size() > maxEntries) - throw new ReviewedStingException("Cannot create a new resource pool. All resources are in use."); + throw new ReviewedGATKException("Cannot create a new resource pool. All resources are in use."); SAMReaders readers = new SAMReaders(readerIDs, validationStringency, removeProgramRecords); allResources.add(readers); availableResources.add(readers); @@ -1087,7 +1087,7 @@ public class SAMDataSource { } } - private class ReleasingIterator implements StingSAMIterator { + private class ReleasingIterator implements GATKSAMIterator { /** * The resource acting as the source of the data. */ @@ -1096,9 +1096,9 @@ public class SAMDataSource { /** * The iterator to wrap. */ - private final StingSAMIterator wrappedIterator; + private final GATKSAMIterator wrappedIterator; - public ReleasingIterator(SAMReaders resource, StingSAMIterator wrapped) { + public ReleasingIterator(SAMReaders resource, GATKSAMIterator wrapped) { this.resource = resource; this.wrappedIterator = wrapped; } @@ -1108,7 +1108,7 @@ public class SAMDataSource { } public void remove() { - throw new UnsupportedOperationException("Can't remove from a StingSAMIterator"); + throw new UnsupportedOperationException("Can't remove from a GATKSAMIterator"); } public void close() { @@ -1146,16 +1146,16 @@ public class SAMDataSource { indexFile = (File)indexFileLocator.invoke(null,bamFile); } catch(ClassNotFoundException ex) { - throw new ReviewedStingException("Unable to locate BAMFileReader class, used to check for index files"); + throw new ReviewedGATKException("Unable to locate BAMFileReader class, used to check for index files"); } catch(NoSuchMethodException ex) { - throw new ReviewedStingException("Unable to locate Picard index file locator."); + throw new ReviewedGATKException("Unable to locate Picard index file locator."); } catch(IllegalAccessException ex) { - throw new ReviewedStingException("Unable to access Picard index file locator."); + throw new ReviewedGATKException("Unable to access Picard index file locator."); } catch(InvocationTargetException ex) { - throw new ReviewedStingException("Unable to invoke Picard index file locator."); + throw new ReviewedGATKException("Unable to invoke Picard index file locator."); } return indexFile; @@ -1191,7 +1191,7 @@ public class SAMDataSource { */ public Iterable createShardIteratorOverIntervals(final GenomeLocSortedSet intervals,final ShardBalancer shardBalancer) { if(intervals == null) - throw new ReviewedStingException("Unable to create schedule from intervals; no intervals were provided."); + throw new ReviewedGATKException("Unable to create schedule from intervals; no intervals were provided."); shardBalancer.initialize(this,IntervalSharder.shardOverIntervals(SAMDataSource.this,intervals,intervalMergingRule),genomeLocParser); return shardBalancer; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderID.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderID.java index 72c037707..ef5aaa040 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderID.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderID.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; -import org.broadinstitute.sting.commandline.Tags; +import org.broadinstitute.gatk.utils.commandline.Tags; import java.io.File; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java index fadeb2452..cc8944ce3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java @@ -23,17 +23,17 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.SAMFileSpan; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.ReadMetrics; -import org.broadinstitute.sting.gatk.ReadProperties; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.HasGenomeLocation; +import org.broadinstitute.gatk.engine.ReadMetrics; +import org.broadinstitute.gatk.engine.ReadProperties; +import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.HasGenomeLocation; import java.util.Collections; import java.util.List; @@ -249,5 +249,5 @@ public abstract class Shard implements HasGenomeLocation { * Gets the iterator over the elements cached in the shard. * @return */ - public StingSAMIterator iterator() { throw new UnsupportedOperationException("This shard does not buffer reads."); } + public GATKSAMIterator iterator() { throw new UnsupportedOperationException("This shard does not buffer reads."); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java index bf00a0ff8..237a38021 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; +package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.PeekableIterator; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocParser; import java.util.Iterator; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java index 41c75421b..f3506f22c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads; \ No newline at end of file +package org.broadinstitute.gatk.engine.datasources.reads; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java index 5f1171582..ca97732cf 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads.utilities; +package org.broadinstitute.gatk.engine.datasources.reads.utilities; import htsjdk.samtools.BAMIndex; import htsjdk.samtools.SAMFileReader; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.CommandLineProgram; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.instrumentation.Sizeof; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.instrumentation.Sizeof; import java.io.File; import java.lang.reflect.Field; @@ -58,7 +58,7 @@ public class BAMFileStat extends CommandLineProgram { public int execute() { switch(command) { case ShowBlocks: - throw new ReviewedStingException("The BAM block inspector has been disabled."); + throw new ReviewedGATKException("The BAM block inspector has been disabled."); case ShowIndex: showIndexBins(new File(bamFileName),range); break; @@ -171,7 +171,7 @@ public class BAMFileStat extends CommandLineProgram { } } catch(IllegalAccessException ex) { - throw new ReviewedStingException("Unable to examine cached index",ex); + throw new ReviewedGATKException("Unable to examine cached index",ex); } System.out.printf("%nOverall: %d bins, %d chunks, %d linear index entries",numBins,numChunks,numLinearIndexEntries); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java index f21f1f76a..bde44a08c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads.utilities; +package org.broadinstitute.gatk.engine.datasources.reads.utilities; import htsjdk.samtools.SAMFileReader; import htsjdk.samtools.SAMFileWriter; import htsjdk.samtools.SAMFileWriterFactory; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.CommandLineProgram; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; import java.io.File; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java index dee62adcc..9105b4cf8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java @@ -23,24 +23,24 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads.utilities; +package org.broadinstitute.gatk.engine.datasources.reads.utilities; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.CommandLineProgram; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.datasources.reads.FilePointer; -import org.broadinstitute.sting.gatk.datasources.reads.IntervalSharder; -import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; -import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; -import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.sting.utils.text.ListFileUtils; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; +import org.broadinstitute.gatk.utils.commandline.Input; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.datasources.reads.FilePointer; +import org.broadinstitute.gatk.engine.datasources.reads.IntervalSharder; +import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; +import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; +import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocSortedSet; +import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; +import org.broadinstitute.gatk.utils.interval.IntervalUtils; +import org.broadinstitute.gatk.utils.text.ListFileUtils; import java.io.File; import java.io.IOException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java index 70d775775..c3edab396 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads.utilities; +package org.broadinstitute.gatk.engine.datasources.reads.utilities; import htsjdk.samtools.GATKBAMFileSpan; import htsjdk.samtools.GATKChunk; import htsjdk.samtools.SAMFileReader; import htsjdk.samtools.SAMRecordIterator; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.CommandLineProgram; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.File; import java.util.regex.Matcher; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java index 7a188c7e0..807e0380d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads.utilities; +package org.broadinstitute.gatk.engine.datasources.reads.utilities; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.CommandLineProgram; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; import java.io.File; import java.io.FileInputStream; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java index 9dbe3e6e4..d65b779e5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads.utilities; +package org.broadinstitute.gatk.engine.datasources.reads.utilities; import htsjdk.samtools.util.BlockGunzipper; -import org.broadinstitute.sting.commandline.CommandLineProgram; -import org.broadinstitute.sting.commandline.Input; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; +import org.broadinstitute.gatk.utils.commandline.Input; import java.io.File; import java.io.FileInputStream; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java index 27f260964..65a909a21 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reads.utilities; \ No newline at end of file +package org.broadinstitute.gatk.engine.datasources.reads.utilities; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java index 8ea4376fd..6fdbea3a0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java @@ -23,18 +23,18 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reference; +package org.broadinstitute.gatk.engine.datasources.reference; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.SAMSequenceRecord; -import org.broadinstitute.sting.gatk.datasources.reads.LocusShard; -import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.engine.datasources.reads.LocusShard; +import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; +import org.broadinstitute.gatk.engine.datasources.reads.Shard; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocSortedSet; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import java.io.File; import java.util.ArrayList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java index 18470599f..581d213dd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.reference; \ No newline at end of file +package org.broadinstitute.gatk.engine.datasources.reference; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java index 07baf19e1..2543c42b7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.rmd; +package org.broadinstitute.gatk.engine.datasources.rmd; /** * Marker interface that represents an arbitrary consecutive segment within a data stream. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java index 6f9ef8db0..eba5b534e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.rmd; +package org.broadinstitute.gatk.engine.datasources.rmd; /** * Models the entire stream of data. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java index 22d238999..0344ff032 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.rmd; +package org.broadinstitute.gatk.engine.datasources.rmd; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.HasGenomeLocation; /** * Models a mapped position within a stream of GATK input data. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java index b2c4832e1..762eb0b44 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java @@ -23,18 +23,18 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.rmd; +package org.broadinstitute.gatk.engine.datasources.rmd; import htsjdk.samtools.SAMSequenceDictionary; -import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator; -import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; -import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder; -import org.broadinstitute.sting.gatk.refdata.utils.FlashBackIterator; -import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.refdata.SeekableRODIterator; +import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack; +import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; +import org.broadinstitute.gatk.engine.refdata.utils.FlashBackIterator; +import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.List; @@ -97,7 +97,7 @@ class ReferenceOrderedDataPool extends ResourcePool 0) - throw new ReviewedStingException("BUG: Tried to create multiple iterators over streaming ROD interface"); + throw new ReviewedGATKException("BUG: Tried to create multiple iterators over streaming ROD interface"); RMDTrack track = builder.createInstanceOfTrack(fileDescriptor); LocationAwareSeekableRODIterator iter = new SeekableRODIterator(track.getHeader(),track.getSequenceDictionary(),referenceSequenceDictionary,genomeLocParser,track.getIterator()); return (flashbackData) ? new FlashBackIterator(iter) : iter; @@ -133,7 +133,7 @@ class ReferenceOrderedDataPool extends ResourcePool { // make sure we actually removed the assignment if (obj == null) - throw new ReviewedStingException("Failed to remove resource assignment; target key had no associated value in the resource assignment map"); + throw new ReviewedGATKException("Failed to remove resource assignment; target key had no associated value in the resource assignment map"); // Return the resource to the pool. if( !allResources.contains(resource) ) - throw new ReviewedStingException("Iterator does not belong to the given pool."); + throw new ReviewedGATKException("Iterator does not belong to the given pool."); availableResources.add(resource); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java index 4f6e4d685..41b7e53b7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.datasources.rmd; \ No newline at end of file +package org.broadinstitute.gatk.engine.datasources.rmd; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtils.java index ecbe7376c..534facd44 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtils.java @@ -23,16 +23,16 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.collections.DefaultHashMap; -import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.pileup.*; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.text.XReadLines; +import org.broadinstitute.gatk.utils.*; +import org.broadinstitute.gatk.utils.collections.DefaultHashMap; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.pileup.*; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.BaseUtils; +import org.broadinstitute.gatk.utils.text.XReadLines; import htsjdk.variant.variantcontext.Allele; import java.io.File; @@ -290,7 +290,7 @@ public class AlleleBiasedDownsamplingUtils { * @return sample-contamination Map */ - public static DefaultHashMap loadContaminationFile(File ContaminationFractionFile, final Double defaultContaminationFraction, final Set AvailableSampleIDs, Logger logger) throws StingException { + public static DefaultHashMap loadContaminationFile(File ContaminationFractionFile, final Double defaultContaminationFraction, final Set AvailableSampleIDs, Logger logger) throws GATKException { DefaultHashMap sampleContamination = new DefaultHashMap(defaultContaminationFraction); Set nonSamplesInContaminationFile = new HashSet(sampleContamination.keySet()); try { @@ -361,7 +361,7 @@ public class AlleleBiasedDownsamplingUtils { return sampleContamination; } catch (IOException e) { - throw new StingException("I/O Error while reading sample-contamination file " + ContaminationFractionFile.getName() + ": " + e.getMessage()); + throw new GATKException("I/O Error while reading sample-contamination file " + ContaminationFractionFile.getName() + ": " + e.getMessage()); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsampleType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsampleType.java index 0917df39c..715ef6eed 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsampleType.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsampleType.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; /** * Type of downsampling method to invoke. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/Downsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/Downsampler.java index 7b42f75f9..8ab0198b1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/Downsampler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/Downsampler.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import java.util.Collection; import java.util.List; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingMethod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingMethod.java index 8e92b1ff3..94a3cc74b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingMethod.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingMethod.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; -import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker; +import org.broadinstitute.gatk.engine.walkers.LocusWalker; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.exceptions.UserException; /** * Describes the method for downsampling reads at a given locus. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIterator.java index 16beeaa6e..6b398aba2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIterator.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; +import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; import java.util.Collection; import java.util.Iterator; @@ -34,14 +34,14 @@ import java.util.NoSuchElementException; /** - * StingSAMIterator wrapper around our generic reads downsampler interface. Converts the push-style + * GATKSAMIterator wrapper around our generic reads downsampler interface. Converts the push-style * downsampler interface to a pull model. * * @author David Roazen */ -public class DownsamplingReadsIterator implements StingSAMIterator { +public class DownsamplingReadsIterator implements GATKSAMIterator { - private StingSAMIterator nestedSAMIterator; + private GATKSAMIterator nestedSAMIterator; private ReadsDownsampler downsampler; private Collection downsampledReadsCache; private SAMRecord nextRead = null; @@ -51,7 +51,7 @@ public class DownsamplingReadsIterator implements StingSAMIterator { * @param iter wrapped iterator from which this iterator will pull reads * @param downsampler downsampler through which the reads will be fed */ - public DownsamplingReadsIterator( StingSAMIterator iter, ReadsDownsampler downsampler ) { + public DownsamplingReadsIterator( GATKSAMIterator iter, ReadsDownsampler downsampler ) { nestedSAMIterator = iter; this.downsampler = downsampler; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingUtils.java index 877083829..39a48c897 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingUtils.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.util.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsampler.java index 5337ffe6d..a2d613c5f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsampler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsampler.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.ArrayList; import java.util.List; @@ -56,7 +56,7 @@ public class FractionalDownsampler extends ReadsDownsampler */ public FractionalDownsampler( final double fraction ) { if ( fraction < 0.0 || fraction > 1.0 ) { - throw new ReviewedStingException("Fraction of reads to include must be between 0.0 and 1.0, inclusive"); + throw new ReviewedGATKException("Fraction of reads to include must be between 0.0 and 1.0, inclusive"); } cutoffForInclusion = (int)(fraction * RANDOM_POOL_SIZE); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerFactory.java index 000badad9..4ddf8dd87 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerFactory.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerFactory.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsampler.java index 3ce4d09d6..4ae7bc581 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsampler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsampler.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; -import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.gatk.utils.MathUtils; import java.util.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PassThroughDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PassThroughDownsampler.java index 907803a1f..a5fdf24a9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PassThroughDownsampler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PassThroughDownsampler.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIterator.java index b13c303d6..118bbbbeb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIterator.java @@ -23,26 +23,26 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMRecordComparator; import htsjdk.samtools.SAMRecordCoordinateComparator; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; +import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; import java.util.*; /** - * StingSAMIterator wrapper around our generic reads downsampler interface + * GATKSAMIterator wrapper around our generic reads downsampler interface * that downsamples reads for each sample independently, and then re-assembles * the reads back into a single merged stream. * * @author David Roazen */ -public class PerSampleDownsamplingReadsIterator implements StingSAMIterator { +public class PerSampleDownsamplingReadsIterator implements GATKSAMIterator { - private StingSAMIterator nestedSAMIterator; + private GATKSAMIterator nestedSAMIterator; private ReadsDownsamplerFactory downsamplerFactory; private Map> perSampleDownsamplers; private PriorityQueue orderedDownsampledReadsCache; @@ -63,7 +63,7 @@ public class PerSampleDownsamplingReadsIterator implements StingSAMIterator { * @param iter wrapped iterator from which this iterator will pull reads * @param downsamplerFactory factory used to create new downsamplers as needed */ - public PerSampleDownsamplingReadsIterator( StingSAMIterator iter, ReadsDownsamplerFactory downsamplerFactory ) { + public PerSampleDownsamplingReadsIterator( GATKSAMIterator iter, ReadsDownsamplerFactory downsamplerFactory ) { nestedSAMIterator = iter; this.downsamplerFactory = downsamplerFactory; perSampleDownsamplers = new HashMap>(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsampler.java index b3d709e69..9263920f9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsampler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsampler.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsamplerFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsamplerFactory.java index 453d34e07..9ef847e67 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsamplerFactory.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsamplerFactory.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsampler.java index 0b637528e..99a0bbd7a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsampler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsampler.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.*; @@ -99,7 +99,7 @@ public class ReservoirDownsampler extends ReadsDownsampler< */ public ReservoirDownsampler ( final int targetSampleSize, final boolean expectFewOverflows ) { if ( targetSampleSize <= 0 ) { - throw new ReviewedStingException("Cannot do reservoir downsampling with a sample size <= 0"); + throw new ReviewedGATKException("Cannot do reservoir downsampling with a sample size <= 0"); } this.targetSampleSize = targetSampleSize; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerFactory.java index 2da45826e..c825bae1f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerFactory.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerFactory.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsampler.java index 79bb97234..af0aa54c0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsampler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsampler.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerFactory.java index 42a43c224..3fc66cafe 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerFactory.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerFactory.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.downsampling; +package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java index d0ba0fa21..9276331e1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java @@ -23,16 +23,16 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.datasources.providers.LocusShardDataProvider; +import org.broadinstitute.gatk.engine.datasources.providers.ShardDataProvider; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocSortedSet; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.ArrayList; import java.util.Iterator; @@ -184,7 +184,7 @@ public abstract class Accumulator { */ public void accumulate( ShardDataProvider provider, Object result ) { if(!(provider instanceof LocusShardDataProvider)) - throw new ReviewedStingException("Unable to reduce by interval on reads traversals at this time."); + throw new ReviewedGATKException("Unable to reduce by interval on reads traversals at this time."); GenomeLoc location = ((LocusShardDataProvider)provider).getLocus(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java index 753e396db..f7e3dbcda 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java @@ -23,23 +23,23 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.tribble.TribbleException; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.io.OutputTracker; -import org.broadinstitute.sting.gatk.io.ThreadGroupOutputTracker; -import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.MultiThreadedErrorTracker; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; +import org.broadinstitute.gatk.engine.datasources.reads.Shard; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.engine.io.OutputTracker; +import org.broadinstitute.gatk.engine.io.ThreadGroupOutputTracker; +import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; +import org.broadinstitute.gatk.engine.walkers.TreeReducible; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.MultiThreadedErrorTracker; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.threading.ThreadPoolMonitor; import java.util.Collection; import java.util.Iterator; @@ -181,13 +181,13 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar try { result = reduceTree.getResult().get(); notifyTraversalDone(walker,result); - } catch (ReviewedStingException ex) { + } catch (ReviewedGATKException ex) { throw ex; } catch ( ExecutionException ex ) { // the thread died and we are failing to get the result, rethrow it as a runtime exception throw notifyOfTraversalError(ex.getCause()); } catch (Exception ex) { - throw new ReviewedStingException("Unable to retrieve result", ex); + throw new ReviewedGATKException("Unable to retrieve result", ex); } // do final cleanup operations @@ -326,7 +326,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar // Specifically catch Tribble I/O exceptions and rethrow them as Reviewed. We don't expect // any issues here because we created the Tribble output file mere moments ago and expect it to // be completely valid. - throw new ReviewedStingException("Unable to merge temporary Tribble output file.",ex); + throw new ReviewedGATKException("Unable to merge temporary Tribble output file.",ex); } } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java index e8952c479..30e03c6a8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; /** * User: hanna * Date: May 29, 2009 diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java index ddc8c6fe4..293bb1ce5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java @@ -23,23 +23,23 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; import htsjdk.samtools.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.io.DirectOutputTracker; -import org.broadinstitute.sting.gatk.io.OutputTracker; -import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.gatk.traversals.TraversalEngine; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.datasources.providers.LocusShardDataProvider; +import org.broadinstitute.gatk.engine.datasources.providers.ReadShardDataProvider; +import org.broadinstitute.gatk.engine.datasources.providers.ShardDataProvider; +import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; +import org.broadinstitute.gatk.engine.datasources.reads.Shard; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.engine.io.DirectOutputTracker; +import org.broadinstitute.gatk.engine.io.OutputTracker; +import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; +import org.broadinstitute.gatk.engine.traversals.TraversalEngine; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.threading.ThreadEfficiencyMonitor; import java.util.Collection; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java index d6e50d748..e192b9a72 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java @@ -23,28 +23,28 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; import com.google.java.contract.Ensures; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.ReadMetrics; -import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.io.OutputTracker; -import org.broadinstitute.sting.gatk.iterators.NullSAMIterator; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.gatk.traversals.*; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.AutoFormattingTime; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.progressmeter.ProgressMeter; -import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.ReadMetrics; +import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; +import org.broadinstitute.gatk.engine.datasources.reads.Shard; +import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.gatk.engine.io.OutputTracker; +import org.broadinstitute.gatk.engine.iterators.NullSAMIterator; +import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; +import org.broadinstitute.gatk.engine.traversals.*; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.AutoFormattingTime; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.progressmeter.ProgressMeter; +import org.broadinstitute.gatk.utils.threading.ThreadEfficiencyMonitor; import javax.management.JMException; import javax.management.MBeanServer; @@ -216,11 +216,11 @@ public abstract class MicroScheduler implements MicroSchedulerMBean { int thisInstance = instanceNumber++; mBeanServer = ManagementFactory.getPlatformMBeanServer(); try { - mBeanName = new ObjectName("org.broadinstitute.sting.gatk.executive:type=MicroScheduler,instanceNumber="+thisInstance); + mBeanName = new ObjectName("org.broadinstitute.gatk.engine.executive:type=MicroScheduler,instanceNumber="+thisInstance); mBeanServer.registerMBean(this, mBeanName); } catch (JMException ex) { - throw new ReviewedStingException("Unable to register microscheduler with JMX", ex); + throw new ReviewedGATKException("Unable to register microscheduler with JMX", ex); } } @@ -317,7 +317,7 @@ public abstract class MicroScheduler implements MicroSchedulerMBean { * @param shard the shard to use when querying reads. * @return an iterator over the reads specified in the shard. */ - protected StingSAMIterator getReadIterator(Shard shard) { + protected GATKSAMIterator getReadIterator(Shard shard) { return (!reads.isEmpty()) ? reads.seek(shard) : new NullSAMIterator(); } @@ -403,7 +403,7 @@ public abstract class MicroScheduler implements MicroSchedulerMBean { mBeanServer.unregisterMBean(mBeanName); } catch (JMException ex) { - throw new ReviewedStingException("Unable to unregister microscheduler with JMX", ex); + throw new ReviewedGATKException("Unable to unregister microscheduler with JMX", ex); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java index bb87eeba7..772fe01dd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; /** * Created by IntelliJ IDEA. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java index bfd5306e7..4e5ef9ff0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; -import org.broadinstitute.sting.gatk.io.storage.Storage; +import org.broadinstitute.gatk.engine.io.storage.Storage; import java.util.ArrayList; import java.util.Collection; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java index 5f4b31f46..e02b846b7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; import java.util.ArrayList; import java.util.LinkedList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java index c52cdf64b..443fdf7e7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java @@ -23,17 +23,17 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.io.ThreadGroupOutputTracker; -import org.broadinstitute.sting.gatk.traversals.TraversalEngine; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.datasources.providers.LocusShardDataProvider; +import org.broadinstitute.gatk.engine.datasources.providers.ShardDataProvider; +import org.broadinstitute.gatk.engine.datasources.reads.Shard; +import org.broadinstitute.gatk.engine.io.ThreadGroupOutputTracker; +import org.broadinstitute.gatk.engine.traversals.TraversalEngine; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.concurrent.Callable; /** @@ -149,7 +149,7 @@ public class ShardTraverser implements Callable { } } catch( InterruptedException ex ) { - throw new ReviewedStingException("Interrupted while waiting for more output to be finalized.",ex); + throw new ReviewedGATKException("Interrupted while waiting for more output to be finalized.",ex); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java index 97ae06778..270b06f33 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; -import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.walkers.TreeReducible; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.concurrent.Callable; import java.util.concurrent.ExecutionException; @@ -106,11 +106,11 @@ public class TreeReducer implements Callable { } catch( InterruptedException ex ) { microScheduler.notifyOfTraversalError(ex); - throw new ReviewedStingException("Hierarchical reduce interrupted", ex); + throw new ReviewedGATKException("Hierarchical reduce interrupted", ex); } catch( ExecutionException ex ) { microScheduler.notifyOfTraversalError(ex); - throw new ReviewedStingException("Hierarchical reduce failed", ex); + throw new ReviewedGATKException("Hierarchical reduce failed", ex); } final long endTime = System.currentTimeMillis(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java index 22e91a4ab..c8483298b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java @@ -23,20 +23,20 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; +package org.broadinstitute.gatk.engine.executive; import htsjdk.samtools.util.PeekableIterator; -import org.broadinstitute.sting.gatk.ReadProperties; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.iterators.GATKSAMIterator; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.locusiterator.LocusIterator; -import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.ReadProperties; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.datasources.reads.Shard; +import org.broadinstitute.gatk.engine.iterators.GATKSAMRecordIterator; +import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.locusiterator.LocusIterator; +import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Collection; import java.util.Iterator; @@ -72,7 +72,7 @@ public class WindowMaker implements Iterable, I /** * Hold the read iterator so that it can be closed later. */ - private final GATKSAMIterator readIterator; + private final GATKSAMRecordIterator readIterator; /** * The data source for reads. Will probably come directly from the BAM file. @@ -107,9 +107,9 @@ public class WindowMaker implements Iterable, I private final LocusIteratorByState libs; - public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, StingSAMIterator iterator, List intervals, Collection sampleNames) { + public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, GATKSAMIterator iterator, List intervals, Collection sampleNames) { this.sourceInfo = shard.getReadProperties(); - this.readIterator = new GATKSAMIterator(iterator); + this.readIterator = new GATKSAMRecordIterator(iterator); this.libs = new LocusIteratorByState(readIterator,sourceInfo,genomeLocParser,sampleNames); this.sourceIterator = new PeekableIterator(libs); @@ -117,7 +117,7 @@ public class WindowMaker implements Iterable, I this.intervalIterator = intervals.size()>0 ? new PeekableIterator(intervals.iterator()) : null; } - public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, StingSAMIterator iterator, List intervals ) { + public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, GATKSAMIterator iterator, List intervals ) { this(shard, genomeLocParser, iterator, intervals, LocusIteratorByState.sampleListForSAMWithoutReadGroups()); } @@ -205,7 +205,7 @@ public class WindowMaker implements Iterable, I break; } else - throw new ReviewedStingException("BUG: filtering locus does not contain, is not before, and is not past the given alignment context"); + throw new ReviewedGATKException("BUG: filtering locus does not contain, is not before, and is not past the given alignment context"); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java index aec0f239b..c0d6e9dcc 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.executive; \ No newline at end of file +package org.broadinstitute.gatk.engine.executive; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java index 5b7885333..fce3a714d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java index cce82536e..c25d8d9ca 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java index e8713c7b4..eb566a249 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.filter.SamRecordFilter; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; import htsjdk.samtools.util.CloserUtil; -import org.broadinstitute.sting.gatk.ReadMetrics; +import org.broadinstitute.gatk.engine.ReadMetrics; import java.util.*; @@ -147,4 +147,4 @@ public class CountingFilteringIterator implements CloseableIterator { return null; } -} \ No newline at end of file +} \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java index bda7b6afc..52861e257 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java index 1a981492f..2cc5e2a8b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java index 64d3e5de8..59c3f151b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.help.GATKDocUtils; -import org.broadinstitute.sting.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.classloader.PluginManager; +import org.broadinstitute.gatk.utils.help.GATKDocUtils; +import org.broadinstitute.gatk.utils.help.HelpConstants; import java.util.Collection; import java.util.List; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java index 39eef52fe..8b0f07624 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.gatk.filters.ReadFilter; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.engine.filters.ReadFilter; /** * Only use reads from the specified library diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java index 7082fa8a0..1b59a06d8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.*; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.ReadProperties; -import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; -import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.ReadProperties; +import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.util.Collections; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java index 4c7af592d..67c62b975 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Argument; /** * Filter out reads with low mapping qualities. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java index 27622c5f1..05df7fb0d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.gatk.utils.QualityUtils; /** * Filter out mapping quality zero reads. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java index b0a0c708b..f3f703278 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java index 98b665407..0818f8fa0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java index 14978916f..cca05ebc7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Argument; /** * Filter out reads that exceed a given max insert size diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java index d686815c0..21b291bb3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java index 81b24a317..65bf1eb02 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java @@ -23,18 +23,18 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.iterators.RNAReadTransformer; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.iterators.RNAReadTransformer; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /** * A read transformer that refactor NDN cigar elements to one N element. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java index 9592fd751..8297903d8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java index d1974368b..b09e1f6d5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java index 94dcb5cb5..79f16a5fc 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; /** * Filter out 454 reads. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java index 1560b3157..8236cc219 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; /** * Filter out PL matching reads. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java index a713b58d7..0d4e2b759 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.util.HashSet; import java.util.Set; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java index 8379d9800..428806d6a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.text.XReadLines; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.text.XReadLines; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java index f8c49728c..a2102a838 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.filter.SamRecordFilter; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; /** * A SamRecordFilter that also depends on the header. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java index 2b900a6c3..7c6bfb0e3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.text.XReadLines; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.text.XReadLines; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java index 5e17f6046..1e44df806 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Argument; /** * Filters out reads whose length is >= some value or < some value. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java index 9e15e28dc..23a5151de 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Argument; /** * Filter out all reads except those with this read name diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java index c3df813f6..fd2876654 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Argument; /** * Filters out reads whose strand is negative or positive diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java index 0a44915cd..0c8a93a83 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Argument; /** * A read filter (transformer) that sets all reads mapping quality to a given value. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java index e732116c6..1c91ee518 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Argument; /** * A read filter (transformer) that changes a given read mapping quality to a different value. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java index b05145c6d..2ec0112ab 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Argument; import java.util.Set; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java index 80c993194..5a9d21476 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Argument; /** * Only use reads from the specified read group. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java index bd3f60905..e9cc30276 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java index 26d13d6e3..7e36ffbdf 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.filters; \ No newline at end of file +package org.broadinstitute.gatk.engine.filters; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java index 60e38aa36..96c9cb24d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.io; +package org.broadinstitute.gatk.engine.io; -import org.broadinstitute.sting.gatk.io.storage.Storage; -import org.broadinstitute.sting.gatk.io.storage.StorageFactory; -import org.broadinstitute.sting.gatk.io.stubs.Stub; +import org.broadinstitute.gatk.engine.io.storage.Storage; +import org.broadinstitute.gatk.engine.io.storage.StorageFactory; +import org.broadinstitute.gatk.engine.io.stubs.Stub; /** * Maps creation of storage directly to output streams in parent. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java index acef3e500..772c327bd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.io; +package org.broadinstitute.gatk.engine.io; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.io.FileNotFoundException; import java.io.PrintStream; @@ -44,7 +44,7 @@ public class FastqFileWriter { try { this.output = new PrintStream(filename); } catch (FileNotFoundException e) { - throw new ReviewedStingException("Can't open file " + filename); + throw new ReviewedGATKException("Can't open file " + filename); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/GATKSAMFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/GATKSAMFileWriter.java index 4da62850b..c60aae842 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/GATKSAMFileWriter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/GATKSAMFileWriter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.io; +package org.broadinstitute.gatk.engine.io; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileWriter; @@ -35,7 +35,7 @@ import htsjdk.samtools.SAMFileWriter; * @author mhanna * @version 0.1 */ -public interface StingSAMFileWriter extends SAMFileWriter { +public interface GATKSAMFileWriter extends SAMFileWriter { /** * Writes the given custom header to SAM file output. * @param header The header to write. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java index 7d3bd174f..2a3b0b02d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java @@ -23,18 +23,18 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.io; +package org.broadinstitute.gatk.engine.io; import htsjdk.samtools.SAMFileReader; -import org.broadinstitute.sting.commandline.ArgumentSource; -import org.broadinstitute.sting.gatk.io.storage.Storage; -import org.broadinstitute.sting.gatk.io.storage.StorageFactory; -import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; -import org.broadinstitute.sting.gatk.io.stubs.Stub; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.classloader.JVMUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder; +import org.broadinstitute.gatk.utils.commandline.ArgumentSource; +import org.broadinstitute.gatk.engine.io.storage.Storage; +import org.broadinstitute.gatk.engine.io.storage.StorageFactory; +import org.broadinstitute.gatk.engine.io.stubs.OutputStreamStub; +import org.broadinstitute.gatk.engine.io.stubs.Stub; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.classloader.JVMUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.sam.SAMFileReaderBuilder; import java.io.OutputStream; import java.lang.reflect.Field; @@ -139,7 +139,7 @@ public abstract class OutputTracker { */ protected T getTargetStream( Stub stub ) { if( !outputs.containsKey(stub) ) - throw new ReviewedStingException("OutputTracker was not notified that this stub exists: " + stub); + throw new ReviewedGATKException("OutputTracker was not notified that this stub exists: " + stub); Storage storage = outputs.get(stub); if( storage == null ) { storage = StorageFactory.createStorage(stub); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java index 2eeab7f68..fdb5fd2cb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.io; +package org.broadinstitute.gatk.engine.io; -import org.broadinstitute.sting.gatk.executive.OutputMergeTask; -import org.broadinstitute.sting.gatk.io.storage.Storage; -import org.broadinstitute.sting.gatk.io.storage.StorageFactory; -import org.broadinstitute.sting.gatk.io.stubs.Stub; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.executive.OutputMergeTask; +import org.broadinstitute.gatk.engine.io.storage.Storage; +import org.broadinstitute.gatk.engine.io.storage.StorageFactory; +import org.broadinstitute.gatk.engine.io.stubs.Stub; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.File; import java.io.IOException; @@ -110,7 +110,7 @@ public class ThreadGroupOutputTracker extends OutputTracker { // make sure something hasn't gone wrong, and we somehow find a map that doesn't include our stub if ( target == null ) - throw new ReviewedStingException("target isn't supposed to be null for " + Thread.currentThread() + throw new ReviewedGATKException("target isn't supposed to be null for " + Thread.currentThread() + " id " + Thread.currentThread().getId() + " map is " + threadLocalOutputStreams); } @@ -126,7 +126,7 @@ public class ThreadGroupOutputTracker extends OutputTracker { } else { // something is terribly wrong, we have a storage lookup for a thread that doesn't have // any map data associated with it! - throw new ReviewedStingException("Couldn't find storage map associated with thread " + thread + " in group " + thread.getThreadGroup()); + throw new ReviewedGATKException("Couldn't find storage map associated with thread " + thread + " in group " + thread.getThreadGroup()); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java index 1cc3a5721..ac348a2ab 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.io.storage; +package org.broadinstitute.gatk.engine.io.storage; -import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.io.stubs.OutputStreamStub; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.*; import java.nio.channels.Channels; @@ -59,7 +59,7 @@ public class OutputStreamStorage extends OutputStream implements Storage, StingSAMFileWriter { +public class SAMFileWriterStub implements Stub, GATKSAMFileWriter { /** * Engine to use for collecting attributes for the output SAM file. */ @@ -189,7 +189,7 @@ public class SAMFileWriterStub implements Stub, StingSAMFileWrite */ public void setCompressionLevel( Integer compressionLevel ) { if(writeStarted) - throw new ReviewedStingException("Attempted to change the compression level of a file with alignments already in it."); + throw new ReviewedGATKException("Attempted to change the compression level of a file with alignments already in it."); this.compressionLevel = compressionLevel; } @@ -243,7 +243,7 @@ public class SAMFileWriterStub implements Stub, StingSAMFileWrite */ public void setPresorted(boolean presorted) { if(writeStarted) - throw new ReviewedStingException("Attempted to change the presorted state of a file with alignments already in it."); + throw new ReviewedGATKException("Attempted to change the presorted state of a file with alignments already in it."); this.presorted = presorted; } @@ -261,7 +261,7 @@ public class SAMFileWriterStub implements Stub, StingSAMFileWrite */ public void setMaxRecordsInRam(int maxRecordsInRam) { if(writeStarted) - throw new ReviewedStingException("Attempted to change the max records in RAM of a file with alignments already in it."); + throw new ReviewedGATKException("Attempted to change the max records in RAM of a file with alignments already in it."); this.maxRecordsInRam = maxRecordsInRam; } @@ -279,7 +279,7 @@ public class SAMFileWriterStub implements Stub, StingSAMFileWrite */ public void writeHeader(SAMFileHeader header) { if(writeStarted) - throw new ReviewedStingException("Attempted to change the header of a file with alignments already in it."); + throw new ReviewedGATKException("Attempted to change the header of a file with alignments already in it."); this.headerOverride = header; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java index 554918ceb..cdfd67ae1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.io.stubs; +package org.broadinstitute.gatk.engine.io.stubs; -import org.broadinstitute.sting.gatk.io.OutputTracker; +import org.broadinstitute.gatk.engine.io.OutputTracker; import java.io.File; import java.io.OutputStream; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java index c05b4ff23..27fa858b1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.io.stubs; +package org.broadinstitute.gatk.engine.io.stubs; import htsjdk.tribble.AbstractFeatureReader; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import htsjdk.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.File; @@ -114,7 +114,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor { @Override public Object createTypeDefault(ParsingEngine parsingEngine, ArgumentSource source, Type type) { if(source.isRequired() || !source.defaultsToStdout()) - throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default."); + throw new ReviewedGATKException("BUG: tried to create type default for argument type descriptor that can't support a type default."); VariantContextWriterStub stub = new VariantContextWriterStub(engine, defaultOutputStream, argumentSources); engine.addOutput(stub); return stub; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java index 7fae815f8..fcfddffdb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.io.stubs; +package org.broadinstitute.gatk.engine.io.stubs; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.tribble.index.IndexCreator; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.io.OutputTracker; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.io.OutputTracker; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.Options; import htsjdk.variant.variantcontext.writer.VariantContextWriter; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java index 0464fa00d..cb696e58e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.MergingSamRecordIterator; import htsjdk.samtools.SAMFileHeader; @@ -67,14 +67,14 @@ import java.util.Iterator; * This class implements a read iterator that is bounded by the number of reads * it will produce over the iteration. */ -public class BoundedReadIterator implements StingSAMIterator { +public class BoundedReadIterator implements GATKSAMIterator { // the genome loc we're bounding final private long readCount; private long currentCount = 0; // the iterator we want to decorate - private final StingSAMIterator iterator; + private final GATKSAMIterator iterator; // our unmapped read flag private boolean doNotUseThatUnmappedReadPile = false; @@ -90,7 +90,7 @@ public class BoundedReadIterator implements StingSAMIterator { * @param iter * @param readCount */ - public BoundedReadIterator(StingSAMIterator iter, long readCount) { + public BoundedReadIterator(GATKSAMIterator iter, long readCount) { this.iterator = iter; this.readCount = readCount; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIterator.java index 0b56c36a2..8ca5cfdbe 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; @@ -48,9 +48,9 @@ import htsjdk.samtools.util.CloseableIterator; * @version 1.0 * @date May 6, 2009 *

- * Interface StingSAMIterator + * Interface GATKSAMIterator *

- * This is the standard interface for all iterators in the Sting package that iterate over SAMRecords + * This is the standard interface for all iterators in the GATK package that iterate over SAMRecords */ -public interface StingSAMIterator extends CloseableIterator, Iterable { +public interface GATKSAMIterator extends CloseableIterator, Iterable { } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapter.java index cce97b30a..0dc3e62a7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; @@ -52,17 +52,17 @@ import java.util.Iterator; * @version 1.0 * @date May 13, 2009 *

- * Class StingSAMIteratorAdapter + * Class GATKSAMIteratorAdapter *

- * This class adapts other SAMRecord iterators to the StingSAMIterator + * This class adapts other SAMRecord iterators to the GATKSAMIterator */ -public class StingSAMIteratorAdapter { +public class GATKSAMIteratorAdapter { - public static StingSAMIterator adapt(Iterator iter) { + public static GATKSAMIterator adapt(Iterator iter) { return new PrivateStringSAMIterator(iter); } - public static StingSAMIterator adapt(CloseableIterator iter) { + public static GATKSAMIterator adapt(CloseableIterator iter) { return new PrivateStringSAMCloseableIterator(iter); } @@ -70,10 +70,10 @@ public class StingSAMIteratorAdapter { /** - * this class wraps iterators in a StingSAMIterator, which means just adding the + * this class wraps iterators in a GATKSAMIterator, which means just adding the * methods that implement the iterable<> interface and the close() method from CloseableIterator */ -class PrivateStringSAMIterator implements StingSAMIterator { +class PrivateStringSAMIterator implements GATKSAMIterator { private Iterator iter = null; PrivateStringSAMIterator(Iterator iter) { @@ -93,7 +93,7 @@ class PrivateStringSAMIterator implements StingSAMIterator { } public void remove() { - throw new UnsupportedOperationException("StingSAMIterator's don't allow remove()ing"); + throw new UnsupportedOperationException("GATKSAMIterator's don't allow remove()ing"); } public Iterator iterator() { @@ -103,10 +103,10 @@ class PrivateStringSAMIterator implements StingSAMIterator { /** - * this class wraps closeable iterators in a StingSAMIterator, which means adding the + * this class wraps closeable iterators in a GATKSAMIterator, which means adding the * methods that implement the iterable<> interface. */ -class PrivateStringSAMCloseableIterator implements StingSAMIterator { +class PrivateStringSAMCloseableIterator implements GATKSAMIterator { private CloseableIterator iter = null; PrivateStringSAMCloseableIterator(CloseableIterator iter) { @@ -126,7 +126,7 @@ class PrivateStringSAMCloseableIterator implements StingSAMIterator { } public void remove() { - throw new UnsupportedOperationException("StingSAMIterator's don't allow remove()ing"); + throw new UnsupportedOperationException("GATKSAMIterator's don't allow remove()ing"); } public Iterator iterator() { diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMRecordIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMRecordIterator.java index 3a966f112..6d02acd4a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMRecordIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMRecordIterator.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Iterator; @@ -38,14 +38,14 @@ import java.util.Iterator; * Date: 1/11/13 * Time: 1:19 PM */ -public class GATKSAMIterator implements CloseableIterator, Iterable { +public class GATKSAMRecordIterator implements CloseableIterator, Iterable { final CloseableIterator it; - public GATKSAMIterator(final CloseableIterator it) { + public GATKSAMRecordIterator(final CloseableIterator it) { this.it = it; } - public GATKSAMIterator(final StingSAMIterator it) { + public GATKSAMRecordIterator(final GATKSAMIterator it) { this.it = it; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java index 398a25463..c76a07e36 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; import java.util.Iterator; import java.util.NoSuchElementException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java index 670bd7b1b..bf8b69741 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import java.util.Iterator; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java index c5df3b711..d3a6bdc4b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.File; import java.util.Iterator; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java index 18988bc60..fa130f930 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; @@ -45,7 +45,7 @@ import java.util.NoSuchElementException; /** * A placeholder for an iterator with no data. */ -public class NullSAMIterator implements StingSAMIterator { +public class NullSAMIterator implements GATKSAMIterator { public NullSAMIterator() {} public Iterator iterator() { return this; } @@ -53,5 +53,5 @@ public class NullSAMIterator implements StingSAMIterator { public boolean hasNext() { return false; } public SAMRecord next() { throw new NoSuchElementException("No next element is available."); } - public void remove() { throw new UnsupportedOperationException("Cannot remove from a StingSAMIterator"); } + public void remove() { throw new UnsupportedOperationException("Cannot remove from a GATKSAMIterator"); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java index 3fc712ae3..f46fb0cce 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; /* diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java index 3344d4f51..2eba344bb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; @@ -33,7 +33,7 @@ import htsjdk.samtools.util.CloseableIterator; * @author hanna * @version 0.1 */ -public class PositionTrackingIterator implements StingSAMIterator { +public class PositionTrackingIterator implements GATKSAMIterator { /** * The iterator being tracked. */ @@ -87,7 +87,7 @@ public class PositionTrackingIterator implements StingSAMIterator { /** * {@inheritDoc} */ - public StingSAMIterator iterator() { + public GATKSAMIterator iterator() { return this; } @@ -101,5 +101,5 @@ public class PositionTrackingIterator implements StingSAMIterator { /** * {@inheritDoc} */ - public void remove() { throw new UnsupportedOperationException("Cannot remove from a StingSAMIterator"); } + public void remove() { throw new UnsupportedOperationException("Cannot remove from a GATKSAMIterator"); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PushbackIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PushbackIterator.java index 7cec77fc6..0bb545b6e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PushbackIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PushbackIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import java.util.Iterator; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java index a412ed701..4cc2a82be 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; /** * diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java index a8f41948e..492227932 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; /** * An iterator which does post-processing of a read, including potentially wrapping @@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.sam.AlignmentUtils; * @author mhanna * @version 0.1 */ -public class ReadFormattingIterator implements StingSAMIterator { +public class ReadFormattingIterator implements GATKSAMIterator { /** * Logger. */ @@ -45,7 +45,7 @@ public class ReadFormattingIterator implements StingSAMIterator { /** * Iterator to which to pass */ - private StingSAMIterator wrappedIterator; + private GATKSAMIterator wrappedIterator; /** * True if original base qualities should be used. @@ -64,7 +64,7 @@ public class ReadFormattingIterator implements StingSAMIterator { * @param useOriginalBaseQualities true if original base qualities should be used * @param defaultBaseQualities if the reads have incomplete quality scores, set them all to defaultBaseQuality. */ - public ReadFormattingIterator(StingSAMIterator wrappedIterator, boolean useOriginalBaseQualities, byte defaultBaseQualities) { + public ReadFormattingIterator(GATKSAMIterator wrappedIterator, boolean useOriginalBaseQualities, byte defaultBaseQualities) { this.wrappedIterator = wrappedIterator; this.useOriginalBaseQualities = useOriginalBaseQualities; this.defaultBaseQualities = defaultBaseQualities; @@ -76,7 +76,7 @@ public class ReadFormattingIterator implements StingSAMIterator { * reset the iterator. * @return An iterator through the current data stream. */ - public StingSAMIterator iterator() { + public GATKSAMIterator iterator() { // NOTE: this iterator doesn't perform any kind of reset operation; it just returns itself. // can we do something better? Do we really have to provide support for the Iterable interface? return this; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java index 799014cd4..b7db50594 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Comparator; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java index 70bf228f9..3fa18c496 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import java.lang.annotation.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java index 1859ea1b8..a34d4de82 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java @@ -23,23 +23,23 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.util.Iterator; /** * Verifies that the incoming stream of reads is correctly sorted */ -public class VerifyingSamIterator implements StingSAMIterator { - StingSAMIterator it; +public class VerifyingSamIterator implements GATKSAMIterator { + GATKSAMIterator it; SAMRecord last = null; boolean checkOrderP = true; - public VerifyingSamIterator(StingSAMIterator it) { + public VerifyingSamIterator(GATKSAMIterator it) { this.it = it; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java index 4e5ce87e7..338789022 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; \ No newline at end of file +package org.broadinstitute.gatk.engine.iterators; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java index e8c8896f6..f8126b9a9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java @@ -23,21 +23,21 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.phonehome; +package org.broadinstitute.gatk.engine.phonehome; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Level; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.crypt.CryptUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.io.IOUtils; -import org.broadinstitute.sting.utils.io.Resource; -import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.crypt.CryptUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.io.IOUtils; +import org.broadinstitute.gatk.utils.io.Resource; +import org.broadinstitute.gatk.utils.threading.ThreadEfficiencyMonitor; import org.jets3t.service.S3Service; import org.jets3t.service.S3ServiceException; import org.jets3t.service.impl.rest.httpclient.RestS3Service; @@ -243,7 +243,7 @@ public class GATKRunReport { */ public GATKRunReport(final Walker walker, final Exception e, final GenomeAnalysisEngine engine, final PhoneHomeOption type) { if ( type == PhoneHomeOption.NO_ET ) - throw new ReviewedStingException("Trying to create a run report when type is NO_ET!"); + throw new ReviewedGATKException("Trying to create a run report when type is NO_ET!"); logger.debug("Aggregating data for run report"); @@ -365,7 +365,7 @@ public class GATKRunReport { // --------------------------------------------------------------------------- /** - * Write an XML representation of this report to the stream, throwing a StingException if the marshalling + * Write an XML representation of this report to the stream, throwing a GATKException if the marshalling * fails for any reason. * * @param stream an output stream to write the report to @@ -453,7 +453,7 @@ public class GATKRunReport { /** * Check that the AWS keys can be decrypted and are what we expect them to be * - * @throws ReviewedStingException if anything goes wrong + * @throws ReviewedGATKException if anything goes wrong */ public static void checkAWSAreValid() { try { @@ -461,14 +461,14 @@ public class GATKRunReport { final String secretKeyMD5 = Utils.calcMD5(getAWSUploadSecretKey()); if ( ! AWS_ACCESS_KEY_MD5.equals(accessKeyMD5) ) { - throw new ReviewedStingException("Invalid AWS access key found, expected MD5 " + AWS_ACCESS_KEY_MD5 + " but got " + accessKeyMD5); + throw new ReviewedGATKException("Invalid AWS access key found, expected MD5 " + AWS_ACCESS_KEY_MD5 + " but got " + accessKeyMD5); } if ( ! AWS_SECRET_KEY_MD5.equals(secretKeyMD5) ) { - throw new ReviewedStingException("Invalid AWS secret key found, expected MD5 " + AWS_SECRET_KEY_MD5 + " but got " + secretKeyMD5); + throw new ReviewedGATKException("Invalid AWS secret key found, expected MD5 " + AWS_SECRET_KEY_MD5 + " but got " + secretKeyMD5); } } catch ( Exception e ) { - throw new ReviewedStingException("Couldn't decrypt AWS keys, something is wrong with the GATK distribution"); + throw new ReviewedGATKException("Couldn't decrypt AWS keys, something is wrong with the GATK distribution"); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java index 431d99867..4de344eb6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.phonehome; +package org.broadinstitute.gatk.engine.phonehome; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.simpleframework.xml.Element; import org.simpleframework.xml.ElementList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RODRecordListImpl.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RODRecordListImpl.java index f8a5aaf37..7296c39ae 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RODRecordListImpl.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RODRecordListImpl.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata; +package org.broadinstitute.gatk.engine.refdata; -import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.HasGenomeLocation; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.*; @@ -73,10 +73,10 @@ public class RODRecordListImpl extends AbstractList implements Comp records.add(r); if ( r == null ) continue; if ( ! this.name.equals(r.getName() ) ) { - throw new ReviewedStingException("Attempt to add GATKFeature with non-matching name "+r.getName()+" to the track "+name); + throw new ReviewedGATKException("Attempt to add GATKFeature with non-matching name "+r.getName()+" to the track "+name); } if ( location != null && ! location.overlapsP(r.getLocation()) ) { - throw new ReviewedStingException("Attempt to add GATKFeature that lies outside of specified interval "+location+"; offending GATKFeature:\n"+r.toString()); + throw new ReviewedGATKException("Attempt to add GATKFeature that lies outside of specified interval "+location+"; offending GATKFeature:\n"+r.toString()); } } } @@ -98,7 +98,7 @@ public class RODRecordListImpl extends AbstractList implements Comp public void add(GATKFeature record, boolean allowNameMismatch) { if ( record != null ) { if ( ! allowNameMismatch && ! name.equals(record.getName() ) ) - throw new ReviewedStingException("Attempt to add GATKFeature with non-matching name "+record.getName()+" to the track "+name); + throw new ReviewedGATKException("Attempt to add GATKFeature with non-matching name "+record.getName()+" to the track "+name); } records.add(record); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTracker.java index 82d5a0fec..7ccf6e572 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTracker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTracker.java @@ -23,17 +23,17 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata; +package org.broadinstitute.gatk.engine.refdata; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; import htsjdk.tribble.Feature; -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.commandline.RodBinding; +import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.util.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceDependentFeatureCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceDependentFeatureCodec.java index c708908ce..9bff00dd8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceDependentFeatureCodec.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceDependentFeatureCodec.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata; +package org.broadinstitute.gatk.engine.refdata; import htsjdk.tribble.FeatureCodec; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocParser; /** * An interface marking that a given Tribble feature/codec is actually dependent on context within the diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceOrderedDatum.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceOrderedDatum.java index a3c0e6433..95de83208 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceOrderedDatum.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceOrderedDatum.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata; +package org.broadinstitute.gatk.engine.refdata; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.HasGenomeLocation; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/SeekableRODIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/SeekableRODIterator.java index dbc477943..ae9e6ca28 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/SeekableRODIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/SeekableRODIterator.java @@ -23,18 +23,18 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata; +package org.broadinstitute.gatk.engine.refdata; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.util.CloseableIterator; -import org.broadinstitute.sting.gatk.iterators.PushbackIterator; -import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.iterators.PushbackIterator; +import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.util.Iterator; import java.util.LinkedList; @@ -193,7 +193,7 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator { */ public RODRecordList next() { if ( ! next_is_allowed ) - throw new ReviewedStingException("Illegal use of iterator: Can not advance iterator with next() after seek-forward query of length > 1"); + throw new ReviewedGATKException("Illegal use of iterator: Can not advance iterator with next() after seek-forward query of length > 1"); curr_position++; // curr_query_end = -1; @@ -243,7 +243,7 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator { r = it.next(); // we got here only if we do need next record, time to load it for real int stop = r.getLocation().getStop(); - if ( stop < curr_position ) throw new ReviewedStingException("DEBUG: encountered contig that should have been loaded earlier"); // this should never happen + if ( stop < curr_position ) throw new ReviewedGATKException("DEBUG: encountered contig that should have been loaded earlier"); // this should never happen if ( stop > max_position ) max_position = stop; // max_position keeps the rightmost stop position across all loaded records records.add(r); } @@ -323,14 +323,14 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator { if ( interval.isBefore(parser.createOverEntireContig(curr_contig)) && !(interval.getStart() == 0 && interval.getStop() == 0 && interval.getContig().equals(curr_contig)) ) // This criteria is syntactic sugar for 'seek to right before curr_contig' - throw new ReviewedStingException("Out of order query: query contig "+interval.getContig()+" is located before "+ + throw new ReviewedGATKException("Out of order query: query contig "+interval.getContig()+" is located before "+ "the iterator's current contig"); if ( interval.getContig().equals(curr_contig) ) { if ( interval.getStart() < curr_position ) - throw new ReviewedStingException("Out of order query: query position "+interval +" is located before "+ + throw new ReviewedGATKException("Out of order query: query position "+interval +" is located before "+ "the iterator's current position "+curr_contig + ":" + curr_position); if ( interval.getStop() < curr_query_end ) - throw new ReviewedStingException("Unsupported querying sequence: current query interval " + + throw new ReviewedGATKException("Unsupported querying sequence: current query interval " + interval+" ends before the end of previous query interval ("+curr_query_end+")"); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/VariantContextAdaptors.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/VariantContextAdaptors.java index 84465ec97..82a826c10 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/VariantContextAdaptors.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/VariantContextAdaptors.java @@ -23,18 +23,18 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata; +package org.broadinstitute.gatk.engine.refdata; import htsjdk.samtools.util.SequenceUtil; import htsjdk.tribble.Feature; import htsjdk.tribble.annotation.Strand; import htsjdk.tribble.dbsnp.OldDbSNPFeature; import htsjdk.tribble.gelitext.GeliTextFeature; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.classloader.PluginManager; +import org.broadinstitute.gatk.utils.codecs.hapmap.RawHapMapFeature; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/package-info.java index 9f9fc1071..e9e9714cb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata; \ No newline at end of file +package org.broadinstitute.gatk.engine.refdata; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManager.java index 0fce83845..d466f3f1e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManager.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManager.java @@ -23,20 +23,20 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.tracks; +package org.broadinstitute.gatk.engine.refdata.tracks; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import htsjdk.tribble.Feature; import htsjdk.tribble.FeatureCodec; import htsjdk.tribble.NameAwareCodec; -import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; -import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.classloader.PluginManager; +import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec; +import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.classloader.PluginManager; import htsjdk.variant.vcf.AbstractVCFCodec; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.help.GATKDocUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.help.GATKDocUtils; import java.io.File; import java.util.*; @@ -170,7 +170,7 @@ public class FeatureManager { if ( canParse.size() == 0 ) return null; else if ( canParse.size() > 1 ) - throw new ReviewedStingException("BUG: multiple feature descriptors can read file " + file + ": " + canParse); + throw new ReviewedGATKException("BUG: multiple feature descriptors can read file " + file + ": " + canParse); else return canParse.get(0); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/IndexDictionaryUtils.java index b98ad4008..5c18d3a8e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/IndexDictionaryUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/IndexDictionaryUtils.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.tracks; +package org.broadinstitute.gatk.engine.refdata.tracks; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import htsjdk.tribble.index.Index; import htsjdk.tribble.index.MutableIndex; -import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; -import org.broadinstitute.sting.utils.SequenceDictionaryUtils; +import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.utils.SequenceDictionaryUtils; import java.util.List; import java.util.Map; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrack.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrack.java index 1b8e12c5b..51cb8f443 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrack.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrack.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.tracks; +package org.broadinstitute.gatk.engine.refdata.tracks; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.util.CloseableIterator; @@ -32,11 +32,11 @@ import htsjdk.tribble.AbstractFeatureReader; import htsjdk.tribble.CloseableTribbleIterator; import htsjdk.tribble.Feature; import htsjdk.tribble.FeatureCodec; -import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator; -import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.refdata.utils.FeatureToGATKFeatureIterator; +import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.File; import java.io.IOException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilder.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilder.java index 4a683e445..dc9e96728 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilder.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilder.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.tracks; +package org.broadinstitute.gatk.engine.refdata.tracks; import htsjdk.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; @@ -34,18 +34,18 @@ import htsjdk.tribble.TribbleException; import htsjdk.tribble.index.Index; import htsjdk.tribble.index.IndexFactory; import htsjdk.tribble.util.LittleEndianOutputStream; -import org.broadinstitute.sting.commandline.Tags; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; -import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor; -import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; -import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.file.FSLockWithShared; -import org.broadinstitute.sting.utils.instrumentation.Sizeof; +import org.broadinstitute.gatk.utils.commandline.Tags; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor; +import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet.RMDStorageType; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.file.FSLockWithShared; +import org.broadinstitute.gatk.utils.instrumentation.Sizeof; import java.io.File; import java.io.FileOutputStream; @@ -160,7 +160,7 @@ public class RMDTrackBuilder { // extends PluginManager { final FeatureManager.FeatureDescriptor descriptor = getFeatureManager().getByCodec(codecClass); if (descriptor == null) - throw new ReviewedStingException("Unable to find type name for codec class " + codecClass.getName()); + throw new ReviewedGATKException("Unable to find type name for codec class " + codecClass.getName()); return createInstanceOfTrack(new RMDTriplet("anonymous",descriptor.getName(),inputFile.getAbsolutePath(),RMDStorageType.FILE,new Tags())); } @@ -224,7 +224,7 @@ public class RMDTrackBuilder { // extends PluginManager { try { Index index = loadIndex(inputFile, createCodec(descriptor, name, inputFile)); try { logger.info(String.format(" Index for %s has size in bytes %d", inputFile, Sizeof.getObjectGraphSize(index))); } - catch (ReviewedStingException e) { } + catch (ReviewedGATKException e) { } sequenceDictionary = IndexDictionaryUtils.getSequenceDictionaryFromProperties(index); @@ -381,7 +381,7 @@ public class RMDTrackBuilder { // extends PluginManager { logger.warn("Unable to write to " + indexFile + " for the index file, creating index in memory only"); try { logger.info(String.format(" Index for %s has size in bytes %d", indexFile, Sizeof.getObjectGraphSize(index))); } - catch ( ReviewedStingException e) { } + catch ( ReviewedGATKException e) { } } finally { if (locked) lock.unlock(); @@ -412,7 +412,7 @@ public class RMDTrackBuilder { // extends PluginManager { * @param index the index file */ public void validateAndUpdateIndexSequenceDictionary(final File inputFile, final Index index, final SAMSequenceDictionary dict) { - if (dict == null) throw new ReviewedStingException("BUG: dict cannot be null"); + if (dict == null) throw new ReviewedGATKException("BUG: dict cannot be null"); // check that every contig in the RMD contig list is at least in the sequence dictionary we're being asked to set final SAMSequenceDictionary currentDict = IndexDictionaryUtils.createSequenceDictionaryFromContigList(index, new SAMSequenceDictionary()); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIterator.java index 595bf39a4..6fb073e12 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIterator.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.utils; +package org.broadinstitute.gatk.engine.refdata.utils; import htsjdk.samtools.util.CloseableIterator; import htsjdk.tribble.CloseableTribbleIterator; import htsjdk.tribble.Feature; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocParser; /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIterator.java index d4a61e76a..8fc549c00 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIterator.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.utils; +package org.broadinstitute.gatk.engine.refdata.utils; import htsjdk.samtools.SAMSequenceDictionary; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.HasGenomeLocation; import java.util.Comparator; import java.util.LinkedList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/GATKFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/GATKFeature.java index 518c19115..4d08f1bca 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/GATKFeature.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/GATKFeature.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.utils; +package org.broadinstitute.gatk.engine.refdata.utils; import htsjdk.tribble.Feature; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.HasGenomeLocation; +import org.broadinstitute.gatk.engine.refdata.ReferenceOrderedDatum; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.HasGenomeLocation; /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/LocationAwareSeekableRODIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/LocationAwareSeekableRODIterator.java index ce3e5fe42..96c60b9d8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/LocationAwareSeekableRODIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/LocationAwareSeekableRODIterator.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.utils; +package org.broadinstitute.gatk.engine.refdata.utils; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.util.CloseableIterator; -import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLoc; /** * @author aaron diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RMDTriplet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RMDTriplet.java index 1477de719..9fa3d1e11 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RMDTriplet.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RMDTriplet.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.utils; +package org.broadinstitute.gatk.engine.refdata.utils; -import org.broadinstitute.sting.commandline.Tags; +import org.broadinstitute.gatk.utils.commandline.Tags; /** * a helper class to manage our triplets of data for the -B command line option (name, type, file) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RODRecordList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RODRecordList.java index 2fc27637a..b859edc10 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RODRecordList.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RODRecordList.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.utils; +package org.broadinstitute.gatk.engine.refdata.utils; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.HasGenomeLocation; import java.util.List; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReport.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReport.java index 9245debd7..660ea95c1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReport.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReport.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.report; +package org.broadinstitute.gatk.engine.report; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.*; import java.util.Collection; @@ -167,7 +167,7 @@ public class GATKReport { public GATKReportTable getTable(String tableName) { GATKReportTable table = tables.get(tableName); if (table == null) - throw new ReviewedStingException("Table is not in GATKReport: " + tableName); + throw new ReviewedGATKException("Table is not in GATKReport: " + tableName); return table; } @@ -195,7 +195,7 @@ public class GATKReport { public void concat(GATKReport input) { if ( !isSameFormat(input) ) { - throw new ReviewedStingException("Failed to combine GATKReport, format doesn't match!"); + throw new ReviewedGATKException("Failed to combine GATKReport, format doesn't match!"); } for ( Map.Entry table : tables.entrySet() ) { @@ -340,11 +340,11 @@ public class GATKReport { public void addRow(final Object... values) { // Must be a simple report if ( tables.size() != 1 ) - throw new ReviewedStingException("Cannot write a row to a complex GATK Report"); + throw new ReviewedGATKException("Cannot write a row to a complex GATK Report"); GATKReportTable table = tables.firstEntry().getValue(); if ( table.getNumColumns() != values.length ) - throw new ReviewedStingException("The number of arguments in writeRow (" + values.length + ") must match the number of columns in the table (" + table.getNumColumns() + ")" ); + throw new ReviewedGATKException("The number of arguments in writeRow (" + values.length + ") must match the number of columns in the table (" + table.getNumColumns() + ")" ); final int rowIndex = table.getNumRows(); for ( int i = 0; i < values.length; i++ ) @@ -360,11 +360,11 @@ public class GATKReport { */ public void addRowList(final List values) { if ( tables.size() != 1 ) - throw new ReviewedStingException("Cannot write a row to a complex GATK Report"); + throw new ReviewedGATKException("Cannot write a row to a complex GATK Report"); GATKReportTable table = tables.firstEntry().getValue(); if ( table.getNumColumns() != values.size() ) - throw new ReviewedStingException("The number of arguments in writeRow() must match the number of columns in the table"); + throw new ReviewedGATKException("The number of arguments in writeRow() must match the number of columns in the table"); final int rowIndex = table.getNumRows(); int idx = 0; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumn.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumn.java index 5f7891622..ffdefff36 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumn.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumn.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.report; +package org.broadinstitute.gatk.engine.report; import org.apache.commons.lang.math.NumberUtils; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumnFormat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumnFormat.java index 0f10f3c51..664b503b0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumnFormat.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumnFormat.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.report; +package org.broadinstitute.gatk.engine.report; /** * Column width and left/right alignment. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportDataType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportDataType.java index 7b100bb2f..acfa74f25 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportDataType.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportDataType.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.report; +package org.broadinstitute.gatk.engine.report; import java.util.EnumSet; import java.util.HashMap; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportGatherer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportGatherer.java index 5e7c3ec86..5f7f7670c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportGatherer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportGatherer.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.report; +package org.broadinstitute.gatk.engine.report; -import org.broadinstitute.sting.commandline.Gatherer; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.commandline.Gatherer; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportTable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportTable.java index fe3df7bf1..6a1e456d4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportTable.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportTable.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.report; +package org.broadinstitute.gatk.engine.report; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.text.TextFormattingUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.text.TextFormattingUtils; import java.io.BufferedReader; import java.io.IOException; @@ -105,7 +105,7 @@ public class GATKReportTable { tableData = reader.readLine().split(SEPARATOR); tableNameData = reader.readLine().split(SEPARATOR); } catch (IOException e) { - throw new ReviewedStingException(COULD_NOT_READ_HEADER + e.getMessage()); + throw new ReviewedGATKException(COULD_NOT_READ_HEADER + e.getMessage()); } // parse the header fields @@ -132,7 +132,7 @@ public class GATKReportTable { try { columnLine = reader.readLine(); } catch (IOException e) { - throw new ReviewedStingException(COULD_NOT_READ_COLUMN_NAMES); + throw new ReviewedGATKException(COULD_NOT_READ_COLUMN_NAMES); } final List columnStarts = TextFormattingUtils.getWordStarts(columnLine); @@ -161,18 +161,18 @@ public class GATKReportTable { } } } catch (IOException e) { - throw new ReviewedStingException(COULD_NOT_READ_DATA_LINE + e.getMessage()); + throw new ReviewedGATKException(COULD_NOT_READ_DATA_LINE + e.getMessage()); } try { reader.readLine(); } catch (IOException e) { - throw new ReviewedStingException(COULD_NOT_READ_EMPTY_LINE + e.getMessage()); + throw new ReviewedGATKException(COULD_NOT_READ_EMPTY_LINE + e.getMessage()); } break; default: - throw new ReviewedStingException(OLD_GATK_TABLE_VERSION); + throw new ReviewedGATKException(OLD_GATK_TABLE_VERSION); } } @@ -197,11 +197,11 @@ public class GATKReportTable { */ public GATKReportTable(final String tableName, final String tableDescription, final int numColumns, final TableSortingWay sortingWay) { if ( !isValidName(tableName) ) { - throw new ReviewedStingException("Attempted to set a GATKReportTable name of '" + tableName + "'. GATKReportTable names must be purely alphanumeric - no spaces or special characters are allowed."); + throw new ReviewedGATKException("Attempted to set a GATKReportTable name of '" + tableName + "'. GATKReportTable names must be purely alphanumeric - no spaces or special characters are allowed."); } if ( !isValidDescription(tableDescription) ) { - throw new ReviewedStingException("Attempted to set a GATKReportTable description of '" + tableDescription + "'. GATKReportTable descriptions must not contain newlines."); + throw new ReviewedGATKException("Attempted to set a GATKReportTable description of '" + tableDescription + "'. GATKReportTable descriptions must not contain newlines."); } this.tableName = tableName; @@ -333,7 +333,7 @@ public class GATKReportTable { */ private void verifyEntry(final int rowIndex, final int colIndex) { if ( rowIndex < 0 || colIndex < 0 || colIndex >= getNumColumns() ) - throw new ReviewedStingException("attempted to access a cell that does not exist in table '" + tableName + "'"); + throw new ReviewedGATKException("attempted to access a cell that does not exist in table '" + tableName + "'"); } /** @@ -394,7 +394,7 @@ public class GATKReportTable { underlyingData.get(rowIndex)[colIndex] = value; column.updateFormatting(value); } else { - throw new ReviewedStingException(String.format("Tried to add an object of type: %s to a column of type: %s", GATKReportDataType.fromObject(value).name(), column.getDataType().name())); + throw new ReviewedGATKException(String.format("Tried to add an object of type: %s to a column of type: %s", GATKReportDataType.fromObject(value).name(), column.getDataType().name())); } } @@ -431,7 +431,7 @@ public class GATKReportTable { } else { Object obj = get(rowID, columnName); if ( !(obj instanceof Integer) ) - throw new ReviewedStingException("Attempting to increment a value in a cell that is not an integer"); + throw new ReviewedGATKException("Attempting to increment a value in a cell that is not an integer"); prevValue = (Integer)obj; } @@ -602,13 +602,13 @@ public class GATKReportTable { case SORT_BY_ROW: // make sure that there are exactly the correct number of ID mappings if ( rowIdToIndex.size() != underlyingData.size() ) - throw new ReviewedStingException("There isn't a 1-to-1 mapping from row ID to index; this can happen when rows are not created consistently"); + throw new ReviewedGATKException("There isn't a 1-to-1 mapping from row ID to index; this can happen when rows are not created consistently"); final TreeMap sortedMap; try { sortedMap = new TreeMap(rowIdToIndex); } catch (ClassCastException e) { - throw new ReviewedStingException("Unable to sort the rows based on the row IDs because the ID Objects are of different types"); + throw new ReviewedGATKException("Unable to sort the rows based on the row IDs because the ID Objects are of different types"); } for ( final Map.Entry rowKey : sortedMap.entrySet() ) writeRow(out, underlyingData.get(rowKey.getValue())); @@ -672,7 +672,7 @@ public class GATKReportTable { */ public void concat(final GATKReportTable table) { if ( !isSameFormat(table) ) - throw new ReviewedStingException("Error trying to concatenate tables with different formats"); + throw new ReviewedGATKException("Error trying to concatenate tables with different formats"); // add the data underlyingData.addAll(table.underlyingData); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportVersion.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportVersion.java index 1140beaa0..226365b80 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportVersion.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportVersion.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.report; +package org.broadinstitute.gatk.engine.report; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; public enum GATKReportVersion { /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java index c95bc9c47..034413520 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.resourcemanagement; +package org.broadinstitute.gatk.engine.resourcemanagement; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; /** * Models how threads are distributed between various components of the GATK. @@ -104,9 +104,9 @@ public class ThreadAllocation { final int numCPUThreadsPerDataThread, final int numIOThreads, final boolean monitorEfficiency) { - if ( numDataThreads < 1 ) throw new ReviewedStingException("numDataThreads cannot be less than 1, but saw " + numDataThreads); - if ( numCPUThreadsPerDataThread < 1 ) throw new ReviewedStingException("numCPUThreadsPerDataThread cannot be less than 1, but saw " + numCPUThreadsPerDataThread); - if ( numIOThreads < 0 ) throw new ReviewedStingException("numIOThreads cannot be less than 0, but saw " + numIOThreads); + if ( numDataThreads < 1 ) throw new ReviewedGATKException("numDataThreads cannot be less than 1, but saw " + numDataThreads); + if ( numCPUThreadsPerDataThread < 1 ) throw new ReviewedGATKException("numCPUThreadsPerDataThread cannot be less than 1, but saw " + numCPUThreadsPerDataThread); + if ( numIOThreads < 0 ) throw new ReviewedGATKException("numIOThreads cannot be less than 0, but saw " + numIOThreads); this.numDataThreads = numDataThreads; this.numCPUThreadsPerDataThread = numCPUThreadsPerDataThread; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java index 2f6e1f9a5..0e5833b99 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.samples; +package org.broadinstitute.gatk.engine.samples; /** * Categorical sample trait for association and analysis diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java index cf2b4ee99..0f26bc630 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.samples; +package org.broadinstitute.gatk.engine.samples; /** * ENUM of possible human genders: male, female, or unknown diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java index 75ef130fa..8946d2808 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.samples; +package org.broadinstitute.gatk.engine.samples; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.text.XReadLines; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.text.XReadLines; import java.io.*; import java.util.*; @@ -250,7 +250,7 @@ public class PedReader { else if ( parts[phenotypePos].equals(MISSING_VALUE2) ) affection = Affection.UNKNOWN; else if ( parts[phenotypePos].equals(PHENOTYPE_UNAFFECTED) ) affection = Affection.UNAFFECTED; else if ( parts[phenotypePos].equals(PHENOTYPE_AFFECTED) ) affection = Affection.AFFECTED; - else throw new ReviewedStingException("Unexpected phenotype type " + parts[phenotypePos] + " at line " + lineNo); + else throw new ReviewedGATKException("Unexpected phenotype type " + parts[phenotypePos] + " at line " + lineNo); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java index bb01b33c6..14fefd2be 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.samples; +package org.broadinstitute.gatk.engine.samples; /** * diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java index 87f0817b7..0d60c39a1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.samples; +package org.broadinstitute.gatk.engine.samples; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.util.ArrayList; import java.util.HashMap; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java index 2530df6ab..141f01b3a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.samples; +package org.broadinstitute.gatk.engine.samples; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.sting.utils.exceptions.StingException; +import org.broadinstitute.gatk.utils.exceptions.GATKException; import htsjdk.variant.variantcontext.Genotype; import java.util.*; @@ -140,7 +140,7 @@ public class SampleDB { samples.add(getSample(name)); } catch (Exception e) { - throw new StingException("Could not get sample with the following ID: " + name, e); + throw new GATKException("Could not get sample with the following ID: " + name, e); } } return samples; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java index 45d5e258f..6fdb9fa0a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.samples; +package org.broadinstitute.gatk.engine.samples; import htsjdk.samtools.SAMFileHeader; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java index 675695112..b5a698b9a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.samples; +package org.broadinstitute.gatk.engine.samples; /** * A class for imposing a trio structure on three samples; a common paradigm diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java index 424bd489e..ebded31d8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.traversals; +package org.broadinstitute.gatk.engine.traversals; -import org.broadinstitute.sting.gatk.downsampling.Downsampler; -import org.broadinstitute.sting.gatk.downsampling.ReservoirDownsampler; -import org.broadinstitute.sting.utils.sam.AlignmentStartComparator; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.downsampling.Downsampler; +import org.broadinstitute.gatk.engine.downsampling.ReservoirDownsampler; +import org.broadinstitute.gatk.utils.sam.AlignmentStartComparator; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.ArrayList; import java.util.Collections; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java index 529b3ef17..25abafd2d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java @@ -23,17 +23,16 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.traversals; +package org.broadinstitute.gatk.engine.traversals; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.ReadMetrics; -import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.progressmeter.ProgressMeter; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.ReadMetrics; +import org.broadinstitute.gatk.engine.datasources.providers.ShardDataProvider; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.progressmeter.ProgressMeter; public abstract class TraversalEngine,ProviderType extends ShardDataProvider> { /** our log, which we want to capture anything from this class */ @@ -76,7 +75,7 @@ public abstract class TraversalEngine,Provide */ public void initialize(final GenomeAnalysisEngine engine, final Walker walker, final ProgressMeter progressMeter) { if ( engine == null ) - throw new ReviewedStingException("BUG: GenomeAnalysisEngine cannot be null!"); + throw new ReviewedGATKException("BUG: GenomeAnalysisEngine cannot be null!"); this.engine = engine; this.progressMeter = progressMeter; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java index f8628bb78..3a8c3ffab 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java @@ -23,32 +23,32 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.traversals; +package org.broadinstitute.gatk.engine.traversals; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.providers.*; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionTraversalParameters; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.activeregion.ActivityProfile; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileState; -import org.broadinstitute.sting.utils.activeregion.BandPassActivityProfile; -import org.broadinstitute.sting.utils.nanoScheduler.NSMapFunction; -import org.broadinstitute.sting.utils.nanoScheduler.NSProgressFunction; -import org.broadinstitute.sting.utils.nanoScheduler.NSReduceFunction; -import org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler; -import org.broadinstitute.sting.utils.progressmeter.ProgressMeter; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.datasources.providers.*; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.ActiveRegionTraversalParameters; +import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.activeregion.ActivityProfile; +import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState; +import org.broadinstitute.gatk.utils.activeregion.BandPassActivityProfile; +import org.broadinstitute.gatk.utils.nanoScheduler.NSMapFunction; +import org.broadinstitute.gatk.utils.nanoScheduler.NSProgressFunction; +import org.broadinstitute.gatk.utils.nanoScheduler.NSReduceFunction; +import org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler; +import org.broadinstitute.gatk.utils.progressmeter.ProgressMeter; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.io.PrintStream; import java.util.Collection; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java index b9ac812ab..6cffe9427 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java @@ -23,18 +23,18 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.traversals; +package org.broadinstitute.gatk.engine.traversals; import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.providers.ReadView; -import org.broadinstitute.sting.gatk.iterators.PushbackIterator; -import org.broadinstitute.sting.gatk.walkers.DuplicateWalker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.datasources.providers.ReadShardDataProvider; +import org.broadinstitute.gatk.engine.datasources.providers.ReadView; +import org.broadinstitute.gatk.engine.iterators.PushbackIterator; +import org.broadinstitute.gatk.engine.walkers.DuplicateWalker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java index 627f98d69..02c1a7e7f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java @@ -23,22 +23,22 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.traversals; +package org.broadinstitute.gatk.engine.traversals; -import org.broadinstitute.sting.gatk.WalkerManager; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.providers.*; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.DataSource; -import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.nanoScheduler.NSMapFunction; -import org.broadinstitute.sting.utils.nanoScheduler.NSProgressFunction; -import org.broadinstitute.sting.utils.nanoScheduler.NSReduceFunction; -import org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.gatk.engine.WalkerManager; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.datasources.providers.*; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.DataSource; +import org.broadinstitute.gatk.engine.walkers.LocusWalker; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.nanoScheduler.NSMapFunction; +import org.broadinstitute.gatk.utils.nanoScheduler.NSProgressFunction; +import org.broadinstitute.gatk.utils.nanoScheduler.NSReduceFunction; +import org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; import java.util.Iterator; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java index 04adaacbc..c68e10908 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java @@ -23,17 +23,17 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.traversals; +package org.broadinstitute.gatk.engine.traversals; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMRecordCoordinateComparator; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.providers.ReadView; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.walkers.DataSource; -import org.broadinstitute.sting.gatk.walkers.ReadPairWalker; -import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.gatk.engine.datasources.providers.ReadShardDataProvider; +import org.broadinstitute.gatk.engine.datasources.providers.ReadView; +import org.broadinstitute.gatk.engine.datasources.reads.Shard; +import org.broadinstitute.gatk.engine.walkers.DataSource; +import org.broadinstitute.gatk.engine.walkers.ReadPairWalker; +import org.broadinstitute.gatk.engine.walkers.Requires; import java.util.ArrayList; import java.util.Collections; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java index a7584cbd2..2ce752b1f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java @@ -23,22 +23,22 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.traversals; +package org.broadinstitute.gatk.engine.traversals; import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.providers.ReadBasedReferenceOrderedView; -import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView; -import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.providers.ReadView; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.utils.nanoScheduler.NSMapFunction; -import org.broadinstitute.sting.utils.nanoScheduler.NSProgressFunction; -import org.broadinstitute.sting.utils.nanoScheduler.NSReduceFunction; -import org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.datasources.providers.ReadBasedReferenceOrderedView; +import org.broadinstitute.gatk.engine.datasources.providers.ReadReferenceView; +import org.broadinstitute.gatk.engine.datasources.providers.ReadShardDataProvider; +import org.broadinstitute.gatk.engine.datasources.providers.ReadView; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.ReadWalker; +import org.broadinstitute.gatk.utils.nanoScheduler.NSMapFunction; +import org.broadinstitute.gatk.utils.nanoScheduler.NSProgressFunction; +import org.broadinstitute.gatk.utils.nanoScheduler.NSReduceFunction; +import org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Iterator; import java.util.LinkedList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java index 809a8a1ac..72d10994d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.traversals; \ No newline at end of file +package org.broadinstitute.gatk.engine.traversals; \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java index 5560946ea..7c428cd6a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.gatk.engine.walkers; -import org.broadinstitute.sting.utils.activeregion.BandPassActivityProfile; +import org.broadinstitute.gatk.utils.activeregion.BandPassActivityProfile; import java.lang.annotation.Documented; import java.lang.annotation.Inherited; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java index e921aed05..3edc8645f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java @@ -23,26 +23,26 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.gatk.engine.walkers; import com.google.java.contract.Ensures; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.tribble.Feature; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.downsampling.DownsampleType; -import org.broadinstitute.sting.gatk.filters.*; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileState; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; -import org.broadinstitute.sting.utils.interval.IntervalSetRule; -import org.broadinstitute.sting.utils.interval.IntervalUtils; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.engine.filters.*; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.GenomeLocSortedSet; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegionReadState; +import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState; +import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; +import org.broadinstitute.gatk.utils.interval.IntervalSetRule; +import org.broadinstitute.gatk.utils.interval.IntervalUtils; import java.io.PrintStream; import java.util.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java index e3827916c..7188fd01c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.gatk.engine.walkers; import java.lang.annotation.*; /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java index a636ed82b..ded2941f3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.gatk.engine.walkers; import java.lang.annotation.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java index c6a621432..931381efb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.gatk.engine.walkers; -import org.broadinstitute.sting.gatk.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import java.lang.annotation.*; @@ -51,6 +51,6 @@ import java.lang.annotation.*; @Retention(RetentionPolicy.RUNTIME) @Target(ElementType.TYPE) public @interface BAQMode { - public abstract org.broadinstitute.sting.utils.baq.BAQ.QualityMode QualityMode() default org.broadinstitute.sting.utils.baq.BAQ.QualityMode.OVERWRITE_QUALS; + public abstract org.broadinstitute.gatk.utils.baq.BAQ.QualityMode QualityMode() default org.broadinstitute.gatk.utils.baq.BAQ.QualityMode.OVERWRITE_QUALS; public abstract ReadTransformer.ApplicationTime ApplicationTime() default ReadTransformer.ApplicationTime.ON_INPUT; } \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java index 792acc961..3962c98e0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.gatk.engine.walkers; import java.lang.annotation.*; /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java index 76bdb5406..fab984084 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.gatk.engine.walkers; /** * User: hanna * Date: May 14, 2009 diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java index 2776b7023..c112d7d26 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.gatk.engine.walkers; -import org.broadinstitute.sting.gatk.downsampling.DownsampleType; +import org.broadinstitute.gatk.engine.downsampling.DownsampleType; import java.lang.annotation.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java index 13542d1a7..96d2d5dad 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.gatk.engine.walkers; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentFilter; -import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.filters.NotPrimaryAlignmentFilter; +import org.broadinstitute.gatk.engine.filters.UnmappedReadFilter; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.List; import java.util.Set; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java index 9997723b8..1e7b0e54c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java @@ -23,16 +23,16 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.gatk.engine.walkers; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.downsampling.DownsampleType; -import org.broadinstitute.sting.gatk.filters.DuplicateReadFilter; -import org.broadinstitute.sting.gatk.filters.FailsVendorQualityCheckFilter; -import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentFilter; -import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.engine.filters.DuplicateReadFilter; +import org.broadinstitute.gatk.engine.filters.FailsVendorQualityCheckFilter; +import org.broadinstitute.gatk.engine.filters.NotPrimaryAlignmentFilter; +import org.broadinstitute.gatk.engine.filters.UnmappedReadFilter; +import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; /** * Created by IntelliJ IDEA. @@ -53,6 +53,6 @@ public abstract class LocusWalker extends Walker extends Walker { final String path; // X.Y.Z diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/GATKReportDiffableReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/GATKReportDiffableReader.java index 55f52a32a..4a78448b6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/GATKReportDiffableReader.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/GATKReportDiffableReader.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.diffengine; +package org.broadinstitute.gatk.engine.walkers.diffengine; -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.gatk.report.GATKReportColumn; -import org.broadinstitute.sting.gatk.report.GATKReportTable; +import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.engine.report.GATKReportColumn; +import org.broadinstitute.gatk.engine.report.GATKReportTable; import java.io.File; import java.io.FileReader; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/VCFDiffableReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/VCFDiffableReader.java index fed18c657..23b213e91 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/VCFDiffableReader.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/VCFDiffableReader.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.diffengine; +package org.broadinstitute.gatk.engine.walkers.diffengine; import org.apache.log4j.Logger; import htsjdk.tribble.AbstractFeatureReader; import htsjdk.tribble.FeatureReader; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.gatk.utils.Utils; import htsjdk.variant.vcf.*; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; 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 331dc1824..631e8e015 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 @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.tools; +package org.broadinstitute.gatk.tools; import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.samtools.reference.ReferenceSequenceFileFactory; @@ -32,19 +32,19 @@ import org.apache.log4j.Level; import htsjdk.tribble.AbstractFeatureReader; import htsjdk.tribble.FeatureReader; import htsjdk.tribble.index.IndexCreator; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.commandline.CommandLineProgram; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.sting.utils.variant.GATKVCFIndexType; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Input; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType; +import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import htsjdk.variant.bcf2.BCF2Codec; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.gatk.utils.collections.Pair; import htsjdk.variant.vcf.VCFCodec; import htsjdk.variant.vcf.VCFHeader; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.Options; import htsjdk.variant.variantcontext.writer.VariantContextWriter; @@ -87,7 +87,7 @@ import java.util.*; * *

Example

* 
- * java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants \
+ * java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants \
  *    -R ref.fasta \
  *    -V input1.vcf \
  *    -V input2.vcf \
@@ -134,7 +134,7 @@ public class CatVariants extends CommandLineProgram {
      * print usage information
      */
     private static void printUsage() {
-        System.err.println("Usage: java -cp target/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants --reference  --variant  --outputFile  [--assumeSorted]");
+        System.err.println("Usage: java -cp target/GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants --reference  --variant  --outputFile  [--assumeSorted]");
         System.err.println("    The output file must be of the same type as all input files.");
         System.err.println("    If the input files are already sorted, then indicate that with --assumeSorted to improve performance.");
     }
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 fabcf828a..72d30defd 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
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.tools;
+package org.broadinstitute.gatk.tools;
 
-import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.help.HelpUtils;
+import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.help.HelpUtils;
 
 /**
  * Utility program to print a list of available annotations
@@ -43,7 +43,7 @@ import org.broadinstitute.sting.utils.help.HelpUtils;
  * classic "CommandLineGATK" arguments.

  *
  * 
Usage

- * 
java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations

+ * 
java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.ListAnnotations

  *
  * @author vdauwera
  * @since 3/14/13
@@ -57,7 +57,7 @@ public class ListAnnotations extends CommandLineProgram {
      * TODO: would be more convenient if we could just call the program by name instead of the full classpath
      */
     private static void printUsage() {
-        System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations");
+        System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.ListAnnotations");
         System.err.println("    Prints a list of available annotations and exits.");
     }
 
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 7c0bcb05b..b6974a6e0 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
@@ -23,18 +23,18 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.MathUtils;
 import htsjdk.variant.vcf.VCFHeaderLineType;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.GenotypesContext;
 import htsjdk.variant.variantcontext.VariantContext;
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 b669c9a7e..abf1cfc30 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
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.MathUtils;
 import htsjdk.variant.vcf.VCFFormatHeaderLine;
 import htsjdk.variant.vcf.VCFHeaderLineType;
 import htsjdk.variant.variantcontext.Allele;
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 f9783c0ad..daf65d275 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
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.BaseUtils;
 import htsjdk.variant.vcf.VCFHeaderLineType;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
 import htsjdk.variant.variantcontext.VariantContext;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCountConstants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCountConstants.java
index f1c57dae1..67fc0a406 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCountConstants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCountConstants.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
 import htsjdk.variant.vcf.VCFConstants;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
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 25e67a2e2..101894cd0 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
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import htsjdk.variant.vcf.VCFHeaderLineType;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
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 a3596056a..1d2617d78 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
@@ -23,19 +23,19 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import htsjdk.variant.vcf.VCFConstants;
 import htsjdk.variant.vcf.VCFFormatHeaderLine;
 import htsjdk.variant.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.GenotypeBuilder;
 import htsjdk.variant.variantcontext.VariantContext;
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 fa656a599..5ed91614b 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
@@ -23,18 +23,18 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.BaseUtils;
 import htsjdk.variant.vcf.VCFHeaderLineType;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
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 49a2247f1..b73acdc08 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
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.RodRequiringAnnotation;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.*;
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 12e923b8f..c82a013b6 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff.EffectType;
+import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff.EffectType;
 
 import java.util.*;
 /**
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 5108c3872..51816d6b9 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
@@ -23,26 +23,26 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.help.HelpUtils;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.gatk.engine.walkers.*;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.downsampling.DownsampleType;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.help.HelpUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.SampleUtils;
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import it.unimi.dsi.fastutil.objects.ObjectOpenHashSet;
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 2f2aba983..d875f15f5 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
@@ -23,19 +23,19 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.vcf.*;
 
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 7c12aefd5..03f707f9d 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
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
@@ -48,7 +48,7 @@ public final class VariantOverlapAnnotator {
     /**
      * Create a new VariantOverlapAnnotator without overall bindings
      *
-     * @see #VariantOverlapAnnotator(org.broadinstitute.sting.commandline.RodBinding, java.util.Map, org.broadinstitute.sting.utils.GenomeLocParser)
+     * @see #VariantOverlapAnnotator(org.broadinstitute.gatk.utils.commandline.RodBinding, java.util.Map, org.broadinstitute.gatk.utils.GenomeLocParser)
      */
     public VariantOverlapAnnotator(RodBinding dbSNPBinding, GenomeLocParser genomeLocParser) {
         this(dbSNPBinding, Collections., String>emptyMap(), genomeLocParser);
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 ec3bf25a4..8a32ae150 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
 import htsjdk.variant.variantcontext.VariantContext;
 
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 59b4b1b3b..8f137ccf9 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
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
-import org.broadinstitute.sting.utils.DeprecatedToolChecks;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.DeprecatedToolChecks;
+import org.broadinstitute.gatk.utils.classloader.PluginManager;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.util.*;
 
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 515efab5b..0051c978f 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
@@ -23,6 +23,6 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
 public interface AnnotationType {}
\ No newline at end of file
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 50255e5f1..f1aeedeaf 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
-import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.List;
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 4161f6c22..9ed24db69 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
@@ -23,6 +23,6 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
 public interface ExperimentalAnnotation extends AnnotationType {}
\ No newline at end of file
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 a02c5528f..a6a81d758 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
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import htsjdk.variant.vcf.VCFFormatHeaderLine;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.GenotypeBuilder;
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 74d676268..55a30d8be 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
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
 import htsjdk.variant.variantcontext.VariantContext;
 
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 4a6a47418..04e545ad0 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
@@ -23,6 +23,6 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
 public interface RodRequiringAnnotation extends AnnotationType {}
\ No newline at end of file
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 62734fe6c..247af00b2 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
@@ -23,6 +23,6 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
 public interface StandardAnnotation extends AnnotationType {}
\ No newline at end of file
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 0812eeaf8..0c689558e 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
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 
 import java.util.List;
 import java.util.Set;
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 14f39de17..9daab4345 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
@@ -23,6 +23,6 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
 public interface WorkInProgressAnnotation extends AnnotationType {}
\ No newline at end of file
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java
index d69bd59e6..726ea9ba4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.beagle;
+package org.broadinstitute.gatk.tools.walkers.beagle;
 
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.codecs.beagle.BeagleFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java
index 70a360272..dab5d160e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java
@@ -23,29 +23,29 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.beagle;
+package org.broadinstitute.gatk.tools.walkers.beagle;
 
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.samples.Gender;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibrationCurve;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.samples.Gender;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.tools.walkers.variantrecalibration.VQSRCalibrationCurve;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.VCFFilterHeaderLine;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 
@@ -267,7 +267,7 @@ public class ProduceBeagleInput extends RodWalker {
                 isValidation = ! isValidationSite;
             } else {
                 // there is magically no genotype for this sample.
-                throw new StingException("Sample "+sample+" arose with no genotype in variant or validation VCF. This should never happen.");
+                throw new GATKException("Sample "+sample+" arose with no genotype in variant or validation VCF. This should never happen.");
             }
 
             /*
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java
index 0689b49f7..c45ceb269 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java
@@ -23,26 +23,26 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.beagle;
+package org.broadinstitute.gatk.tools.walkers.beagle;
 
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Input;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
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 2e38f5daa..1757e7bc0 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
@@ -23,23 +23,23 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.coverage;
+package org.broadinstitute.gatk.tools.walkers.coverage;
 
-import org.broadinstitute.sting.commandline.Advanced;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.By;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.commandline.Advanced;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.By;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.LocusWalker;
+import org.broadinstitute.gatk.utils.*;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
 
 import java.io.File;
 import java.io.FileNotFoundException;
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 b8f66add3..9ab8555cd 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
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.coverage;
+package org.broadinstitute.gatk.tools.walkers.coverage;
 
 import htsjdk.tribble.bed.BEDFeature;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Input;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 
 import java.io.PrintStream;
 import java.util.Arrays;
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 e7635f1e8..7514fa5a8 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
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.coverage;
+package org.broadinstitute.gatk.tools.walkers.coverage;
 
 import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.fragments.FragmentCollection;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.fragments.FragmentCollection;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
 
 import java.util.*;
 
@@ -98,7 +98,7 @@ public class CoverageUtils {
         } else if ( type == DoCOutputType.Partition.sample_by_platform_by_center ) {
             return String.format("%s_pl_%s_cn_%s",r.getSample(),r.getPlatform(),r.getSequencingCenter());
         } else {
-            throw new ReviewedStingException("Invalid type ID sent to getTypeID. This is a BUG!");
+            throw new ReviewedGATKException("Invalid type ID sent to getTypeID. This is a BUG!");
         }
     }
 
@@ -224,7 +224,7 @@ public class CoverageUtils {
             try {
                 counts[BaseUtils.simpleBaseToBaseIndex(e.getBase())]++;
             } catch (ArrayIndexOutOfBoundsException exc) {
-                throw new ReviewedStingException("Expected a simple base, but actually received"+(char)e.getBase());
+                throw new ReviewedGATKException("Expected a simple base, but actually received"+(char)e.getBase());
             }
         }
     }
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 045e61b26..36f5a6c87 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
@@ -23,34 +23,34 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.coverage;
+package org.broadinstitute.gatk.tools.walkers.coverage;
 
 import htsjdk.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.commandline.Advanced;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
-import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
-import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.engine.walkers.*;
+import org.broadinstitute.gatk.utils.commandline.Advanced;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.downsampling.DownsampleType;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.refdata.SeekableRODIterator;
+import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack;
+import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder;
+import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature;
+import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator;
+import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.codecs.refseq.RefSeqCodec;
+import org.broadinstitute.gatk.utils.codecs.refseq.RefSeqFeature;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 
 import java.io.File;
 import java.io.PrintStream;
@@ -366,7 +366,7 @@ public class DepthOfCoverage extends LocusWalker maxWindowElements() || elementsToRight > maxWindowElements() )
-            throw new ReviewedStingException("Too large a window requested");
+            throw new ReviewedGATKException("Too large a window requested");
         if ( elementsToLeft < 0 || elementsToRight < 0 )
-            throw new ReviewedStingException("Window size cannot be negative");
+            throw new ReviewedGATKException("Window size cannot be negative");
 
         FiltrationContext[] array = new FiltrationContext[elementsToLeft + elementsToRight + 1];
         ListIterator iter = window.listIterator(currentContext - elementsToLeft);
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 564d9d7c0..7d833405b 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
@@ -23,25 +23,25 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.filters;
+package org.broadinstitute.gatk.tools.walkers.filters;
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.Reference;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.Window;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 
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 822b73769..ce6fe0633 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
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
 
 import htsjdk.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.filters.ReadFilter;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.filters.ReadFilter;
 
 /**
  * Filter out reads with low mapping qualities.
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 e76cb5130..4201ef0dc 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
@@ -23,4 +23,4 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.gatk.tools.walkers;
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 b6a3853f8..a3848dccc 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
@@ -23,27 +23,27 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Input;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.LocusWalker;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.engine.walkers.TreeReducible;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.codecs.sampileup.SAMPileupFeature;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
 
 import java.io.PrintStream;
 import java.util.Arrays;
@@ -241,7 +241,7 @@ public class CheckPileup extends LocusWalker implemen
         else if( pileupArg.hasIndelGenotype() )
             return pileupArg.getIndelGenotype();
         else
-            throw new ReviewedStingException("Unsupported pileup type: " + pileupArg);
+            throw new ReviewedGATKException("Unsupported pileup type: " + pileupArg);
     }
 }
 
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 8b82e50a7..1500ce37d 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
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 /**
  * Walks over the input data set, calculating the number of bases seen for diagnostic purposes.
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 89dc7ebcb..221c4a9a2 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
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RefWalker;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Input;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RefWalker;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 
 import java.io.PrintStream;
 import java.util.Collections;
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 d999dfebf..51c161731 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
@@ -23,18 +23,18 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.LocusWalker;
+import org.broadinstitute.gatk.engine.walkers.NanoSchedulable;
+import org.broadinstitute.gatk.engine.walkers.TreeReducible;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 
 import java.io.PrintStream;
 
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 7279a64a4..d665e618e 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
@@ -23,20 +23,20 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.samples.Gender;
-import org.broadinstitute.sting.gatk.samples.Sample;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.samples.Gender;
+import org.broadinstitute.gatk.engine.samples.Sample;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
 
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 9070f4436..e068ff7ad 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
@@ -23,29 +23,29 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Input;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList;
+import org.broadinstitute.gatk.engine.walkers.NanoSchedulable;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.TreeReducible;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.collections.ExpandingArrayList;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 
 import java.io.PrintStream;
 import java.util.*;
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 31842be64..40471b50b 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
@@ -23,21 +23,21 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RefWalker;
-import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Input;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RefWalker;
+import org.broadinstitute.gatk.utils.collections.ExpandingArrayList;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 
 import java.util.Collections;
 import java.util.List;
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 547eaa52f..998448ecf 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
@@ -23,21 +23,21 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import htsjdk.samtools.CigarOperator;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.report.GATKReport;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.report.GATKReport;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.ReadUtils;
 
 import java.io.PrintStream;
 import java.util.ArrayList;
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 45beea28f..33d22cab1 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
@@ -23,18 +23,18 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.NanoSchedulable;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 /**
  * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
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 3746bb067..90a131c2a 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
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
 import java.util.List;
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 c0e2422c7..b5a1e742d 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
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.variantcontext.VariantContext;
 
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 1de0f2030..6e872e3d4 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
@@ -23,22 +23,21 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
-import org.broadinstitute.sting.gatk.walkers.RefWalker;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Input;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.NanoSchedulable;
+import org.broadinstitute.gatk.engine.walkers.RefWalker;
+import org.broadinstitute.gatk.engine.walkers.TreeReducible;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 
 /**
  * A walker that simply throws errors.  Allows us to test that the engine is behaving as expected with error handling
@@ -94,8 +93,8 @@ public class ErrorThrowing extends RefWalker implements TreeRed
             throw new UserException("UserException");
         } else if ( exceptionToThrow.equals("NullPointerException") ) {
             throw new NullPointerException();
-        } else if ( exceptionToThrow.equals("ReviewedStingException") ) {
-            throw new ReviewedStingException("ReviewedStingException");
+        } else if ( exceptionToThrow.equals("ReviewedGATKException") ) {
+            throw new ReviewedGATKException("ReviewedGATKException");
         } else if ( exceptionToThrow.equals("SamError1") ) {
             throw new RuntimeException(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_1);
         } else if ( exceptionToThrow.equals("SamError2") ) {
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 17fb4e322..83c2cc48b 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
@@ -23,19 +23,19 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.NanoSchedulable;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
 import java.text.DecimalFormat;
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 9708a8caa..322cea6d9 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
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.LocusWalker;
+import org.broadinstitute.gatk.engine.walkers.NanoSchedulable;
+import org.broadinstitute.gatk.engine.walkers.TreeReducible;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
 
 import java.io.PrintStream;
 import java.util.ArrayList;
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 cc37414ed..22ab7d1a7 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
@@ -23,19 +23,19 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.commandline.Input;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 
 import java.io.PrintStream;
 
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 0c02f8cc1..ee8b68fbf 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
@@ -23,20 +23,20 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.reference.ReferenceSequence;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RefWalker;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RefWalker;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 
 import java.io.PrintStream;
 
@@ -79,7 +79,7 @@ public class QCRef extends RefWalker {
     }
 
     private final void throwError(ReferenceContext ref, String message) {
-        throw new StingException(String.format("Site %s failed: %s", ref.getLocus(), message));
+        throw new GATKException(String.format("Site %s failed: %s", ref.getLocus(), message));
     }
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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 16b8a2d22..14a1de5f5 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
@@ -23,26 +23,26 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.commandline.Advanced;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.commandline.Advanced;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
 import java.util.Arrays;
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 9174651ca..5f1d39693 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
@@ -23,18 +23,18 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList;
+import org.broadinstitute.gatk.engine.walkers.Reference;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.Window;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.io.*;
@@ -78,7 +78,7 @@ public class RodSystemValidation extends RodWalker {
         try {
             digest = MessageDigest.getInstance("MD5");
         } catch (NoSuchAlgorithmException e) {
-            throw new ReviewedStingException("Unable to find MD5 checksumer");
+            throw new ReviewedGATKException("Unable to find MD5 checksumer");
         }
         out.println("Header:");
         // enumerate the list of ROD's we've loaded
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 4dac4cc9d..de3c0dcec 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
@@ -23,32 +23,32 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.readutils;
+package org.broadinstitute.gatk.tools.walkers.readutils;
 
 import htsjdk.samtools.reference.ReferenceSequence;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
 import htsjdk.samtools.util.StringUtil;
-import org.broadinstitute.sting.commandline.Advanced;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.clipping.ClippingOp;
-import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;
-import org.broadinstitute.sting.utils.clipping.ReadClipper;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.commandline.Advanced;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Hidden;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.clipping.ClippingOp;
+import org.broadinstitute.gatk.utils.clipping.ClippingRepresentation;
+import org.broadinstitute.gatk.utils.clipping.ReadClipper;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.io.File;
 import java.io.PrintStream;
@@ -172,7 +172,7 @@ public class ClipReads extends ReadWalker 0 is provided, then the quality score based read clipper will be applied to the reads using this
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 1221820ff..f8d8b529b 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
@@ -23,27 +23,27 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.readutils;
+package org.broadinstitute.gatk.tools.walkers.readutils;
 
 import htsjdk.samtools.SAMFileWriter;
 import htsjdk.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformersMode;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.engine.walkers.*;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Hidden;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformersMode;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.baq.BAQ;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.io.File;
 import java.util.*;
@@ -107,7 +107,7 @@ import java.util.*;
 public class PrintReads extends ReadWalker implements NanoSchedulable {
 
     @Output(doc="Write output to this BAM filename instead of STDOUT")
-    StingSAMFileWriter out;
+    GATKSAMFileWriter out;
 
     @Argument(fullName = "readGroup", shortName = "readGroup", doc="Exclude all reads with this read group from the output", required = false)
     String readGroup = null;
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 24cc3eae3..6f0ee85ff 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
@@ -23,25 +23,28 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.readutils;
+package org.broadinstitute.gatk.tools.walkers.readutils;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.SAMFileWriter;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.Advanced;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.engine.walkers.NanoSchedulable;
+import org.broadinstitute.gatk.engine.walkers.PartitionBy;
+import org.broadinstitute.gatk.engine.walkers.PartitionType;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.utils.commandline.Advanced;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Hidden;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.util.ArrayList;
 import java.util.Arrays;
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 9a518a265..b19a2d735 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
@@ -23,25 +23,25 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.readutils;
+package org.broadinstitute.gatk.tools.walkers.readutils;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileWriter;
 import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.WalkerName;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.engine.walkers.WalkerName;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.ReadUtils;
 
 import java.util.ArrayList;
 import java.util.HashMap;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmplicons.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmplicons.java
index 077534125..45e408ffa 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmplicons.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmplicons.java
@@ -23,29 +23,29 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.validation;
+package org.broadinstitute.gatk.tools.walkers.validation;
 
 import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMSequenceDictionary;
-import org.broadinstitute.sting.alignment.Alignment;
-import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
-import org.broadinstitute.sting.alignment.bwa.BWTFiles;
-import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.codecs.table.TableFeature;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.engine.alignment.Alignment;
+import org.broadinstitute.gatk.engine.alignment.bwa.BWAConfiguration;
+import org.broadinstitute.gatk.engine.alignment.bwa.BWTFiles;
+import org.broadinstitute.gatk.engine.alignment.bwa.c.BWACAligner;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.codecs.table.TableFeature;
+import org.broadinstitute.gatk.engine.walkers.DataSource;
+import org.broadinstitute.gatk.engine.walkers.Requires;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.io.File;
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 1c5b47312..67c1fcb3f 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
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval;
+package org.broadinstitute.gatk.tools.walkers.varianteval;
 
 import com.google.java.contract.Requires;
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
@@ -31,30 +31,30 @@ import htsjdk.samtools.util.IntervalTree;
 import htsjdk.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.IntervalStratification;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.VariantEvalUtils;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.engine.walkers.*;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.IntervalStratification;
+import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.VariantStratifier;
+import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.StratificationManager;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.EvaluationContext;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.VariantEvalUtils;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
@@ -343,7 +343,7 @@ public class VariantEval extends RodWalker implements TreeRedu
             try {
                 ancestralAlignments = new IndexedFastaSequenceFile(ancestralAlignmentsFile);
             } catch (FileNotFoundException e) {
-                throw new ReviewedStingException(String.format("The ancestral alignments file, '%s', could not be found", ancestralAlignmentsFile.getAbsolutePath()));
+                throw new ReviewedGATKException(String.format("The ancestral alignments file, '%s', could not be found", ancestralAlignmentsFile.getAbsolutePath()));
             }
         }
 
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 a63f32485..7244a9417 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
@@ -23,20 +23,20 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval;
+package org.broadinstitute.gatk.tools.walkers.varianteval;
 
-import org.broadinstitute.sting.gatk.report.GATKReport;
-import org.broadinstitute.sting.gatk.report.GATKReportTable;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.AnalysisModuleScanner;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.gatk.engine.report.GATKReport;
+import org.broadinstitute.gatk.engine.report.GATKReportTable;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.VariantStratifier;
+import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.StratificationManager;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.AnalysisModuleScanner;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.EvaluationContext;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
 
 import java.io.PrintStream;
 import java.lang.reflect.Field;
@@ -86,10 +86,10 @@ public class VariantEvalReportWriter {
                         final Object fieldValue = field.get(ve);
 
                         if ( fieldValue == null || ! (fieldValue instanceof Map) )
-                            throw new ReviewedStingException("BUG field " + field.getName() + " must be a non-null instance of Map in " + scanner.getAnalysis().name());
+                            throw new ReviewedGATKException("BUG field " + field.getName() + " must be a non-null instance of Map in " + scanner.getAnalysis().name());
                         final Map map = (Map)fieldValue;
                         if ( map.isEmpty() )
-                            throw new ReviewedStingException("BUG: map is null or empty in analysis " + scanner.getAnalysis());
+                            throw new ReviewedGATKException("BUG: map is null or empty in analysis " + scanner.getAnalysis());
                         
                         int counter = 0; // counter is used to ensure printing order is as defined by entrySet
                         for ( Map.Entry keyValue : map.entrySet() ) {
@@ -106,7 +106,7 @@ public class VariantEvalReportWriter {
                         }
                     }
                 } catch (IllegalAccessException e) {
-                    throw new ReviewedStingException("BUG: analysis field not public: " + e);
+                    throw new ReviewedGATKException("BUG: analysis field not public: " + e);
                 }
             }
         }
@@ -132,7 +132,7 @@ public class VariantEvalReportWriter {
             final String columnName = vs.getName();
             final Object strat = stratAndState.getSecond();
             if ( columnName == null || strat == null )
-                throw new ReviewedStingException("Unexpected null variant stratifier state at " + table + " key = " + primaryKey);
+                throw new ReviewedGATKException("Unexpected null variant stratifier state at " + table + " key = " + primaryKey);
             table.set(primaryKey, columnName, strat);
         }
     }
@@ -181,7 +181,7 @@ public class VariantEvalReportWriter {
                 table.addColumn(scanner.getMoltenAnnotation().valueName(), scanner.getMoltenAnnotation().valueFormat());
             } else {
                 if ( datamap.isEmpty() )
-                    throw new ReviewedStingException("Datamap is empty for analysis " + scanner.getAnalysis());
+                    throw new ReviewedGATKException("Datamap is empty for analysis " + scanner.getAnalysis());
                 
                 // add DataPoint's for each field marked as such
                 for (final Map.Entry field : datamap.entrySet()) {
@@ -192,7 +192,7 @@ public class VariantEvalReportWriter {
                         final String format = field.getValue().format();
                         table.addColumn(field.getKey().getName(), format);
                     } catch (SecurityException e) {
-                        throw new StingException("SecurityException: " + e);
+                        throw new GATKException("SecurityException: " + e);
                     }
                 }
             }
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 5b45434c1..7ebf96e7c 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
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 
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 4e95d964a..89b37f0f2 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
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
 
@@ -152,7 +152,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     nSymbolic++;
                     break;
                 default:
-                    throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
+                    throw new ReviewedGATKException("Unexpected VariantContext type " + vc1.getType());
             }
         }
 
@@ -200,7 +200,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                 case UNAVAILABLE:
                     break;
                 default:
-                    throw new ReviewedStingException("BUG: Unexpected genotype type: " + g);
+                    throw new ReviewedGATKException("BUG: Unexpected genotype type: " + g);
             }
         }
     }
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 ee0feb3be..8e202a74a 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
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Molten;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Molten;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 
@@ -91,7 +91,7 @@ public class IndelLengthHistogram extends VariantEvaluator implements StandardEv
                 // only if we are actually polymorphic in the subsetted samples should we count the allele
                 for ( Allele alt : eval.getAlternateAlleles() ) {
                     final int alleleSize = alt.length() - eval.getReference().length();
-                    if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
+                    if ( alleleSize == 0 ) throw new ReviewedGATKException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
                     updateLengthHistogram(eval.getReference(), alt);
                 }
             }
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 a496bcc78..484541e88 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
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
@@ -198,7 +198,7 @@ public class IndelSummary extends VariantEvaluator implements StandardEval {
 
                     // ins : del ratios
                     final int alleleSize = alt.length() - eval.getReference().length();
-                    if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
+                    if ( alleleSize == 0 ) throw new ReviewedGATKException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
                     if ( alleleSize > 0 ) n_insertions++;
                     if ( alleleSize < 0 ) n_deletions++;
 
@@ -206,7 +206,7 @@ public class IndelSummary extends VariantEvaluator implements StandardEval {
                     if ( eval.getAttributeAsString("SNPEFF_GENE_BIOTYPE", "missing").equals("protein_coding") ) {
                         final String effect = eval.getAttributeAsString("SNPEFF_EFFECT", "missing");
                         if ( effect.equals("missing") ) 
-                            throw new ReviewedStingException("Saw SNPEFF_GENE_BIOTYPE but unexpected no SNPEFF_EFFECT at " + eval);
+                            throw new ReviewedGATKException("Saw SNPEFF_GENE_BIOTYPE but unexpected no SNPEFF_EFFECT at " + eval);
                         if ( effect.equals("FRAME_SHIFT") )
                             n_coding_indels_frameshifting++;
                         else if ( effect.startsWith("CODON") )
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 e6a49a4e1..c01aae1cc 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
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.samples.Sample;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.MendelianViolation;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.samples.Sample;
+import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.utils.MendelianViolation;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Map;
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 6478fa87f..88543b505 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
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 
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 fb1c33786..0d3d4cf27 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
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
 import htsjdk.variant.variantcontext.VariantContext;
 
 @Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites")
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 206fc9560..c3b75c1e6 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
@@ -23,6 +23,6 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
 public interface StandardEval {}
\ No newline at end of file
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 288144b28..60a488117 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
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
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 b0318eef7..1919c5f5e 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
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.variantcontext.VariantContext;
 
 @Analysis(description = "Ti/Tv Variant Evaluator")
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 8d87fa1bc..664e5f245 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
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
 import htsjdk.variant.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 
@@ -109,7 +109,7 @@ public class ValidationReport extends VariantEvaluator implements StandardEval {
                 nComp += getCounts(x, y);
 
         if ( nComp != TP + FN + FP + TN + CompFiltered )
-            throw new ReviewedStingException("BUG: nComp != TP + FN + FP + TN + CompFiltered!");
+            throw new ReviewedGATKException("BUG: nComp != TP + FN + FP + TN + CompFiltered!");
 
         sensitivity = (100.0 * TP) / (TP + FN);
         specificity = (TN+FP > 0) ? (100.0 * TN) / (TN + FP) : 100.0;
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 3905aec86..0984a2e73 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
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import htsjdk.variant.variantcontext.VariantContext;
 
 public abstract class VariantEvaluator implements Comparable {
@@ -119,7 +119,7 @@ public abstract class VariantEvaluator implements Comparable {
      * @param other a VariantEvaluator of the same type of this object
      */
     public void combine(final VariantEvaluator other) {
-        throw new ReviewedStingException(getSimpleName() + " doesn't support combining results, sorry");
+        throw new ReviewedGATKException(getSimpleName() + " doesn't support combining results, sorry");
     }
 
     /**
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 c17394678..91473306a 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
@@ -23,21 +23,21 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
 import htsjdk.samtools.util.IntervalTree;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
+import org.broadinstitute.gatk.utils.interval.IntervalUtils;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
 
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 2129a2fb6..1f7ed14fc 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
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantSummary;
 import htsjdk.variant.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 
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 097b41c61..349979ada 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
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.MathUtils;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Collections;
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 9e196db3a..f131ca751 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
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Collections;
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 b80f021a9..f90e7c5bc 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
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
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 dc5d10512..97e5e7222 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
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
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 6c46e8ff7..03cba8cfc 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
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
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 7e61d6bb0..1c428982c 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
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
 import htsjdk.variant.variantcontext.VariantContext;
 
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 1e8a12bb4..8fdd00726 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
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
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 685891143..c37f0031c 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
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
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 17c90ad72..08ff9d4f5 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
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
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 f6e51fdde..e5cb24077 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
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Collections;
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 fcfcaa747..8ee4e79b2 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
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
 import htsjdk.samtools.util.IntervalTree;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.interval.IntervalUtils;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.*;
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 da8175170..00fec2a81 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
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.SortableJexlVCMatchExp;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextUtils;
 
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 1987a1ccb..0114bf24d 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
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.*;
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 0b9aabf7e..7ad45e040 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
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
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 de4ab5db8..946c723fc 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
@@ -23,6 +23,6 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
 public interface RequiredStratification {}
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 1aaa9503d..bd0b6f1e2 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
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantSummary;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.*;
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 f254f0e41..c2ddd803f 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
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
-import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff.EffectType;
-import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff.InfoFieldKey;
-import org.broadinstitute.sting.gatk.walkers.annotator.SnpEffUtil;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff;
+import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff.EffectType;
+import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff.InfoFieldKey;
+import org.broadinstitute.gatk.tools.walkers.annotator.SnpEffUtil;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
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 5267513ad..41c52c2f0 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
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
 public interface StandardStratification {
 }
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 9432a18ad..6eba4b450 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
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
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 53c7f2198..0832ebd13 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
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.Stratifier;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.Stratifier;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
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 cf5493511..0ba5b6077 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
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.Collections;
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 4ab6262be..0db937052 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
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.*;
 
@@ -79,7 +79,7 @@ class StratNode implements Iterable> {
     @Requires("key >= 0")
     public void setKey(final int key) {
         if ( ! isLeaf() )
-            throw new ReviewedStingException("Cannot set key of non-leaf node");
+            throw new ReviewedGATKException("Cannot set key of non-leaf node");
         this.key = key;
     }
 
@@ -115,7 +115,7 @@ class StratNode implements Iterable> {
                 // loop over all of the states at this offset
                 final StratNode subnode = subnodes.get(state);
                 if ( subnode == null )
-                    throw new ReviewedStingException("Couldn't find state for " + state + " at node " + this);
+                    throw new ReviewedGATKException("Couldn't find state for " + state + " at node " + this);
                 else
                     subnode.find(multipleStates, offset+1, keys);
             }
@@ -125,7 +125,7 @@ class StratNode implements Iterable> {
     @Ensures("result >= 0")
     public int getKey() {
         if ( ! isLeaf() )
-            throw new ReviewedStingException("Cannot get key of non-leaf node");
+            throw new ReviewedGATKException("Cannot get key of non-leaf node");
         else
             return key;
     }
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 87fb3dfa4..a789b70e1 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.*;
 
@@ -64,6 +64,6 @@ class StratNodeIterator implements Iterator>
 
     @Override
     public void remove() {
-        throw new ReviewedStingException("Cannot remove from StratNode iterator");
+        throw new ReviewedGATKException("Cannot remove from StratNode iterator");
     }
 }
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 681d32f2d..729001677 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
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager;
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.*;
 
@@ -74,7 +74,7 @@ public class StratificationManager implements Map data
         this.valuesByKey = new ArrayList(size());
@@ -109,7 +109,7 @@ public class StratificationManager implements Map states = first.getAllStates();
             
             if ( states.isEmpty() )
-                throw new ReviewedStingException("State " + first + " is empty!");
+                throw new ReviewedGATKException("State " + first + " is empty!");
             
             final LinkedHashMap> subNodes = new LinkedHashMap>(states.size());
             for ( final Object state : states ) {
@@ -147,13 +147,13 @@ public class StratificationManager implements Map stateValues : stratifierValuesByKey )
             if ( stateValues == null )
-                throw new ReviewedStingException("Found a null state value set that's null");
+                throw new ReviewedGATKException("Found a null state value set that's null");
     }
 
     private void assignStratifierValuesByKey(final StratNode node, final LinkedList states) {
         if ( node.isLeaf() ) { // we're here!
             if ( states.isEmpty() )
-                throw new ReviewedStingException("Found a leaf node with an empty state values vector");
+                throw new ReviewedGATKException("Found a leaf node with an empty state values vector");
             stratifierValuesByKey.set(node.getKey(), Collections.unmodifiableList(new ArrayList(states)));
         } else {
             for ( Map.Entry> entry : node.getSubnodes().entrySet() ) {
@@ -299,37 +299,37 @@ public class StratificationManager implements Map objects, final V v) {
-        throw new ReviewedStingException("put() not implemented for StratificationManager");
+        throw new ReviewedGATKException("put() not implemented for StratificationManager");
     }
 
     @Override
     public V remove(final Object o) {
-        throw new ReviewedStingException("remove() not implemented for StratificationManager");
+        throw new ReviewedGATKException("remove() not implemented for StratificationManager");
     }
 
     @Override
     public void putAll(final Map, ? extends V> map) {
-        throw new ReviewedStingException("clear() not implemented for StratificationManager");
+        throw new ReviewedGATKException("clear() not implemented for StratificationManager");
     }
 
     @Override
     public void clear() {
-        throw new ReviewedStingException("clear() not implemented for StratificationManager");
+        throw new ReviewedGATKException("clear() not implemented for StratificationManager");
     }
 
     @Override
     public Set> keySet() {
-        throw new ReviewedStingException("Not yet implemented");
+        throw new ReviewedGATKException("Not yet implemented");
     }
 
     @Override
     public Set, V>> entrySet() {
-        throw new ReviewedStingException("Not yet implemented");
+        throw new ReviewedGATKException("Not yet implemented");
     }
 
     // -------------------------------------------------------------------------------------
@@ -387,16 +387,16 @@ public class StratificationManager implements Map remappedStates) {
         // make sure the mapping is reasonable
         if ( ! newStratifier.getAllStates().containsAll(remappedStates.values()) )
-            throw new ReviewedStingException("combineStrats: remapped states contains states not found in newStratifer state set");
+            throw new ReviewedGATKException("combineStrats: remapped states contains states not found in newStratifer state set");
 
         if ( ! remappedStates.keySet().containsAll(stratifierToReplace.getAllStates()) )
-            throw new ReviewedStingException("combineStrats: remapped states missing mapping for some states");
+            throw new ReviewedGATKException("combineStrats: remapped states missing mapping for some states");
 
         // the new strats are the old ones with the single replacement
         final List newStrats = new ArrayList(getStratifiers());
         final int stratOffset = newStrats.indexOf(stratifierToReplace);
         if ( stratOffset == -1 )
-            throw new ReviewedStingException("Could not find strat to replace " + stratifierToReplace + " in existing strats " + newStrats);
+            throw new ReviewedGATKException("Could not find strat to replace " + stratifierToReplace + " in existing strats " + newStrats);
         newStrats.set(stratOffset, newStratifier);
 
         // create an empty but fully initialized new manager
@@ -412,7 +412,7 @@ public class StratificationManager implements Map 0 )
-                throw new ReviewedStingException("Analysis " + analysis.name() + " has an @Molten field as well as @DataPoint fields, which is forbidden");
+                throw new ReviewedGATKException("Analysis " + analysis.name() + " has an @Molten field as well as @DataPoint fields, which is forbidden");
         }
     }
 
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 34c9368f2..0805cb5e7 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
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.util;
+package org.broadinstitute.gatk.tools.walkers.varianteval.util;
 
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
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 cf738b7a5..7e9f2da36 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
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.util;
+package org.broadinstitute.gatk.tools.walkers.varianteval.util;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.StratificationManager;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
@@ -59,9 +59,9 @@ public final class EvaluationContext {
                 if ( doInitialize ) eval.initialize(walker);
                 evaluationInstances.add(eval);
             } catch (InstantiationException e) {
-                throw new ReviewedStingException("Unable to instantiate eval module '" + c.getSimpleName() + "'", e);
+                throw new ReviewedGATKException("Unable to instantiate eval module '" + c.getSimpleName() + "'", e);
             } catch (IllegalAccessException e) {
-                throw new ReviewedStingException("Illegal access error when trying to instantiate eval module '" + c.getSimpleName() + "'", e);
+                throw new ReviewedGATKException("Illegal access error when trying to instantiate eval module '" + c.getSimpleName() + "'", e);
             }
         }
     }
@@ -92,7 +92,7 @@ public final class EvaluationContext {
                     evaluation.update2(eval, comp, tracker, ref, context);
                     break;
                 default:
-                    throw new ReviewedStingException("BUG: Unexpected evaluation order " + evaluation);
+                    throw new ReviewedGATKException("BUG: Unexpected evaluation order " + evaluation);
             }
         }
     }
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 d65887090..57c4fbc06 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
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.util;
+package org.broadinstitute.gatk.tools.walkers.varianteval.util;
 
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
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 eb8129ba7..a759eb258 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
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.util;
+package org.broadinstitute.gatk.tools.walkers.varianteval.util;
 
 import org.apache.commons.jexl2.Expression;
 import htsjdk.variant.variantcontext.VariantContextUtils;
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 7c4168379..6f623d48b 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
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.varianteval.util;
+package org.broadinstitute.gatk.tools.walkers.varianteval.util;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.StandardEval;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.RequiredStratification;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.StandardStratification;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.StandardEval;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.RequiredStratification;
+import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.StandardStratification;
+import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.VariantStratifier;
+import org.broadinstitute.gatk.utils.classloader.PluginManager;
 import htsjdk.variant.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
 import htsjdk.variant.variantcontext.VariantContextUtils;
@@ -130,9 +130,9 @@ public class VariantEvalUtils {
 
                     strats.add(vs);
                 } catch (InstantiationException e) {
-                    throw new StingException("Unable to instantiate stratification module '" + c.getSimpleName() + "'");
+                    throw new GATKException("Unable to instantiate stratification module '" + c.getSimpleName() + "'");
                 } catch (IllegalAccessException e) {
-                    throw new StingException("Illegal access error when trying to instantiate stratification module '" + c.getSimpleName() + "'");
+                    throw new GATKException("Illegal access error when trying to instantiate stratification module '" + c.getSimpleName() + "'");
                 }
             }
         }
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 a04da2930..355441d5b 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
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
+package org.broadinstitute.gatk.tools.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.text.XReadLines;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.io.File;
@@ -108,7 +108,7 @@ public class VQSRCalibrationCurve {
                 return r.getTruePositiveRate();
         }
 
-        throw new ReviewedStingException("BUG: should not be able to reach this code");
+        throw new ReviewedGATKException("BUG: should not be able to reach this code");
     }
 
     public double probTrueVariant(String VQSRQualKey, VariantContext vc) {
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 a49e26889..beb453b7b 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
@@ -23,26 +23,26 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.Reference;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.TreeReducible;
+import org.broadinstitute.gatk.engine.walkers.Window;
+import org.broadinstitute.gatk.tools.walkers.annotator.ChromosomeCountConstants;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
 import htsjdk.variant.variantcontext.VariantContextUtils;
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
old mode 100755
new mode 100644
index db555b1d8..2b1897c04
--- 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
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.vcf.VCFHeader;
 
@@ -73,7 +73,7 @@ public class ConcordanceMetrics {
     public GenotypeConcordanceTable getGenotypeConcordance(String sample) {
         GenotypeConcordanceTable table = perSampleGenotypeConcordance.get(sample);
         if ( table == null )
-            throw new ReviewedStingException("Attempted to request the concordance table for sample "+sample+" on which it was not calculated");
+            throw new ReviewedGATKException("Attempted to request the concordance table for sample "+sample+" on which it was not calculated");
         return table;
     }
 
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 a29818458..73995bf93 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
@@ -23,22 +23,24 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.engine.walkers.Reference;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.Window;
+import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.variantcontext.VariantContext;
 
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
old mode 100755
new mode 100644
index 1bba62eb9..9ddcc34e7
--- 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
@@ -23,20 +23,20 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.report.GATKReport;
-import org.broadinstitute.sting.gatk.report.GATKReportTable;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.report.GATKReport;
+import org.broadinstitute.gatk.engine.report.GATKReportTable;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.vcf.VCFHeader;
 
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 be9b205c1..641047800 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
@@ -23,34 +23,33 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.Reference;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.Window;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
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 71776c432..710aad576 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
@@ -23,29 +23,29 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import htsjdk.samtools.liftover.LiftOver;
 import htsjdk.samtools.util.Interval;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileReader;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
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 13576a767..d50b4f20d 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
@@ -23,25 +23,25 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
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 0fcb2b1fb..c9842c8bc 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
@@ -23,28 +23,28 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import org.apache.commons.io.FilenameUtils;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.interval.IntervalSetRule;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.TreeReducible;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.interval.IntervalMergingRule;
+import org.broadinstitute.gatk.utils.interval.IntervalSetRule;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.text.ListFileUtils;
+import org.broadinstitute.gatk.utils.text.ListFileUtils;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.io.File;
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 02b5d7cf6..206d6dc7a 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
@@ -23,28 +23,28 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants;
-import org.broadinstitute.sting.utils.MendelianViolation;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.TreeReducible;
+import org.broadinstitute.gatk.tools.walkers.annotator.ChromosomeCountConstants;
+import org.broadinstitute.gatk.utils.MendelianViolation;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.text.XReadLines;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 
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 1f2d55751..6b6e6ca82 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
@@ -23,23 +23,23 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import htsjdk.tribble.TribbleException;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.Reference;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.Window;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFConstants;
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 6bef27d0e..9031bf7c1 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
@@ -23,22 +23,24 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.engine.walkers.Reference;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.Window;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.QualityUtils;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
@@ -255,7 +257,7 @@ public class VariantValidationAssessor extends RodWalker
 
     private double hardyWeinbergCalculation(VariantContext vc) {
         //if ( popFile != null ) {
-        //    throw new StingException("We still need to implement this!");
+        //    throw new GATKException("We still need to implement this!");
         //} else {
         return GATKVariantContextUtils.computeHardyWeinbergPvalue(vc);
         //}
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 b7971e335..1f7b20ca3 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
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
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 d42dfb96e..b51349afe 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
@@ -23,28 +23,27 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import htsjdk.tribble.TribbleException;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.Reference;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.Window;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.QualityUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
 import htsjdk.variant.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.text.XReadLines;
 import htsjdk.variant.variantcontext.*;
 
 import java.io.*;
@@ -188,7 +187,7 @@ public class VariantsToBinaryPed extends RodWalker {
                         printMap.put(sample,new PrintStream(temp));
                         tempFiles.put(sample,temp);
                     } catch (IOException e) {
-                        throw new ReviewedStingException("Error creating temporary file",e);
+                        throw new ReviewedGATKException("Error creating temporary file",e);
                     }
                     genotypeBuffer.put(sample,new byte[BUFFER_SIZE]);
                 }
@@ -272,7 +271,7 @@ public class VariantsToBinaryPed extends RodWalker {
                     try {
                         samOut.write(genotypeBuffer.get(sample));
                     } catch ( IOException e ) {
-                        throw new ReviewedStingException("Error writing to temporary bed file.",e);
+                        throw new ReviewedGATKException("Error writing to temporary bed file.",e);
                     }
                     // reset the buffer for this sample
                     genotypeBuffer.put(sample,new byte[BUFFER_SIZE]);
@@ -303,7 +302,7 @@ public class VariantsToBinaryPed extends RodWalker {
         try {
             outBed.write(bytes);
         } catch (IOException e) {
-            throw new ReviewedStingException("Error writing to output bed file",e);
+            throw new ReviewedGATKException("Error writing to output bed file",e);
         }
     }
 
@@ -331,13 +330,13 @@ public class VariantsToBinaryPed extends RodWalker {
                 int lim = byteCount + (genotypeCount > 0 ? 1 : 0);
                 printMap.get(sample).write(genotypeBuffer.get(sample),0,lim);
             } catch (IOException e) {
-                throw new ReviewedStingException("Error closing temporary file.",e);
+                throw new ReviewedGATKException("Error closing temporary file.",e);
             }
 
             try {
                printMap.get(sample).close();
             } catch (IOException e) {
-                throw new ReviewedStingException("Error closing temporary file.",e);
+                throw new ReviewedGATKException("Error closing temporary file.",e);
             }
         }
         for ( String sample : famOrder ) {
@@ -346,7 +345,7 @@ public class VariantsToBinaryPed extends RodWalker {
             try {
                 inStream = new FileInputStream(tempFiles.get(sample));
             } catch (IOException e) {
-                throw new ReviewedStingException("Error opening temp file for input.",e);
+                throw new ReviewedGATKException("Error opening temp file for input.",e);
             }
 
 
@@ -366,7 +365,7 @@ public class VariantsToBinaryPed extends RodWalker {
                 }
                 inStream.close();
             } catch (IOException e) {
-                throw new ReviewedStingException("Error reading form temp file for input.",e);
+                throw new ReviewedGATKException("Error reading form temp file for input.",e);
             }
         }
     }
@@ -448,7 +447,7 @@ public class VariantsToBinaryPed extends RodWalker {
             outBed.write(new byte[] { (byte) 0x6c, (byte) 0x1b, (byte) (mode == OutputMode.INDIVIDUAL_MAJOR ? 0x0 : 0x1)});
             // ultimately, the bed will be in individual-major mode
         } catch (IOException e) {
-            throw new ReviewedStingException("error writing to output file.");
+            throw new ReviewedGATKException("error writing to output file.");
         }
     }
 
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 77ac085d3..9a65a7062 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
@@ -23,25 +23,25 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.VCFConstants;
 import htsjdk.variant.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.io.PrintStream;
 import java.lang.reflect.Array;
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 8b2b4f58a..3e0e2ab5c 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
@@ -23,33 +23,33 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.gatk.walkers.annotator.VariantOverlapAnnotator;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.refdata.VariantContextAdaptors;
+import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder;
+import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature;
+import org.broadinstitute.gatk.engine.walkers.Reference;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.Window;
+import org.broadinstitute.gatk.tools.walkers.annotator.VariantOverlapAnnotator;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.codecs.hapmap.RawHapMapFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java
index e74e4f690..31032e3f6 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import java.util.concurrent.TimeUnit;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java
index 4f744ee6a..ec53225ee 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java
@@ -23,12 +23,12 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import htsjdk.samtools.util.StringUtil;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.util.Arrays;
 import java.util.Comparator;
@@ -644,7 +644,7 @@ public class BaseUtils {
             case 'N':
                 return 'N';
             default:
-                throw new ReviewedStingException("base must be A, C, G or T. " + (char) base + " is not a valid base.");
+                throw new ReviewedGATKException("base must be A, C, G or T. " + (char) base + " is not a valid base.");
         }
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java
index 94ff2f9dd..a9ab00de3 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import java.util.BitSet;
 import java.util.HashMap;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java
index 12dda4fd2..f3f93b411 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import htsjdk.samtools.SAMSequenceDictionary;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java
index f867f76c2..9fcd848f2 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import it.unimi.dsi.fastutil.objects.Object2ObjectMap;
 import it.unimi.dsi.fastutil.objects.Object2ObjectOpenHashMap;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java
index b85b583ad..fe880ec8a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
@@ -34,8 +34,8 @@ import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 /**
  * Factory class for creating GenomeLocs
@@ -314,7 +314,7 @@ public final class GenomeLocParser {
         try {
             validateGenomeLoc(contig, getContigIndexWithoutException(contig), start, stop, mustBeOnReference);
             return true;
-        } catch ( ReviewedStingException e) {
+        } catch ( ReviewedGATKException e) {
             return false;
         }
     }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java
index 86817c43c..694c27187 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.interval.IntervalMergingRule;
+import org.broadinstitute.gatk.utils.interval.IntervalUtils;
 
 import java.util.*;
 
@@ -390,7 +390,7 @@ public class GenomeLocSortedSet extends AbstractSet {
             } else if ( e.getStop() < p.getStart() ) {
                 toExclude.pop();                 // p starts after e stops, e is done
             } else {
-                throw new ReviewedStingException("BUG: unexpected condition: p=" + p + ", e=" + e);
+                throw new ReviewedGATKException("BUG: unexpected condition: p=" + p + ", e=" + e);
             }
 
             if ( i++ % 10000 == 0 )
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java
index 3d5891f2e..041bf76ba 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.lang.management.ManagementFactory;
 import java.lang.management.MemoryMXBean;
@@ -67,7 +67,7 @@ public class HeapSizeMonitor {
             monitorThread.join();
         }
         catch(InterruptedException ex) {
-            throw new ReviewedStingException("Unable to connect to monitor thread");
+            throw new ReviewedGATKException("Unable to connect to monitor thread");
         }
         monitorThread = null;        
     }
@@ -99,7 +99,7 @@ public class HeapSizeMonitor {
                     Thread.sleep(monitorFrequencyMillis);
                 }
                 catch(InterruptedException ex) {
-                    throw new ReviewedStingException("Unable to continue monitoring heap consumption",ex);
+                    throw new ReviewedGATKException("Unable to continue monitoring heap consumption",ex);
                 }
             }
         }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java
index 95a6d5700..81a2bdc52 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
@@ -253,7 +253,7 @@ public class IndelUtils {
         if (k >=0 && k < COLUMN_KEYS.length)
             return COLUMN_KEYS[k];
         else
-            throw new ReviewedStingException("Invalid index when trying to get indel classification name");
+            throw new ReviewedGATKException("Invalid index when trying to get indel classification name");
     }
 
     public static boolean isInsideExtendedIndel(VariantContext vc, ReferenceContext ref) {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java
index 913080a63..df2e829ab 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import java.util.LinkedHashMap;
 import java.util.Map;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java
index 94bdeca27..8c0e68064 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java
@@ -23,13 +23,13 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 /**
  * A wrapper class that provides efficient most recently used caching for the global
@@ -97,7 +97,7 @@ final class MRUCachingSAMSequenceDictionary {
      * Same as SAMSequenceDictionary.getSequence but uses a MRU cache for efficiency
      *
      * @param contig the contig name we want to get the sequence record of
-     * @throws ReviewedStingException if contig isn't present in the dictionary
+     * @throws ReviewedGATKException if contig isn't present in the dictionary
      * @return the sequence record for contig
      */
     @Requires("contig != null")
@@ -113,7 +113,7 @@ final class MRUCachingSAMSequenceDictionary {
      * Same as SAMSequenceDictionary.getSequence but uses a MRU cache for efficiency
      *
      * @param index the contig index we want to get the sequence record of
-     * @throws ReviewedStingException if contig isn't present in the dictionary
+     * @throws ReviewedGATKException if contig isn't present in the dictionary
      * @return the sequence record for contig
      */
     @Requires("index >= 0")
@@ -129,7 +129,7 @@ final class MRUCachingSAMSequenceDictionary {
      * Same as SAMSequenceDictionary.getSequenceIndex but uses a MRU cache for efficiency
      *
      * @param contig the contig we want to get the sequence record of
-     * @throws ReviewedStingException if index isn't present in the dictionary
+     * @throws ReviewedGATKException if index isn't present in the dictionary
      * @return the sequence record index for contig
      */
     @Requires("contig != null")
@@ -167,7 +167,7 @@ final class MRUCachingSAMSequenceDictionary {
      *
      * @param contig the contig we want to look up.  If null, index is used instead
      * @param index the contig index we want to look up.  Only used if contig is null
-     * @throws ReviewedStingException if index isn't present in the dictionary
+     * @throws ReviewedGATKException if index isn't present in the dictionary
      * @return the SAMSequenceRecord for contig / index
      */
     @Requires("contig != null || index >= 0")
@@ -175,7 +175,7 @@ final class MRUCachingSAMSequenceDictionary {
     private SAMSequenceRecord updateCache(final String contig, int index ) {
         SAMSequenceRecord rec = contig == null ? dict.getSequence(index) : dict.getSequence(contig);
         if ( rec == null ) {
-            throw new ReviewedStingException("BUG: requested unknown contig=" + contig + " index=" + index);
+            throw new ReviewedGATKException("BUG: requested unknown contig=" + contig + " index=" + index);
         } else {
             lastSSR = rec;
             lastContig = rec.getSequenceName();
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java
index 74009682a..a918c0a0e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import cern.jet.math.Arithmetic;
 import cern.jet.random.Normal;
@@ -32,9 +32,9 @@ import com.google.java.contract.Requires;
 import org.apache.commons.math.MathException;
 import org.apache.commons.math.distribution.NormalDistribution;
 import org.apache.commons.math.distribution.NormalDistributionImpl;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
 
 import java.io.Serializable;
 import java.util.Comparator;
@@ -332,7 +332,7 @@ public class MannWhitneyU {
     @Requires({"m > 0","n > 0","u >= 0"})
     @Ensures({"result != null","! Double.isInfinite(result.getFirst())", "! Double.isInfinite(result.getSecond())"})
     public static Pair calculatePRecursively(int n, int m, long u, boolean twoSided, ExactMode mode) {
-        if ( m > 8 && n > 5 ) { throw new StingException(String.format("Please use the appropriate (normal or sum of uniform) approximation. Values n: %d, m: %d",n,m)); }
+        if ( m > 8 && n > 5 ) { throw new GATKException(String.format("Please use the appropriate (normal or sum of uniform) approximation. Values n: %d, m: %d",n,m)); }
         double p = mode == ExactMode.POINT ? cpr(n,m,u) : cumulativeCPR(n,m,u);
         //p *= twoSided ? 2.0 : 1.0;
         double z;
@@ -355,7 +355,7 @@ public class MannWhitneyU {
             }
 
         } catch (MathException me) {
-            throw new StingException("A math exception occurred in inverting the probability",me);
+            throw new GATKException("A math exception occurred in inverting the probability",me);
         }
 
         return new Pair(z,(twoSided ? 2.0*p : p));
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java
index b1501f490..1e70d8502 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.apache.commons.math.distribution.ExponentialDistribution;
 import org.apache.commons.math.distribution.ExponentialDistributionImpl;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.math.BigDecimal;
 import java.util.*;
@@ -190,7 +190,7 @@ public class MathUtils {
             if ( num == 0 && denom == 0) {
                 return 0.0;
             } else {
-                throw new ReviewedStingException(String.format("The denominator of a ratio cannot be zero or less than zero: %d/%d",num,denom));
+                throw new ReviewedGATKException(String.format("The denominator of a ratio cannot be zero or less than zero: %d/%d",num,denom));
             }
         }
     }
@@ -202,7 +202,7 @@ public class MathUtils {
             if ( num == 0L && denom == 0L ) {
                 return 0.0;
             } else {
-                throw new ReviewedStingException(String.format("The denominator of a ratio cannot be zero or less than zero: %d/%d",num,denom));
+                throw new ReviewedGATKException(String.format("The denominator of a ratio cannot be zero or less than zero: %d/%d",num,denom));
             }
         }
     }
@@ -1104,7 +1104,7 @@ public class MathUtils {
      */
     public static double logDotProduct(final double [] x, final double[] y) {
         if (x.length != y.length)
-            throw new ReviewedStingException("BUG: Vectors of different lengths");
+            throw new ReviewedGATKException("BUG: Vectors of different lengths");
 
         double tmpVec[] = new double[x.length];
 
@@ -1438,7 +1438,7 @@ public class MathUtils {
      */
     public static double[] vectorSum(final double[]x, final double[] y) {
         if (x.length != y.length)
-            throw new ReviewedStingException("BUG: Lengths of x and y must be the same");
+            throw new ReviewedGATKException("BUG: Lengths of x and y must be the same");
 
         double[] result = new double[x.length];
         for (int k=0; k  Byte.MAX_VALUE )
                 throw new UserException.MisencodedBAM(read, "we encountered an extremely high quality score (" + (int)read.getBaseQualities()[i] + ") with BAQ correction factor of " + baq_i);
@@ -542,9 +542,9 @@ public class BAQ {
 //    int n = 0;
     public BAQCalculationResult calcBAQFromHMM(byte[] ref, byte[] query, byte[] quals, int queryStart, int queryEnd ) {
 //        total.restart();
-        if ( queryStart < 0 ) throw new ReviewedStingException("BUG: queryStart < 0: " + queryStart);
-        if ( queryEnd < 0 ) throw new ReviewedStingException("BUG: queryEnd < 0: " + queryEnd);
-        if ( queryEnd < queryStart ) throw new ReviewedStingException("BUG: queryStart < queryEnd : " + queryStart + " end =" + queryEnd);
+        if ( queryStart < 0 ) throw new ReviewedGATKException("BUG: queryStart < 0: " + queryStart);
+        if ( queryEnd < 0 ) throw new ReviewedGATKException("BUG: queryEnd < 0: " + queryEnd);
+        if ( queryEnd < queryStart ) throw new ReviewedGATKException("BUG: queryStart < queryEnd : " + queryStart + " end =" + queryEnd);
 
         // note -- assumes ref is offset from the *CLIPPED* start
         BAQCalculationResult baqResult = new BAQCalculationResult(query, quals, ref);
@@ -584,7 +584,7 @@ public class BAQ {
                     // in the else case we aren't including soft clipped bases, so we don't update
                     // queryStart or queryStop
                     break;
-                default: throw new ReviewedStingException("BUG: Unexpected CIGAR element " + elt + " in read " + read.getReadName());
+                default: throw new ReviewedGATKException("BUG: Unexpected CIGAR element " + elt + " in read " + read.getReadName());
             }
         }
 
@@ -633,7 +633,7 @@ public class BAQ {
                     readI += l; refI += l;
                     break;
                 default:
-                    throw new ReviewedStingException("BUG: Unexpected CIGAR element " + elt + " in read " + read.getReadName());
+                    throw new ReviewedGATKException("BUG: Unexpected CIGAR element " + elt + " in read " + read.getReadName());
             }
         }
         if ( readI != read.getReadLength() ) // odd cigar string
@@ -683,7 +683,7 @@ public class BAQ {
                         case ADD_TAG:         addBAQTag(read, hmmResult.bq); break;
                         case OVERWRITE_QUALS: System.arraycopy(hmmResult.bq, 0, read.getBaseQualities(), 0, hmmResult.bq.length); break;
                         case DONT_MODIFY:     BAQQuals = hmmResult.bq; break;
-                        default:              throw new ReviewedStingException("BUG: unexpected qmode " + qmode);
+                        default:              throw new ReviewedGATKException("BUG: unexpected qmode " + qmode);
                     }
                 } else if ( readHasBAQTag ) {
                     // remove the BAQ tag if it's there because we cannot trust it
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQReadTransformer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQReadTransformer.java
index 7a87235d8..c9192e12f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQReadTransformer.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQReadTransformer.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.baq;
+package org.broadinstitute.gatk.utils.baq;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.WalkerManager;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
-import org.broadinstitute.sting.gatk.walkers.BAQMode;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.WalkerManager;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
+import org.broadinstitute.gatk.engine.walkers.BAQMode;
+import org.broadinstitute.gatk.engine.walkers.Walker;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 /**
  * Applies Heng's BAQ calculation to a stream of incoming reads
@@ -53,7 +53,7 @@ public class BAQReadTransformer extends ReadTransformer {
         baqHMM = new BAQ(engine.getArguments().BAQGOP);
 
         if ( qmode == BAQ.QualityMode.DONT_MODIFY )
-            throw new ReviewedStingException("BUG: shouldn't create BAQ transformer with quality mode DONT_MODIFY");
+            throw new ReviewedGATKException("BUG: shouldn't create BAQ transformer with quality mode DONT_MODIFY");
 
         if ( mode.ApplicationTime() == ReadTransformer.ApplicationTime.FORBIDDEN && enabled() )
             throw new UserException.BadArgumentValue("baq", "Walker cannot accept BAQ'd base qualities, and yet BAQ mode " + cmode + " was requested.");
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/ReadTransformingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/ReadTransformingIterator.java
index 523f71bc2..18ca02f61 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/ReadTransformingIterator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/ReadTransformingIterator.java
@@ -23,29 +23,29 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.baq;
+package org.broadinstitute.gatk.utils.baq;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.util.Iterator;
 
 /**
  * Iterator that applies a ReadTransformer to a stream of reads
  */
-public class ReadTransformingIterator implements StingSAMIterator {
-    private final StingSAMIterator it;
+public class ReadTransformingIterator implements GATKSAMIterator {
+    private final GATKSAMIterator it;
     private final ReadTransformer transformer;
 
     /**
      * Creates a new ReadTransforming iterator
      */
     @Requires({"it != null", "transformer != null", "transformer.isInitialized()"})
-    public ReadTransformingIterator(final StingSAMIterator it, final ReadTransformer transformer) {
+    public ReadTransformingIterator(final GATKSAMIterator it, final ReadTransformer transformer) {
         if ( ! transformer.isInitialized() )
             throw new IllegalStateException("Creating a read transformer stream for an uninitialized read transformer: " + transformer);
         if ( transformer.getApplicationTime() == ReadTransformer.ApplicationTime.FORBIDDEN )
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java
index 8f4958f6c..d695543c4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.classloader;
+package org.broadinstitute.gatk.utils.classloader;
 
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
 import org.reflections.util.ClasspathHelper;
 
 import java.io.File;
@@ -138,7 +138,7 @@ public class JVMUtils {
             field.set(instance, value);
         }
         catch( IllegalAccessException ex ) {
-            throw new ReviewedStingException(String.format("Could not set %s in instance %s to %s",field.getName(),instance.getClass().getName(),value.toString()));
+            throw new ReviewedGATKException(String.format("Could not set %s in instance %s to %s",field.getName(),instance.getClass().getName(),value.toString()));
         }
     }
 
@@ -154,7 +154,7 @@ public class JVMUtils {
             return field.get(instance);
         }
         catch( IllegalAccessException ex ) {
-            throw new ReviewedStingException(String.format("Could not retrieve %s in instance %s",field.getName(),instance.getClass().getName()));
+            throw new ReviewedGATKException(String.format("Could not retrieve %s in instance %s",field.getName(),instance.getClass().getName()));
         }
     }
 
@@ -169,9 +169,9 @@ public class JVMUtils {
         // TODO: Make JVM utils.
         Collection selectedObjects = getObjectsOfType(objectsToFilter,type);
         if(selectedObjects.size() > 1)
-            throw new ReviewedStingException("User asked for a single instance of the type, multiple were present");
+            throw new ReviewedGATKException("User asked for a single instance of the type, multiple were present");
         if(selectedObjects.size() == 0)
-            throw new ReviewedStingException("User asked for a single instance of the type, but none were present");
+            throw new ReviewedGATKException("User asked for a single instance of the type, but none were present");
         return selectedObjects.iterator().next();
     }
 
@@ -222,7 +222,7 @@ public class JVMUtils {
         } else if (type instanceof Class) {
             classes.add((Class) type);
         } else {
-            throw new StingException("Unknown type: " + type + " (" + type.getClass().getName() + ")");
+            throw new GATKException("Unknown type: " + type + " (" + type.getClass().getName() + ")");
         }
     }
 
@@ -230,10 +230,10 @@ public class JVMUtils {
         if ( t instanceof ParameterizedType ) {
             ParameterizedType parameterizedType = (ParameterizedType)t;
             if ( parameterizedType.getActualTypeArguments().length != 1 )
-                throw new ReviewedStingException("BUG: more than 1 generic type found on class" + t);
+                throw new ReviewedGATKException("BUG: more than 1 generic type found on class" + t);
             return (Class)parameterizedType.getActualTypeArguments()[0];
         } else
-            throw new ReviewedStingException("BUG: could not find generic type on class " + t);
+            throw new ReviewedGATKException("BUG: could not find generic type on class " + t);
     }
 
     /**
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java
index 38bd9bdcc..7313e19e6 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.classloader;
+package org.broadinstitute.gatk.utils.classloader;
 
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.WalkerManager;
-import org.broadinstitute.sting.gatk.filters.FilterManager;
-import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.WalkerManager;
+import org.broadinstitute.gatk.engine.filters.FilterManager;
+import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.reflections.Reflections;
 import org.reflections.scanners.SubTypesScanner;
 import org.reflections.util.ConfigurationBuilder;
@@ -209,7 +209,7 @@ public class PluginManager {
                   method.setAccessible(true);
               method.invoke(ClassLoader.getSystemClassLoader(), url);
           } catch (Exception e) {
-              throw new ReviewedStingException("Error adding url to the current classloader.", e);
+              throw new ReviewedGATKException("Error adding url to the current classloader.", e);
           }
       }
     }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java
index 3196a2eda..7c7a776a0 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java
@@ -23,6 +23,6 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.classloader;
+package org.broadinstitute.gatk.utils.classloader;
 
 public interface ProtectedPackageSource {}
\ No newline at end of file
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java
index bcb4c1564..5321466d4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java
@@ -23,6 +23,6 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.classloader;
+package org.broadinstitute.gatk.utils.classloader;
 
 public interface PublicPackageSource {}
\ No newline at end of file
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java
index 09b387645..d08c5d2ce 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.clipping;
+package org.broadinstitute.gatk.utils.clipping;
 
 import com.google.java.contract.Requires;
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
-import org.broadinstitute.sting.utils.recalibration.EventType;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.recalibration.EventType;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.util.Iterator;
 import java.util.List;
@@ -71,7 +71,7 @@ public class ClippingOp {
         try {
             read = (GATKSAMRecord) originalRead.clone();
         } catch (CloneNotSupportedException e) {
-            throw new ReviewedStingException("Where did the clone go?");
+            throw new ReviewedGATKException("Where did the clone go?");
         }
         byte[] quals = read.getBaseQualities();
         byte[] bases = read.getReadBases();
@@ -175,7 +175,7 @@ public class ClippingOp {
         try {
             unclipped = (GATKSAMRecord) read.clone();
         } catch (CloneNotSupportedException e) {
-            throw new ReviewedStingException("Where did the clone go?");
+            throw new ReviewedGATKException("Where did the clone go?");
         }
 
         Cigar unclippedCigar = new Cigar();
@@ -380,7 +380,7 @@ public class ClippingOp {
         try {
             hardClippedRead = (GATKSAMRecord) read.clone();
         } catch (CloneNotSupportedException e) {
-            throw new ReviewedStingException("Where did the clone go?");
+            throw new ReviewedGATKException("Where did the clone go?");
         }
 
         hardClippedRead.resetSoftStartAndEnd();                                                                         // reset the cached soft start and end because they may have changed now that the read was hard clipped. No need to calculate them now. They'll be lazily calculated on the next call to getSoftStart()/End()
@@ -420,7 +420,7 @@ public class ClippingOp {
                 if (cigarElementIterator.hasNext())
                     cigarElement = cigarElementIterator.next();
                 else
-                    throw new ReviewedStingException("Read is entirely hardclipped, shouldn't be trying to clip it's cigar string");
+                    throw new ReviewedGATKException("Read is entirely hardclipped, shouldn't be trying to clip it's cigar string");
             }
             // keep clipping until we hit stop
             while (index <= stop) {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java
index 67316a54a..5d86e0bf7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.clipping;
+package org.broadinstitute.gatk.utils.clipping;
 
 /**
  * How should we represent a clipped bases in a read?
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java
index d5be8dc11..c31784fa4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.clipping;
+package org.broadinstitute.gatk.utils.clipping;
 
 import com.google.java.contract.Requires;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.recalibration.EventType;
-import org.broadinstitute.sting.utils.sam.CigarUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.recalibration.EventType;
+import org.broadinstitute.gatk.utils.sam.CigarUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.ReadUtils;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -538,25 +538,25 @@ public class ReadClipper {
         // Determine the read coordinate to start and stop hard clipping
         if (refStart < 0) {
             if (refStop < 0)
-                throw new ReviewedStingException("Only one of refStart or refStop must be < 0, not both (" + refStart + ", " + refStop + ")");
+                throw new ReviewedGATKException("Only one of refStart or refStop must be < 0, not both (" + refStart + ", " + refStop + ")");
             start = 0;
             stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop, ReadUtils.ClippingTail.LEFT_TAIL);
         }
         else {
             if (refStop >= 0)
-                throw new ReviewedStingException("Either refStart or refStop must be < 0 (" + refStart + ", " + refStop + ")");
+                throw new ReviewedGATKException("Either refStart or refStop must be < 0 (" + refStart + ", " + refStop + ")");
             start = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart, ReadUtils.ClippingTail.RIGHT_TAIL);
             stop = read.getReadLength() - 1;
         }
 
         if (start < 0 || stop > read.getReadLength() - 1)
-            throw new ReviewedStingException("Trying to clip before the start or after the end of a read");
+            throw new ReviewedGATKException("Trying to clip before the start or after the end of a read");
 
         if ( start > stop )
-            throw new ReviewedStingException(String.format("START (%d) > (%d) STOP -- this should never happen, please check read: %s (CIGAR: %s)", start, stop, read, read.getCigarString()));
+            throw new ReviewedGATKException(String.format("START (%d) > (%d) STOP -- this should never happen, please check read: %s (CIGAR: %s)", start, stop, read, read.getCigarString()));
 
         if ( start > 0 && stop < read.getReadLength() - 1)
-            throw new ReviewedStingException(String.format("Trying to clip the middle of the read: start %d, stop %d, cigar: %s", start, stop, read.getCigarString()));
+            throw new ReviewedGATKException(String.format("Trying to clip the middle of the read: start %d, stop %d, cigar: %s", start, stop, read.getCigarString()));
 
         this.addOp(new ClippingOp(start, stop));
         GATKSAMRecord clippedRead = clipRead(ClippingRepresentation.HARDCLIP_BASES);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java
index 66a49e862..915900388 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.beagle;
+package org.broadinstitute.gatk.utils.codecs.beagle;
 /*
  * Copyright (c) 2010 The Broad Institute
  *
@@ -53,9 +53,9 @@ package org.broadinstitute.sting.utils.codecs.beagle;
 import htsjdk.tribble.AsciiFeatureCodec;
 import htsjdk.tribble.exception.CodecLineParsingException;
 import htsjdk.tribble.readers.LineIterator;
-import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
 
 import java.io.IOException;
 import java.util.*;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java
index f4db16b31..bd9e4ef4c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.beagle;
+package org.broadinstitute.gatk.utils.codecs.beagle;
 
 import htsjdk.tribble.Feature;
 import htsjdk.variant.variantcontext.Allele;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java
index 050a24d3d..ac50853e0 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.hapmap;
+package org.broadinstitute.gatk.utils.codecs.hapmap;
 
 import htsjdk.tribble.AsciiFeatureCodec;
 import htsjdk.tribble.FeatureCodecHeader;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java
index 36edef068..a9b878847 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.hapmap;
+package org.broadinstitute.gatk.utils.codecs.hapmap;
 
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.annotation.Strand;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java
index 86f6863e6..9d60076ca 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.refseq;
+package org.broadinstitute.gatk.utils.codecs.refseq;
 
 import htsjdk.tribble.AsciiFeatureCodec;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.TribbleException;
 import htsjdk.tribble.readers.LineIterator;
-import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.util.ArrayList;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java
index 0fbe03211..226a35307 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.refseq;
+package org.broadinstitute.gatk.utils.codecs.refseq;
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature;
+import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.*;
 
@@ -73,7 +73,7 @@ public class RefSeqFeature implements Transcript, Feature {
 
     /** Genomic location of the n-th exon; throws an exception if n is out of bounds */
     public GenomeLoc getExonLocation(int n) {
-        if ( n >= exons.size() || n < 0 ) throw new ReviewedStingException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n);
+        if ( n >= exons.size() || n < 0 ) throw new ReviewedGATKException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n);
         return exons.get(n);
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java
index 5a029653b..1671c79fc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.refseq;
+package org.broadinstitute.gatk.utils.codecs.refseq;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.HasGenomeLocation;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.HasGenomeLocation;
 
 import java.util.List;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java
index bef638e47..8c4385448 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.sampileup;
+package org.broadinstitute.gatk.utils.codecs.sampileup;
 
 import htsjdk.tribble.AsciiFeatureCodec;
 import htsjdk.tribble.exception.CodecLineParsingException;
@@ -34,7 +34,7 @@ import java.util.ArrayList;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.VariantType;
+import static org.broadinstitute.gatk.utils.codecs.sampileup.SAMPileupFeature.VariantType;
 
 /**
  * Decoder for SAM pileup data.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java
index ad39851e8..89f168b67 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.sampileup;
+package org.broadinstitute.gatk.utils.codecs.sampileup;
 
 import htsjdk.samtools.util.StringUtil;
 import htsjdk.tribble.Feature;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java
index fd2db5b83..d83ce6d8d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.samread;
+package org.broadinstitute.gatk.utils.codecs.samread;
 
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.TextCigarCodec;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java
index 13e004625..129ae6e66 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.samread;
+package org.broadinstitute.gatk.utils.codecs.samread;
 
 import htsjdk.tribble.Feature;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java
index 56c6bdd96..9a0115f66 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.table;
+package org.broadinstitute.gatk.utils.codecs.table;
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
+import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec;
 
 import java.util.Arrays;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java
index 6f713ef8c..1058d3e90 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.table;
+package org.broadinstitute.gatk.utils.codecs.table;
 
 import htsjdk.tribble.AsciiFeatureCodec;
 import htsjdk.tribble.readers.LineIterator;
-import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java
index 8a564ec9e..58b06c954 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.table;
+package org.broadinstitute.gatk.utils.codecs.table;
 
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.Utils;
 
 import java.util.List;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java
index b3a9760a4..2c543dd4a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.collections;
+package org.broadinstitute.gatk.utils.collections;
 
 import java.util.HashMap;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java
index 24a42716f..b2b23d36d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.collections;
+package org.broadinstitute.gatk.utils.collections;
 
 import java.util.ArrayList;
 import java.util.Collection;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java
index 192d5bc7e..3117852f5 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.collections;
+package org.broadinstitute.gatk.utils.collections;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.PrintStream;
 
@@ -61,7 +61,7 @@ public class LoggingNestedIntegerArray extends NestedIntegerArray {
         super(dimensions);
 
         if ( log == null ) {
-            throw new ReviewedStingException("Log output stream must not be null");
+            throw new ReviewedGATKException("Log output stream must not be null");
         }
         this.log = log;
         this.logEntryLabel = logEntryLabel != null ? logEntryLabel : "";
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java
index f7fe71f13..02dd15a17 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.collections;
+package org.broadinstitute.gatk.utils.collections;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -53,7 +53,7 @@ public class NestedIntegerArray {
     public NestedIntegerArray(final int... dimensions) {
         numDimensions = dimensions.length;
         if ( numDimensions == 0 )
-            throw new ReviewedStingException("There must be at least one dimension to an NestedIntegerArray");
+            throw new ReviewedGATKException("There must be at least one dimension to an NestedIntegerArray");
         this.dimensions = dimensions.clone();
 
         int dimensionsToPreallocate = Math.min(dimensions.length, NUM_DIMENSIONS_TO_PREALLOCATE);
@@ -126,13 +126,13 @@ public class NestedIntegerArray {
      */
     public boolean put(final T value, final int... keys) { // WARNING! value comes before the keys!
         if ( keys.length != numDimensions )
-            throw new ReviewedStingException("Exactly " + numDimensions + " keys should be passed to this NestedIntegerArray but " + keys.length + " were provided");
+            throw new ReviewedGATKException("Exactly " + numDimensions + " keys should be passed to this NestedIntegerArray but " + keys.length + " were provided");
 
         final int numNestedDimensions = numDimensions - 1;
         Object[] myData = data;
         for ( int i = 0; i < numNestedDimensions; i++ ) {
             if ( keys[i] >= dimensions[i] )
-                throw new ReviewedStingException("Key " + keys[i] + " is too large for dimension " + i + " (max is " + (dimensions[i]-1) + ")");
+                throw new ReviewedGATKException("Key " + keys[i] + " is too large for dimension " + i + " (max is " + (dimensions[i]-1) + ")");
 
             // If we're at or beyond the last dimension that was pre-allocated, we need to do a synchronized
             // check to see if the next branch exists, and if it doesn't, create it
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java
index 4c00331a9..b09c9dfc9 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.collections;
+package org.broadinstitute.gatk.utils.collections;
 
 
 public class Pair {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java
index dad6f3b4c..2b759ced7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.collections;
+package org.broadinstitute.gatk.utils.collections;
 
 
 /** This class is used to group together multiple Pair classes for
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java
index cc77098c4..7af62bd9e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.collections;
+package org.broadinstitute.gatk.utils.collections;
 
-import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
-import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator;
+import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.Collection;
 import java.util.Iterator;
@@ -45,10 +45,10 @@ public class RODMergingIterator implements Iterator, Iterable it) {
             if ( it instanceof LocationAwareSeekableRODIterator) {
                 this.it = (LocationAwareSeekableRODIterator)it;
-                if ( ! it.hasNext() ) throw new ReviewedStingException("Iterator is empty");
+                if ( ! it.hasNext() ) throw new ReviewedGATKException("Iterator is empty");
                 update();
             } else {
-                throw new ReviewedStingException("Iterator passed to RODMergingIterator is not LocationAwareSeekableRODIterator");
+                throw new ReviewedGATKException("Iterator passed to RODMergingIterator is not LocationAwareSeekableRODIterator");
             }
         }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java
index 191198dca..3995ff71c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.lang.annotation.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java
index 96731584b..66c562934 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.lang.annotation.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java
index f9994734e..c142f06e3 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.lang.annotation.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java
index 795b9521b..f2e7e6ef0 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.lang.annotation.Annotation;
 import java.util.List;
@@ -292,6 +292,6 @@ public class ArgumentDefinition {
      */
     private void validateName(final String name) {
         if ( name != null && name.startsWith("-") )
-            throw new ReviewedStingException("Invalid argument definition: " + name + " begins with a -");
+            throw new ReviewedGATKException("Invalid argument definition: " + name + " begins with a -");
     }
 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java
index 0679ade26..b6bb16ca3 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.ArrayList;
 import java.util.Collections;
@@ -67,7 +67,7 @@ public class ArgumentDefinitionGroup implements Iterable {
      */
     public ArgumentDefinitionGroup merge( ArgumentDefinitionGroup other ) {
         if( !groupNameMatches(other) )
-            throw new ReviewedStingException("Unable to merge two argument groups with differing names.");
+            throw new ReviewedGATKException("Unable to merge two argument groups with differing names.");
 
         // Create a merged definition group.
         List mergedDefinitions = new ArrayList();
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java
index 964a1786d..45c104b0a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.Collection;
 import java.util.HashSet;
@@ -56,9 +56,9 @@ public class ArgumentDefinitions implements Iterable {
             if( definition.fullName.length() == 0 )
                 throw new IllegalArgumentException( "Argument cannot have 0-length fullname." );
             if( hasArgumentDefinition( definition.fullName, FullNameDefinitionMatcher ) )
-                throw new ReviewedStingException("Duplicate definition of argument with full name: " + definition.fullName);
+                throw new ReviewedGATKException("Duplicate definition of argument with full name: " + definition.fullName);
             if( definition.shortName != null && hasArgumentDefinition( definition.shortName, ShortNameDefinitionMatcher ) )
-                throw new ReviewedStingException("Duplicate definition of argument with short name: " + definition.shortName);
+                throw new ReviewedGATKException("Duplicate definition of argument with short name: " + definition.shortName);
 
             argumentDefinitions.add( definition );
         }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java
index 5c5105afe..a55da890a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 /**
  * Generic class for handling misc parsing exceptions.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java
index 5921fb4be..27b816324 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.lang.annotation.Annotation;
 
@@ -47,6 +47,6 @@ public enum ArgumentIOType {
         for (ArgumentIOType ioType: ArgumentIOType.values())
             if (ioType.annotationClass.isAssignableFrom(annotation.getClass()))
                 return ioType;
-        throw new ReviewedStingException("Unknown annotation type: " + annotation);
+        throw new ReviewedGATKException("Unknown annotation type: " + annotation);
     }
 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java
index e354601da..9064930c0 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.gatk.walkers.Multiplexer;
+import org.broadinstitute.gatk.engine.walkers.Multiplexer;
 
 import java.util.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java
index ef8201e98..3b9c8d3d8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.io.File;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java
index b0e06cdc7..967d4c60a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 /**
  * Which source and the index within the source where an argument match was found.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java
index 575d4bd83..a7ce7bad7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 /**
  * Where an argument match originated, via the commandline or a custom provider.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java
index 2400951a1..9dee5be28 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 /**
  * Type of where an argument match originated, via the commandline or a some other provider.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java
index cf273d554..9f772bc89 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.io.File;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java
index e34af1732..f37d5382b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.io.File;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java
index 983222956..2d81cfcaa 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.gatk.walkers.Multiplexer;
+import org.broadinstitute.gatk.engine.walkers.Multiplexer;
 
 import java.util.*;
 /**
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java
index 12bf548d5..79e07a6bd 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.lang.reflect.Field;
 import java.util.Arrays;
@@ -229,7 +229,7 @@ public class ArgumentSource {
      */
     public MultiplexArgumentTypeDescriptor createDependentTypeDescriptor(ParsingEngine parsingEngine,Object containingObject) {
         if(!isDependent())
-            throw new ReviewedStingException("Field " + field.getName() + " is independent; no dependent type descriptor can be derived.");
+            throw new ReviewedGATKException("Field " + field.getName() + " is independent; no dependent type descriptor can be derived.");
         return ((MultiplexArgumentTypeDescriptor)typeDescriptor).createCustomTypeDescriptor(parsingEngine,this,containingObject);
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java
index fb39575e6..b900ad085 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java
@@ -23,18 +23,18 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import org.apache.log4j.Logger;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
-import org.broadinstitute.sting.gatk.walkers.Multiplex;
-import org.broadinstitute.sting.gatk.walkers.Multiplexer;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager;
+import org.broadinstitute.gatk.engine.walkers.Multiplex;
+import org.broadinstitute.gatk.engine.walkers.Multiplexer;
+import org.broadinstitute.gatk.utils.classloader.JVMUtils;
+import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.text.XReadLines;
 
 import java.io.File;
 import java.io.IOException;
@@ -53,7 +53,7 @@ public abstract class ArgumentTypeDescriptor {
     private static Class[] ARGUMENT_ANNOTATIONS = {Input.class, Output.class, Argument.class};
 
     /**
-     * our log, which we want to capture anything from org.broadinstitute.sting
+     * our log, which we want to capture anything from org.broadinstitute.gatk
      */
     protected static final Logger logger = Logger.getLogger(ArgumentTypeDescriptor.class);
 
@@ -68,7 +68,7 @@ public abstract class ArgumentTypeDescriptor {
             if( descriptor.supports(type) )
                 return descriptor;
         }
-        throw new ReviewedStingException("Can't process command-line arguments of type: " + type.getName());
+        throw new ReviewedGATKException("Can't process command-line arguments of type: " + type.getName());
     }
 
     /**
@@ -234,7 +234,7 @@ public abstract class ArgumentTypeDescriptor {
         Tags tags = new Tags();
         for(ArgumentMatch match: matches) {
             if(!tags.isEmpty() && !match.tags.isEmpty())
-                throw new ReviewedStingException("BUG: multiple conflicting sets of tags are available, and the type descriptor specifies no way of resolving the conflict.");
+                throw new ReviewedGATKException("BUG: multiple conflicting sets of tags are available, and the type descriptor specifies no way of resolving the conflict.");
             tags = match.tags;
         }
         return tags;
@@ -266,7 +266,7 @@ public abstract class ArgumentTypeDescriptor {
         for (Class annotation: ARGUMENT_ANNOTATIONS)
             if (source.field.isAnnotationPresent(annotation))
                 return source.field.getAnnotation(annotation);
-        throw new ReviewedStingException("ArgumentAnnotation is not present for the argument field: " + source.field.getName());
+        throw new ReviewedGATKException("ArgumentAnnotation is not present for the argument field: " + source.field.getName());
     }
 
     /**
@@ -722,7 +722,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 for (Object val : vals) {
                     if (String.valueOf(val).equalsIgnoreCase(value == null ? null : value.asString())) return val;
                     try { if (type.getField(val.toString()).isAnnotationPresent(EnumerationArgumentDefault.class)) defaultEnumeration = val; }
-                    catch (NoSuchFieldException e) { throw new ReviewedStingException("parsing " + type.toString() + "doesn't contain the field " + val.toString()); }
+                    catch (NoSuchFieldException e) { throw new ReviewedGATKException("parsing " + type.toString() + "doesn't contain the field " + val.toString()); }
                 }
                 // if their argument has no value (null), and there's a default, return that default for the enum value
                 if (defaultEnumeration != null && value == null)
@@ -811,11 +811,11 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             }
             catch (InstantiationException e) {
                 logger.fatal("ArgumentParser: InstantiationException: cannot convert field " + source.field.getName());
-                throw new ReviewedStingException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
+                throw new ReviewedGATKException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
             }
             catch (IllegalAccessException e) {
                 logger.fatal("ArgumentParser: IllegalAccessException: cannot convert field " + source.field.getName());
-                throw new ReviewedStingException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage());
+                throw new ReviewedGATKException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage());
             }
 
             for( ArgumentMatch match: matches ) {
@@ -851,7 +851,7 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             }
         }
         else
-            throw new ReviewedStingException("Unsupported compound argument type: " + type);
+            throw new ReviewedGATKException("Unsupported compound argument type: " + type);
 
         return result;
     }
@@ -916,7 +916,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     @Override
     public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) {
         if(multiplexer == null || multiplexedIds == null)
-            throw new ReviewedStingException("No multiplexed ids available");
+            throw new ReviewedGATKException("No multiplexed ids available");
 
         Map multiplexedMapping = new HashMap();
         Class componentType = makeRawTypeIfNecessary(getCollectionComponentType(source.field));
@@ -939,7 +939,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     @Override
     public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches) {
         if(multiplexedIds == null)
-            throw new ReviewedStingException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first.");
+            throw new ReviewedGATKException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first.");
 
         Map multiplexedMapping = new HashMap();
 
@@ -970,14 +970,14 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 if(!source.field.getName().equals(sourceField))
                     continue;
                 if(source.field.isAnnotationPresent(Multiplex.class))
-                    throw new ReviewedStingException("Command-line arguments can only depend on independent fields");
+                    throw new ReviewedGATKException("Command-line arguments can only depend on independent fields");
                 sourceTypes[currentField] = source.field.getType();
                 sourceValues[currentField] = JVMUtils.getFieldValue(source.field,containingObject);
                 currentField++;
                 fieldFound = true;
             }
             if(!fieldFound)
-                throw new ReviewedStingException(String.format("Unable to find source field %s, referred to by dependent field %s",sourceField,dependentArgument.field.getName()));
+                throw new ReviewedGATKException(String.format("Unable to find source field %s, referred to by dependent field %s",sourceField,dependentArgument.field.getName()));
         }
 
         Class multiplexerType = dependentArgument.field.getAnnotation(Multiplex.class).value();
@@ -987,7 +987,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             multiplexerConstructor.setAccessible(true);
         }
         catch(NoSuchMethodException ex) {
-            throw new ReviewedStingException(String.format("Unable to find constructor for class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new ReviewedGATKException(String.format("Unable to find constructor for class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
 
         Multiplexer multiplexer;
@@ -995,13 +995,13 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             multiplexer = multiplexerConstructor.newInstance(sourceValues);
         }
         catch(IllegalAccessException ex) {
-            throw new ReviewedStingException(String.format("Constructor for class %s with parameters %s is inaccessible",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new ReviewedGATKException(String.format("Constructor for class %s with parameters %s is inaccessible",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
         catch(InstantiationException ex) {
-            throw new ReviewedStingException(String.format("Can't create class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new ReviewedGATKException(String.format("Can't create class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
         catch(InvocationTargetException ex) {
-            throw new ReviewedStingException(String.format("Can't invoke constructor of class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new ReviewedGATKException(String.format("Can't invoke constructor of class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
 
         return new MultiplexArgumentTypeDescriptor(multiplexer,multiplexer.multiplex());
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java
index 0d5bf9d6e..d57d32668 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.lang.annotation.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java
index 8b1a390f4..80ebe2c23 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import org.apache.log4j.FileAppender;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.PatternLayout;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.help.ApplicationDetails;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.help.HelpFormatter;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.help.ApplicationDetails;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.help.HelpFormatter;
 
 import java.io.IOException;
 import java.util.*;
@@ -75,7 +75,7 @@ public abstract class CommandLineProgram {
 
     static {
         /**
-         * The very first thing that any Sting application does is forces the JVM locale into US English, so that we don't have
+         * The very first thing that any GATK application does is forces the JVM locale into US English, so that we don't have
          * to think about number formatting issues.
          */
         forceJVMLocaleToUSEnglish();
@@ -386,7 +386,7 @@ public abstract class CommandLineProgram {
 
     public static void exitSystemWithUserError(final Exception e) {
         if ( e.getMessage() == null )
-            throw new ReviewedStingException("UserException found with no message!", e);
+            throw new ReviewedGATKException("UserException found with no message!", e);
 
         errorPrintf("------------------------------------------------------------------------------------------%n");
         errorPrintf("A USER ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber());
@@ -408,7 +408,7 @@ public abstract class CommandLineProgram {
 
     public static void exitSystemWithSamError(final Throwable t) {
         if ( t.getMessage() == null )
-            throw new ReviewedStingException("SamException found with no message!", t);
+            throw new ReviewedGATKException("SamException found with no message!", t);
 
         errorPrintf("------------------------------------------------------------------------------------------%n");
         errorPrintf("A BAM ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber());
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java
index cb9a781c3..70f5532a4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import org.apache.log4j.Appender;
 import org.apache.log4j.ConsoleAppender;
 import org.apache.log4j.Logger;
 import org.apache.log4j.PatternLayout;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.lang.annotation.Annotation;
 import java.util.Collections;
@@ -136,7 +136,7 @@ public class CommandLineUtils {
         try {
             return annotation.getClass().getMethod(method).invoke(annotation);
         } catch (Exception e) {
-            throw new ReviewedStingException("Unable to access method " + method + " on annotation " + annotation.getClass(), e);
+            throw new ReviewedGATKException("Unable to access method " + method + " on annotation " + annotation.getClass(), e);
         }
     }
 
@@ -151,11 +151,11 @@ public class CommandLineUtils {
     }
 
     /**
-     * Returns the root logger for all Sting code.
-     * @return the root logger for all Sting code.
+     * Returns the root logger for all GATK code.
+     * @return the root logger for all GATK  code.
      */
     public static Logger getStingLogger() {
-        return Logger.getLogger("org.broadinstitute.sting");
+        return Logger.getLogger("org.broadinstitute.gatk");
     }
 
     /**
@@ -171,7 +171,7 @@ public class CommandLineUtils {
                     return;
             }
         }
-        // Extracted from BasicConfigurator.configure(), but only applied to the Sting logger.
+        // Extracted from BasicConfigurator.configure(), but only applied to the GATK logger.
         Logger.getRootLogger().addAppender(new ConsoleAppender(
                     new PatternLayout(PatternLayout.TTCC_CONVERSION_PATTERN), ConsoleAppender.SYSTEM_ERR));
     }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java
index 44b97b63f..3bbdedb01 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.lang.annotation.ElementType;
 import java.lang.annotation.Retention;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java
index 7adb4fc1e..b29166352 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.lang.annotation.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java
index a325d8a23..761611f97 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.io.File;
 import java.util.List;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java
index c9be94821..02325a767 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.lang.annotation.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java
index 2ab896b60..8ec048389 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.lang.annotation.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java
index 34d96d979..e31dca30c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.interval.IntervalSetRule;
+import org.broadinstitute.gatk.utils.interval.IntervalMergingRule;
+import org.broadinstitute.gatk.utils.interval.IntervalSetRule;
 
 import java.util.List;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java
index 7bd80d5d2..59048a93b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java
@@ -23,20 +23,20 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import com.google.java.contract.Requires;
 import htsjdk.tribble.AbstractFeatureReader;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.FeatureCodec;
 import htsjdk.tribble.FeatureReader;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec;
+import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.interval.IntervalUtils;
 
 import java.util.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java
index e21c8c4f8..f8f3895ad 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.gatk.utils.Utils;
 
 /**
  * Specifies that a value was missing when attempting to populate an argument.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java
index 0db870f2e..88057a235 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.lang.annotation.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java
index 8da02c576..45cc055a8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 /**
  * Represents a collection of parsed arguments for an argument source.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java
index 0d06ab6b2..aa9e186d0 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import org.apache.commons.lang.StringUtils;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java
index ad64aaa1d..6cc9ae97c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java
@@ -23,19 +23,19 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import com.google.java.contract.Requires;
 import org.apache.commons.io.FileUtils;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.ApplicationDetails;
-import org.broadinstitute.sting.utils.help.HelpFormatter;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.classloader.JVMUtils;
+import org.broadinstitute.gatk.utils.classloader.PluginManager;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.help.ApplicationDetails;
+import org.broadinstitute.gatk.utils.help.HelpFormatter;
 
 import java.io.File;
 import java.io.IOException;
@@ -44,7 +44,7 @@ import java.lang.reflect.Field;
 import java.util.*;
 
 /**
- * A parser for Sting command-line arguments.
+ * A parser for command-line arguments.
  */
 public class ParsingEngine {
 
@@ -98,7 +98,7 @@ public class ParsingEngine {
             new PluginManager(ParsingEngineArgumentProvider.class);
 
     /**
-     * our log, which we want to capture anything from org.broadinstitute.sting
+     * our log, which we want to capture anything from org.broadinstitute.gatk
      */
     protected static Logger logger = Logger.getLogger(ParsingEngine.class);
 
@@ -453,7 +453,7 @@ public class ParsingEngine {
         // Grab the first argument definition and report that one as the failure.  Theoretically, we should notify of all failures.
         List definitions = argumentSource.createArgumentDefinitions();
         if(definitions.size() < 1)
-            throw new ReviewedStingException("Internal error.  Argument source creates no definitions.");
+            throw new ReviewedGATKException("Internal error.  Argument source creates no definitions.");
         ArgumentDefinition definition = definitions.get(0);
         throw new UserException.DeprecatedArgument(definition.fullName,definition.doc);
     }
@@ -479,7 +479,7 @@ public class ParsingEngine {
 
         // Abort if no home is found for the object.
         if( targets.size() == 0 )
-            throw new ReviewedStingException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);
+            throw new ReviewedGATKException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);
 
         for( Object target: targets ) {
             Object value;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java
index 786c72ed0..0361c4cc0 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.io.File;
 import java.util.ArrayList;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java
index 2e009ab2b..d53a36ca1 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.util.List;
 import java.util.SortedMap;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java
index 033700965..a93974231 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.gatk.utils.Utils;
 
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java
index 98a06313a..2c557872c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java
index a806788de..faf456538 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import com.google.java.contract.Ensures;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java
index cff2b60cd..2b1c7f7ce 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.util.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java
index 72c7e102c..f572d3485 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java
@@ -23,4 +23,4 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
\ No newline at end of file
+package org.broadinstitute.gatk.utils.commandline;
\ No newline at end of file
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/CryptUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/CryptUtils.java
index 6658c8163..d6ccd3231 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/CryptUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/CryptUtils.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.crypt;
+package org.broadinstitute.gatk.utils.crypt;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.io.IOUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.io.IOUtils;
 
 import javax.crypto.Cipher;
 import java.io.File;
@@ -128,10 +128,10 @@ public class CryptUtils {
             return keyGen.generateKeyPair();
         }
         catch ( NoSuchAlgorithmException e ) {
-            throw new ReviewedStingException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
+            throw new ReviewedGATKException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
         }
         catch ( Exception e ) {
-            throw new ReviewedStingException("Error while generating key pair", e);
+            throw new ReviewedGATKException("Error while generating key pair", e);
         }
     }
 
@@ -155,7 +155,7 @@ public class CryptUtils {
             return SecureRandom.getInstance(randAlgorithm);
         }
         catch ( NoSuchAlgorithmException e ) {
-            throw new ReviewedStingException(String.format("Could not find an implementation of the requested random-number generation algorithm %s", randAlgorithm), e);
+            throw new ReviewedGATKException(String.format("Could not find an implementation of the requested random-number generation algorithm %s", randAlgorithm), e);
         }
     }
 
@@ -216,10 +216,10 @@ public class CryptUtils {
             return keyFactory.generatePublic(keySpec);
         }
         catch ( NoSuchAlgorithmException e ) {
-            throw new ReviewedStingException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
+            throw new ReviewedGATKException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
         }
         catch ( InvalidKeySpecException e ) {
-            throw new ReviewedStingException("Unable to use X.509 key specification to decode the given key", e);
+            throw new ReviewedGATKException("Unable to use X.509 key specification to decode the given key", e);
         }
     }
 
@@ -258,10 +258,10 @@ public class CryptUtils {
             return keyFactory.generatePrivate(keySpec);
         }
         catch ( NoSuchAlgorithmException e ) {
-            throw new ReviewedStingException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
+            throw new ReviewedGATKException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
         }
         catch ( InvalidKeySpecException e ) {
-            throw new ReviewedStingException("Unable to use the PKCS #8 key specification to decode the given key", e);
+            throw new ReviewedGATKException("Unable to use the PKCS #8 key specification to decode the given key", e);
         }
     }
 
@@ -276,7 +276,7 @@ public class CryptUtils {
         InputStream publicKeyInputStream = ClassLoader.getSystemResourceAsStream(GATK_DISTRIBUTED_PUBLIC_KEY_FILE_NAME);
 
         if ( publicKeyInputStream == null ) {
-            throw new ReviewedStingException(String.format("Could not locate the GATK public key %s in the classpath",
+            throw new ReviewedGATKException(String.format("Could not locate the GATK public key %s in the classpath",
                                                            GATK_DISTRIBUTED_PUBLIC_KEY_FILE_NAME));
         }
 
@@ -341,14 +341,14 @@ public class CryptUtils {
             return cipher.doFinal(data);
         }
         catch ( NoSuchAlgorithmException e ) {
-            throw new ReviewedStingException(String.format("Could not find an implementation of the requested algorithm %s",
+            throw new ReviewedGATKException(String.format("Could not find an implementation of the requested algorithm %s",
                                              key.getAlgorithm()), e);
         }
         catch ( InvalidKeyException e ) {
-            throw new ReviewedStingException("Key is invalid", e);
+            throw new ReviewedGATKException("Key is invalid", e);
         }
         catch ( GeneralSecurityException e ) {
-            throw new ReviewedStingException("Error during encryption", e);
+            throw new ReviewedGATKException("Error during encryption", e);
         }
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/GATKKey.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/GATKKey.java
index 1a3244135..ab21a2a17 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/GATKKey.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/GATKKey.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.crypt;
+package org.broadinstitute.gatk.utils.crypt;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.io.IOUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.io.IOUtils;
 
 import java.io.*;
 import java.security.*;
@@ -131,7 +131,7 @@ public class GATKKey {
      */
     public GATKKey ( PrivateKey privateKey, PublicKey publicKey, String emailAddress, String signingAlgorithm ) {
         if ( privateKey == null || publicKey == null || emailAddress == null || emailAddress.length() == 0 || signingAlgorithm == null ) {
-            throw new ReviewedStingException("Cannot construct GATKKey using null/empty arguments");
+            throw new ReviewedGATKException("Cannot construct GATKKey using null/empty arguments");
         }
 
         this.privateKey = privateKey;
@@ -143,7 +143,7 @@ public class GATKKey {
         generateSignature();
 
         if ( ! isValid() ) {
-            throw new ReviewedStingException("Newly-generated GATK key fails validation -- this should never happen!");
+            throw new ReviewedGATKException("Newly-generated GATK key fails validation -- this should never happen!");
         }
     }
 
@@ -175,7 +175,7 @@ public class GATKKey {
      */
     public GATKKey ( PublicKey publicKey, File keyFile, String signingAlgorithm ) {
         if ( publicKey == null || keyFile == null || signingAlgorithm == null ) {
-            throw new ReviewedStingException("Cannot construct GATKKey using null arguments");
+            throw new ReviewedGATKException("Cannot construct GATKKey using null arguments");
         }
 
         this.publicKey = publicKey;
@@ -219,11 +219,11 @@ public class GATKKey {
             return sig.verify(signature);
         }
         catch ( NoSuchAlgorithmException e ) {
-            throw new ReviewedStingException(String.format("Signing algorithm %s not found", signingAlgorithm), e);
+            throw new ReviewedGATKException(String.format("Signing algorithm %s not found", signingAlgorithm), e);
         }
         catch ( InvalidKeyException e ) {
             // If the GATK public key is invalid, it's likely our problem, not the user's:
-            throw new ReviewedStingException(String.format("Public key %s is invalid", publicKey), e);
+            throw new ReviewedGATKException(String.format("Public key %s is invalid", publicKey), e);
         }
         catch ( SignatureException e ) {
             throw new UserException.UnreadableKeyException("Signature is invalid or signing algorithm was unable to process the input data", e);
@@ -246,13 +246,13 @@ public class GATKKey {
             signature = sig.sign();
         }
         catch ( NoSuchAlgorithmException e ) {
-            throw new ReviewedStingException(String.format("Signing algorithm %s not found", signingAlgorithm), e);
+            throw new ReviewedGATKException(String.format("Signing algorithm %s not found", signingAlgorithm), e);
         }
         catch ( InvalidKeyException e ) {
-            throw new ReviewedStingException(String.format("Private key %s is invalid", privateKey), e);
+            throw new ReviewedGATKException(String.format("Private key %s is invalid", privateKey), e);
         }
         catch ( SignatureException e ) {
-            throw new ReviewedStingException(String.format("Error creating signature for email address %s", emailAddress), e);
+            throw new ReviewedGATKException(String.format("Error creating signature for email address %s", emailAddress), e);
         }
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java
index afd51eb26..acd6319a2 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java
@@ -23,18 +23,18 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.duplicates;
+package org.broadinstitute.gatk.utils.duplicates;
 
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.QualityUtils;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.util.Arrays;
 import java.util.List;
@@ -44,7 +44,7 @@ public class DupUtils {
         try {
             return (GATKSAMRecord)read.clone();
         } catch ( CloneNotSupportedException e ) {
-            throw new ReviewedStingException("Unexpected Clone failure!");
+            throw new ReviewedGATKException("Unexpected Clone failure!");
         }
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java
index 1a110714a..9213a3e32 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.duplicates;
+package org.broadinstitute.gatk.utils.duplicates;
 
 public class DuplicateComp {
     public int getQLarger() {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java
index 0f1b473c3..1c5342068 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.exceptions;
+package org.broadinstitute.gatk.utils.exceptions;
 
 import java.lang.reflect.InvocationTargetException;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java
index 52f80077b..07db4fcf3 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java
@@ -23,30 +23,30 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.exceptions;
+package org.broadinstitute.gatk.utils.exceptions;
 
 import htsjdk.samtools.CigarOperator;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMSequenceDictionary;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.sam.ReadUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType;
 import htsjdk.variant.variantcontext.VariantContext;
 
 import java.io.File;
 
 /**
- * Represents the common user errors detected by Sting / GATK
+ * Represents the common user errors detected by GATK
  *
  * Root class for all GATK user errors, as well as the container for errors themselves
  */
 @DocumentedGATKFeature(
         groupName = HelpConstants.DOCS_CAT_USRERR,
         summary = "Errors caused by incorrect user behavior, such as bad files, bad arguments, etc." )
-public class UserException extends ReviewedStingException {
+public class UserException extends ReviewedGATKException {
     /**
      * The URL where people can get help messages.  Printed when an error occurs
      */
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java
index e02511f53..bf03ec625 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.fasta;
+package org.broadinstitute.gatk.utils.fasta;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
@@ -59,7 +59,7 @@ public class ArtificialFastaUtils {
         try {
             s = new PrintStream(new FileOutputStream(fileName));
         } catch (FileNotFoundException e) {
-            throw new ReviewedStingException("Filename " + fileName + " passed to the ArtificialFastaUtils generated a FileNotFound exception", e);
+            throw new ReviewedGATKException("Filename " + fileName + " passed to the ArtificialFastaUtils generated a FileNotFound exception", e);
         }
         generateFakeFasta(contigNames, contigSizes, pattern, s);
     }
@@ -83,7 +83,7 @@ public class ArtificialFastaUtils {
      */
     private static void generateFakeFasta(List contigNames, List contigSizes, BASE_PATTERN pattern, PrintStream s) {
         if (contigNames.size() != contigSizes.size()) {
-            throw new ReviewedStingException("ArtificialContig name and size arrays are not equal sizes");
+            throw new ReviewedGATKException("ArtificialContig name and size arrays are not equal sizes");
         }
         for (int x = 0; x < contigNames.size(); x++) {
             ArtificialContig tig = new ArtificialContig(contigNames.get(x), contigSizes.get(x), pattern);
@@ -147,7 +147,7 @@ class ArtificialContig {
             case ALL_G:
                 return "G";
             default:
-                throw new ReviewedStingException("Unknown base pattern");
+                throw new ReviewedGATKException("Unknown base pattern");
         }
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java
index ed4dc7437..05f2ccfd7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.fasta;
+package org.broadinstitute.gatk.utils.fasta;
 
 import picard.PicardException;
 import htsjdk.samtools.reference.FastaSequenceIndex;
@@ -32,8 +32,8 @@ import htsjdk.samtools.reference.ReferenceSequence;
 import htsjdk.samtools.SAMSequenceRecord;
 import htsjdk.samtools.util.StringUtil;
 import org.apache.log4j.Priority;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.BaseUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -297,7 +297,7 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
             try {
                 result = new ReferenceSequence(myCache.seq.getName(), myCache.seq.getContigIndex(), Arrays.copyOfRange(myCache.seq.getBases(), cacheOffsetStart, cacheOffsetStop));
             } catch ( ArrayIndexOutOfBoundsException e ) {
-                throw new ReviewedStingException(String.format("BUG: bad array indexing.  Cache start %d and end %d, request start %d end %d, offset start %d and end %d, base size %d",
+                throw new ReviewedGATKException(String.format("BUG: bad array indexing.  Cache start %d and end %d, request start %d end %d, offset start %d and end %d, base size %d",
                         myCache.start, myCache.stop, start, stop, cacheOffsetStart, cacheOffsetStop, myCache.seq.getBases().length), e);
             }
         }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java
index 1af538b27..ec94dac77 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java
@@ -23,4 +23,4 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.fasta;
\ No newline at end of file
+package org.broadinstitute.gatk.utils.fasta;
\ No newline at end of file
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java
index 87e89e0f1..934a022d8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.file;
+package org.broadinstitute.gatk.utils.file;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.IOException;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java
index d24e02e94..67d55ffff 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.fragments;
+package org.broadinstitute.gatk.utils.fragments;
 
 import java.util.Collection;
 import java.util.Collections;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java
index 364cc3d8f..689fdf6f8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.fragments;
+package org.broadinstitute.gatk.utils.fragments;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
@@ -32,14 +32,14 @@ import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.clipping.ReadClipper;
-import org.broadinstitute.sting.utils.recalibration.EventType;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.gatk.utils.clipping.ReadClipper;
+import org.broadinstitute.gatk.utils.recalibration.EventType;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.ReadUtils;
 
 import java.util.*;
 
@@ -196,7 +196,7 @@ public final class FragmentUtils {
     }
 
     public static void adjustQualsOfOverlappingPairedFragments( final List overlappingPair ) {
-        if( overlappingPair.size() != 2 ) { throw new ReviewedStingException("Found overlapping pair with " + overlappingPair.size() + " reads, but expecting exactly 2."); }
+        if( overlappingPair.size() != 2 ) { throw new ReviewedGATKException("Found overlapping pair with " + overlappingPair.size() + " reads, but expecting exactly 2."); }
 
         final GATKSAMRecord firstRead = overlappingPair.get(0);
         final GATKSAMRecord secondRead = overlappingPair.get(1);
@@ -260,7 +260,7 @@ public final class FragmentUtils {
     }
 
     public static List mergeOverlappingPairedFragments( final List overlappingPair ) {
-        if( overlappingPair.size() != 2 ) { throw new ReviewedStingException("Found overlapping pair with " + overlappingPair.size() + " reads, but expecting exactly 2."); }
+        if( overlappingPair.size() != 2 ) { throw new ReviewedGATKException("Found overlapping pair with " + overlappingPair.size() + " reads, but expecting exactly 2."); }
 
         final GATKSAMRecord firstRead = overlappingPair.get(0);
         final GATKSAMRecord secondRead = overlappingPair.get(1);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java
index ceae4bb47..f836f4456 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.genotyper;
+package org.broadinstitute.gatk.utils.genotyper;
 
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.BaseUtils;
 
 public enum DiploidGenotype {
     AA ('A', 'A'),
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java
index 40a70dfd8..65c1fd058 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.genotyper;
+package org.broadinstitute.gatk.utils.genotyper;
 
-import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.gatk.utils.MathUtils;
 import htsjdk.variant.variantcontext.Allele;
 
 /**
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java
index 859fd345b..49d8962b9 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.genotyper;
+package org.broadinstitute.gatk.utils.genotyper;
 
 
 import com.google.java.contract.Ensures;
-import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtils;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import htsjdk.variant.variantcontext.Allele;
 
 import java.util.*;
@@ -321,7 +321,7 @@ public class PerReadAlleleLikelihoodMap {
      *
      * Goes through each read in this map, and if it is poorly modelled removes it from the map.
      *
-     * @see #readIsPoorlyModelled(org.broadinstitute.sting.utils.sam.GATKSAMRecord, java.util.Collection, double)
+     * @see #readIsPoorlyModelled(org.broadinstitute.gatk.utils.sam.GATKSAMRecord, java.util.Collection, double)
      * for more information about the poorly modelled test.
      *
      * @param maxErrorRatePerBase see equivalent parameter in #readIsPoorlyModelled
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java
index da9df6594..60dcd4943 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.haplotype;
+package org.broadinstitute.gatk.utils.haplotype;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
@@ -31,10 +31,10 @@ import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
@@ -168,7 +168,7 @@ public class EventMap extends TreeMap {
                 case H:
                 case P:
                 default:
-                    throw new ReviewedStingException( "Unsupported cigar operator created during SW alignment: " + ce.getOperator() );
+                    throw new ReviewedGATKException( "Unsupported cigar operator created during SW alignment: " + ce.getOperator() );
             }
         }
     }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java
index 30603df29..7b31b2a7b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java
@@ -23,18 +23,18 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.haplotype;
+package org.broadinstitute.gatk.utils.haplotype;
 
 import com.google.java.contract.Requires;
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
 import org.apache.commons.lang.ArrayUtils;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
+import org.broadinstitute.gatk.utils.sam.ReadUtils;
 import htsjdk.variant.variantcontext.Allele;
 
 import java.util.Arrays;
@@ -254,7 +254,7 @@ public class Haplotype extends Allele {
         }
 
         if (refAllele == null)
-            throw new ReviewedStingException("BUG: no ref alleles in input to makeHaplotypeListfrom Alleles at loc: "+ startPos);
+            throw new ReviewedGATKException("BUG: no ref alleles in input to makeHaplotypeListfrom Alleles at loc: "+ startPos);
 
         final byte[] refBases = ref.getBases();
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java
index 191442e3e..8d1dfff73 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.haplotype;
+package org.broadinstitute.gatk.utils.haplotype;
 
 import java.util.Comparator;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java
index 40146ba88..7818d3e8a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.haplotype;
+package org.broadinstitute.gatk.utils.haplotype;
 
 import java.util.Comparator;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java
index 9981ce495..48180682b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.haplotype;
+package org.broadinstitute.gatk.utils.haplotype;
 
 import java.util.Comparator;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java
index a801f53d0..a0c7afbf1 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
-import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
+import org.broadinstitute.gatk.utils.classloader.JVMUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.IOException;
 import java.util.Collections;
@@ -82,7 +82,7 @@ public class ApplicationDetails {
             runningInstructions = JVMUtils.getLocationFor( application ).getName();
         }
         catch( IOException ex ) {
-            throw new ReviewedStingException("Unable to determine running instructions", ex);
+            throw new ReviewedGATKException("Unable to determine running instructions", ex);
         }
 
         if( runningInstructions.endsWith(".jar") )
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java
index 1e9a37cb7..324fcfc84 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 import com.sun.javadoc.FieldDoc;
 import com.sun.javadoc.PackageDoc;
 import com.sun.javadoc.ProgramElementDoc;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.gatk.utils.classloader.JVMUtils;
 
 import java.lang.reflect.Field;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java
index 0afcdae02..eed95b4a6 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 import java.lang.annotation.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java
index db67b2145..c2c6e5bc2 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 import com.sun.javadoc.ClassDoc;
 import com.sun.javadoc.RootDoc;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java
index ad0959bfe..45f0c147f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 /**
  * Documentation unit.  Effectively a class version of the DocumentedGATKFeature.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java
index 5302bd81a..fbf65287a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 import com.google.gson.Gson;
 import org.apache.commons.io.IOUtils;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java
index a2869c786..7b95b500d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 import java.util.HashMap;
 import java.util.Map;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java
index e8596aa78..2ca7656d2 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 public class GATKDocUtils {
     /**
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java
index 847e55c00..6b1f42443 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 import com.sun.javadoc.ClassDoc;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java
index 2bb49e53b..88469dbaf 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 import com.sun.javadoc.ClassDoc;
 import com.sun.javadoc.RootDoc;
@@ -35,11 +35,11 @@ import org.apache.commons.io.FileUtils;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.FeatureCodec;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.walkers.qc.DocumentationTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.tools.walkers.qc.DocumentationTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.text.XReadLines;
 
 import java.io.*;
 import java.util.*;
@@ -295,7 +295,7 @@ public class GATKDoclet {
             if (clazz != null && testOnly && !testOnlyKeepers.contains(clazz))
                 continue;
 
-            //if ( clazz != null && clazz.getName().equals("org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance"))
+            //if ( clazz != null && clazz.getName().equals("org.broadinstitute.gatk.tools.walkers.annotator.AlleleBalance"))
             //    logger.debug("foo");
 
             DocumentedGATKFeatureObject feature = getFeatureForClassDoc(doc);
@@ -399,7 +399,7 @@ public class GATKDoclet {
             temp.process(groupIndexData(indexData), out);
             out.flush();
         } catch (TemplateException e) {
-            throw new ReviewedStingException("Failed to create GATK documentation", e);
+            throw new ReviewedGATKException("Failed to create GATK documentation", e);
         }
     }
 
@@ -520,7 +520,7 @@ public class GATKDoclet {
             temp.process(unit.forTemplate, out);
             out.flush();
         } catch (TemplateException e) {
-            throw new ReviewedStingException("Failed to create GATK documentation", e);
+            throw new ReviewedGATKException("Failed to create GATK documentation", e);
         }
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java
index c5bcde444..a53e9119f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
@@ -33,17 +33,17 @@ import com.sun.javadoc.Tag;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.gatk.engine.walkers.*;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.classloader.JVMUtils;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
 
 import java.io.IOException;
 import java.lang.annotation.Annotation;
@@ -139,7 +139,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         for (final Class extraDocClass : toProcess.annotation.extraDocs()) {
             final GATKDocWorkUnit otherUnit = getDoclet().findWorkUnitForClass(extraDocClass);
             if (otherUnit == null)
-                throw new ReviewedStingException("Requested extraDocs for class without any documentation: " + extraDocClass);
+                throw new ReviewedGATKException("Requested extraDocs for class without any documentation: " + extraDocClass);
             extraDocsData.add(
                     new HashMap() {{
                         put("filename", otherUnit.filename);
@@ -250,7 +250,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
             if (argumentSource.createsTypeDefault()) {
                 try { // handle the case where there's an implicit default
                     return argumentSource.typeDefaultDocString();
-                } catch (ReviewedStingException e) {
+                } catch (ReviewedGATKException e) {
                     ; // failed to create type default, don't worry about it
                 }
             }
@@ -733,7 +733,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
             if (field.isAnnotationPresent(ArgumentCollection.class)) {
                 ClassDoc typeDoc = getRootDoc().classNamed(fieldDoc.type().qualifiedTypeName());
                 if (typeDoc == null)
-                    throw new ReviewedStingException("Tried to get javadocs for ArgumentCollection field " + fieldDoc + " but could't find the class in the RootDoc");
+                    throw new ReviewedGATKException("Tried to get javadocs for ArgumentCollection field " + fieldDoc + " but could't find the class in the RootDoc");
                 else {
                     FieldDoc result = getFieldDoc(typeDoc, name, false);
                     if (result != null)
@@ -804,7 +804,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         } else if (type instanceof Class) {
             return ((Class) type).getSimpleName();
         } else {
-            throw new StingException("Unknown type: " + type);
+            throw new GATKException("Unknown type: " + type);
         }
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java
index 783e7aa90..a5ee420c7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 public class HelpConstants {
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java
index f2e3fad4b..a8d469302 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java
@@ -23,23 +23,23 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.text.TextFormattingUtils;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.text.TextFormattingUtils;
 
 import java.net.InetAddress;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.*;
 /**
- * Print out help for Sting command-line applications.
+ * Print out help for GATK command-line applications.
  */
 
 public class HelpFormatter {
-    /** our log, which we want to capture anything from org.broadinstitute.sting */
+    /** our log, which we want to capture anything from org.broadinstitute.gatk */
     private static Logger logger = Logger.getLogger(HelpFormatter.class);
 
     public static final int FIELD_SEPARATION_WIDTH = 3;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpUtils.java
index 74516672d..0efca21f4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpUtils.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotationType;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.gatk.utils.classloader.PluginManager;
 
 import java.util.List;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java
index ac85d7aff..f28130b69 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.help;
+package org.broadinstitute.gatk.utils.help;
 
 import com.sun.javadoc.*;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.gatk.engine.walkers.Walker;
+import org.broadinstitute.gatk.utils.Utils;
 
 import java.io.*;
 import java.util.*;
@@ -115,7 +115,7 @@ public class ResourceBundleExtractorDoclet {
             renderHelpText(currentPackage.name(),currentPackage);
 
         try {
-            resourceText.store(out,"Strings displayed by the Sting help system");
+            resourceText.store(out,"Strings displayed by the GATK help system");
         } catch ( FileNotFoundException e ) {
             throw new RuntimeException(e);
         } catch ( IOException e ) {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java
index 10289ed97..a31c49857 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.instrumentation;
+package org.broadinstitute.gatk.utils.instrumentation;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.lang.instrument.Instrumentation;
 import java.lang.reflect.Array;
@@ -74,7 +74,7 @@ public class Sizeof {
      */
     public static long getObjectSize(Object o) {
         if(!isEnabled())
-            throw new ReviewedStingException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
+            throw new ReviewedGATKException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
         return instrumentation.getObjectSize(o);
     }
 
@@ -85,7 +85,7 @@ public class Sizeof {
      */
     public static long getObjectGraphSize(Object o) {
         if(!isEnabled())
-            throw new ReviewedStingException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
+            throw new ReviewedGATKException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
         IdentityHashMap objectsSeen = new IdentityHashMap();
         return getObjectGraphSize(o,objectsSeen);
     }
@@ -135,7 +135,7 @@ public class Sizeof {
                     fieldValue = field.get(o);
                 }
                 catch(IllegalAccessException ex) {
-                    throw new ReviewedStingException("Unable to access field " + field.getName(),ex);
+                    throw new ReviewedGATKException("Unable to access field " + field.getName(),ex);
                 }
                 totalSize += getObjectGraphSize(fieldValue,objectsSeen);
             }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java
index fbd3478b6..3e5eb4548 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.interval;
+package org.broadinstitute.gatk.utils.interval;
 
 
 /**
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java
index c2f69ed41..e9d20eed3 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.interval;
+package org.broadinstitute.gatk.utils.interval;
 
 /**
  * set operators for combining lists of intervals
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java
index 18e9ad3f0..53c8d55cc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.interval;
+package org.broadinstitute.gatk.utils.interval;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
@@ -32,17 +32,17 @@ import htsjdk.samtools.util.IntervalList;
 import htsjdk.samtools.SAMFileHeader;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.IntervalArgumentCollection;
-import org.broadinstitute.sting.commandline.IntervalBinding;
-import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.gatk.utils.commandline.IntervalArgumentCollection;
+import org.broadinstitute.gatk.utils.commandline.IntervalBinding;
+import org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.GenomeLocSortedSet;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.text.XReadLines;
 
 import java.io.File;
 import java.io.IOException;
@@ -50,7 +50,7 @@ import java.util.*;
 
 /**
  * Parse text representations of interval strings that
- * can appear in Sting-based applications.
+ * can appear in GATK-based applications.
  *
  * @author mhanna
  * @version 0.1
@@ -129,7 +129,7 @@ public class IntervalUtils {
         // case: BED file
         if ( file_name.toUpperCase().endsWith(".BED") ) {
             // this is now supported in Tribble
-            throw new ReviewedStingException("BED files must be parsed through Tribble; parsing them as intervals through the GATK engine is no longer supported");
+            throw new ReviewedGATKException("BED files must be parsed through Tribble; parsing them as intervals through the GATK engine is no longer supported");
         }
         else {
             /**
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java
index 269660db9..e099a45fb 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.io;
+package org.broadinstitute.gatk.utils.io;
 
 import java.io.File;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java
index aad655cba..1d041b66a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.io;
+package org.broadinstitute.gatk.utils.io;
 
 import org.apache.commons.io.output.ThresholdingOutputStream;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java
index 59466dad3..7defceac7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.io;
+package org.broadinstitute.gatk.utils.io;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.io.LineIterator;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.io.*;
 import java.nio.ByteBuffer;
@@ -282,7 +282,7 @@ public class IOUtils {
         if (file instanceof FileExtension)
             return ((FileExtension)file).withPath(path);
         if (!File.class.equals(file.getClass()))
-            throw new StingException("Sub classes of java.io.File must also implement FileExtension");
+            throw new GATKException("Sub classes of java.io.File must also implement FileExtension");
         return new File(path);
     }
 
@@ -365,7 +365,7 @@ public class IOUtils {
             outputStream = FileUtils.openOutputStream(file);
             org.apache.commons.io.IOUtils.copy(inputStream, outputStream);
         } catch (IOException e) {
-            throw new StingException(String.format("Unable to copy resource '%s' to '%s'", path, file), e);
+            throw new GATKException(String.format("Unable to copy resource '%s' to '%s'", path, file), e);
         } finally {
             org.apache.commons.io.IOUtils.closeQuietly(inputStream);
             org.apache.commons.io.IOUtils.closeQuietly(outputStream);
@@ -423,7 +423,7 @@ public class IOUtils {
      */
     public static byte[] readFileIntoByteArray ( File source, int readBufferSize ) {
         if ( source == null ) {
-            throw new ReviewedStingException("Source file was null");
+            throw new ReviewedGATKException("Source file was null");
         }
 
         byte[] fileContents;
@@ -462,10 +462,10 @@ public class IOUtils {
      */
     public static byte[] readStreamIntoByteArray ( InputStream in, int readBufferSize ) {
         if ( in == null ) {
-            throw new ReviewedStingException("Input stream was null");
+            throw new ReviewedGATKException("Input stream was null");
         }
         else if ( readBufferSize <= 0 ) {
-            throw new ReviewedStingException("Read buffer size must be > 0");
+            throw new ReviewedGATKException("Read buffer size must be > 0");
         }
 
         // Use a fixed-size buffer for each read, but a dynamically-growing buffer
@@ -500,7 +500,7 @@ public class IOUtils {
      */
     public static void writeByteArrayToFile ( byte[] bytes, File destination ) {
         if ( destination == null ) {
-            throw new ReviewedStingException("Destination file was null");
+            throw new ReviewedGATKException("Destination file was null");
         }
 
         try {
@@ -519,7 +519,7 @@ public class IOUtils {
      */
     public static void writeByteArrayToStream ( byte[] bytes, OutputStream out ) {
         if ( bytes == null || out == null ) {
-            throw new ReviewedStingException("Data to write or output stream was null");
+            throw new ReviewedGATKException("Data to write or output stream was null");
         }
 
         try {
@@ -544,7 +544,7 @@ public class IOUtils {
      */
     public static int getGZIPFileUncompressedSize ( File gzipFile ) {
         if ( gzipFile == null ) {
-            throw new ReviewedStingException("GZIP file to examine was null");
+            throw new ReviewedGATKException("GZIP file to examine was null");
         }
 
         try {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java
index 85ca5ce1c..abebe5299 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.io;
+package org.broadinstitute.gatk.utils.io;
 
 import java.io.File;
 import java.io.InputStream;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java
index d374a2ca6..0c14ffa1b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.clibrary;
+package org.broadinstitute.gatk.utils.jna.clibrary;
 
 import com.sun.jna.Platform;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java
index c7d24b89b..dd2d7e7b0 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.clibrary;
+package org.broadinstitute.gatk.utils.jna.clibrary;
 
 import com.sun.jna.LastErrorException;
 import com.sun.jna.Native;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java
index a41416065..1a99bfa40 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.drmaa.v1_0;
+package org.broadinstitute.gatk.utils.jna.drmaa.v1_0;
 
 import org.ggf.drmaa.DrmaaException;
 import org.ggf.drmaa.JobInfo;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java
index 2962bad0c..b8add996a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.drmaa.v1_0;
+package org.broadinstitute.gatk.utils.jna.drmaa.v1_0;
 
 import com.sun.jna.Pointer;
 import org.ggf.drmaa.*;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java
index 5488808ba..67eaad7c9 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.drmaa.v1_0;
+package org.broadinstitute.gatk.utils.jna.drmaa.v1_0;
 
 import com.sun.jna.Memory;
 import com.sun.jna.NativeLong;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java
index ab4bafaa2..f4dbc98d4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.drmaa.v1_0;
+package org.broadinstitute.gatk.utils.jna.drmaa.v1_0;
 
 import org.ggf.drmaa.Session;
 import org.ggf.drmaa.SessionFactory;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java
index 390ad4c01..3e5c4e45c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.drmaa.v1_0;
+package org.broadinstitute.gatk.utils.jna.drmaa.v1_0;
 
 import com.sun.jna.*;
 import com.sun.jna.ptr.IntByReference;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java
index f34bf925d..e66a40dab 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.lsf.v7_0_6;
+package org.broadinstitute.gatk.utils.jna.lsf.v7_0_6;
 
 import com.sun.jna.*;
 import com.sun.jna.ptr.*;
-import org.broadinstitute.sting.jna.clibrary.JNAUtils;
-import org.broadinstitute.sting.jna.clibrary.LibC;
+import org.broadinstitute.gatk.utils.jna.clibrary.JNAUtils;
+import org.broadinstitute.gatk.utils.jna.clibrary.LibC;
 
 /*
   NOTE: This library uses Pointer for some Struct.ByReference members going
@@ -84,7 +84,7 @@ public class LibBat {
         LSF 7.0.6 on the mac is missing the unsatisfied exported symbol for environ which was removed on MacOS X 10.5+.
         nm $LSF_LIBDIR/liblsf.dylib | grep environ
         See "man environ" for more info, along with http://lists.apple.com/archives/java-dev/2007/Dec/msg00096.html
-        For now, we export environ ourselves using libenvironhack.dylib available in Sting/c/libenvironhack.
+        For now, we export environ ourselves using libenvironhack.dylib available in c/libenvironhack.
         */
         if (Platform.isMac())
             NativeLibrary.getInstance("environhack");
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java
index bd63d1ba8..cc4721d79 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.lsf.v7_0_6;
+package org.broadinstitute.gatk.utils.jna.lsf.v7_0_6;
 
 import com.sun.jna.*;
 import com.sun.jna.ptr.FloatByReference;
 import com.sun.jna.ptr.IntByReference;
 import com.sun.jna.ptr.PointerByReference;
-import org.broadinstitute.sting.jna.clibrary.JNAUtils;
-import org.broadinstitute.sting.jna.clibrary.LibC.timeval;
+import org.broadinstitute.gatk.utils.jna.clibrary.JNAUtils;
+import org.broadinstitute.gatk.utils.jna.clibrary.LibC.timeval;
 
 /*
   NOTE: This library uses Pointer for some Struct.ByReference members going
@@ -76,7 +76,7 @@ public class LibLsf {
         LSF 7.0.6 on the mac is missing the unsatisfied exported symbol for environ which was removed on MacOS X 10.5+.
         nm $LSF_LIBDIR/liblsf.dylib | grep environ
         See "man environ" for more info, along with http://lists.apple.com/archives/java-dev/2007/Dec/msg00096.html
-        For now, we export environ ourselves using libenvironhack.dylib available in Sting/c/libenvironhack.
+        For now, we export environ ourselves using libenvironhack.dylib available in c/libenvironhack.
         */
         if (Platform.isMac())
             NativeLibrary.getInstance("environhack");
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java
index c40e5fc91..f94038698 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
@@ -31,11 +31,11 @@ import com.google.java.contract.Requires;
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 /**
  * Steps a single read along its alignment to the genome
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java
index d2a53f657..01bf17d6b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 /**
  * Simple wrapper about the information LIBS needs about downsampling
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java
index 0e018703d..d9b158f85 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.SAMFileHeader;
@@ -31,17 +31,17 @@ import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.SAMRecordIterator;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.gatk.ReadProperties;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.iterators.GATKSAMIterator;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
+import org.broadinstitute.gatk.utils.commandline.Input;
+import org.broadinstitute.gatk.engine.ReadProperties;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMRecordIterator;
+import org.broadinstitute.gatk.utils.*;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -82,7 +82,7 @@ public class LIBSPerformance extends CommandLineProgram {
             rawIterator = reader.query(loc.getContig(), loc.getStart(), loc.getStop(), false);
         }
 
-        final GATKSAMIterator iterator = new GATKSAMIterator(rawIterator);
+        final GATKSAMRecordIterator iterator = new GATKSAMRecordIterator(rawIterator);
 
         final Set samples = new HashSet();
         for ( final SAMReadGroupRecord rg : reader.getFileHeader().getReadGroups() )
@@ -156,8 +156,8 @@ public class LIBSPerformance extends CommandLineProgram {
 //                        case NEW_LIBS:
 //                        {
 //                            final List reads = Collections.nCopies(30, read);
-//                            final org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState libs =
-//                                    new org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState(
+//                            final org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState libs =
+//                                    new org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState(
 //                                            new LocusIteratorByStateBaseTest.FakeCloseableIterator(reads.iterator()),
 //                                            LocusIteratorByStateBaseTest.createTestReadProperties(),
 //                                            genomeLocParser,
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java
index 6a1451b18..72764e4df 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import htsjdk.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
 
 import java.util.Iterator;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java
index 942bb833b..aaf61900e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
@@ -32,17 +32,17 @@ import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.util.CloseableIterator;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.ReadProperties;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
-import org.broadinstitute.sting.gatk.iterators.GATKSAMIterator;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.gatk.engine.ReadProperties;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.downsampling.DownsampleType;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMRecordIterator;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.ReadUtils;
 
 import java.util.*;
 
@@ -156,7 +156,7 @@ public final class LocusIteratorByState extends LocusIterator {
      * @param it an iterator from reader that has the reads we want to use to create ReadBackPileups
      */
     public LocusIteratorByState(final SAMFileReader reader, final CloseableIterator it) {
-        this(new GATKSAMIterator(it),
+        this(new GATKSAMRecordIterator(it),
                 new LIBSDownsamplingInfo(false, 0),
                 true,
                 new GenomeLocParser(reader.getFileHeader().getSequenceDictionary()),
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java
index b3676189b..e6d49c354 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.CigarOperator;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.downsampling.Downsampler;
-import org.broadinstitute.sting.gatk.downsampling.LevelingDownsampler;
+import org.broadinstitute.gatk.engine.downsampling.Downsampler;
+import org.broadinstitute.gatk.engine.downsampling.LevelingDownsampler;
 
 import java.util.Iterator;
 import java.util.LinkedList;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java
index 40f8b53c8..0014753f6 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.util.PeekableIterator;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.util.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java
index e755835aa..825cb350a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.downsampling.Downsampler;
-import org.broadinstitute.sting.gatk.downsampling.PassThroughDownsampler;
-import org.broadinstitute.sting.gatk.downsampling.ReservoirDownsampler;
+import org.broadinstitute.gatk.engine.downsampling.Downsampler;
+import org.broadinstitute.gatk.engine.downsampling.PassThroughDownsampler;
+import org.broadinstitute.gatk.engine.downsampling.ReservoirDownsampler;
 
 import java.util.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java
index d188de0ac..c5255e42e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
 /**
  * Wrapper to hold data that distinguishing an special EOF marker from a real object
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java
index 0bcf7d426..3a67b4328 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
 import org.apache.log4j.Logger;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java
index d82ae27dd..d6628a5bc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
 /**
  * Holds the results of a map job suitable for producer/consumer threading
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java
index cb5c64ff9..afeafb5e2 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
-import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
+import org.broadinstitute.gatk.utils.collections.ExpandingArrayList;
 
 /**
  * Created with IntelliJ IDEA.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java
index 81e849eef..dbd58b44a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
 /**
  * A function that maps from InputType -> ResultType
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java
index ccf3b696c..27d713ead 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
 /**
  * Created with IntelliJ IDEA.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java
index a9ee45a2a..acb0a78bf 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
 /**
  * A function that combines a value of MapType with an existing ReduceValue into a new ResultType
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java
index 318097fb6..8b027214e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.MultiThreadedErrorTracker;
-import org.broadinstitute.sting.utils.threading.NamedThreadFactory;
+import org.broadinstitute.gatk.utils.MultiThreadedErrorTracker;
+import org.broadinstitute.gatk.utils.threading.NamedThreadFactory;
 
 import java.util.Iterator;
 import java.util.List;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java
index fdebc6440..41b612f0f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
 import com.google.java.contract.Ensures;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.MultiThreadedErrorTracker;
+import org.broadinstitute.gatk.utils.MultiThreadedErrorTracker;
 
 import java.util.concurrent.locks.Lock;
 import java.util.concurrent.locks.ReentrantLock;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java
index 6468753d2..231156489 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pairhmm;
+package org.broadinstitute.gatk.utils.pairhmm;
 
-import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.gatk.utils.haplotype.Haplotype;
 
 import java.util.List;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java
index 0ee08e560..4d84fc5e6 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pairhmm;
+package org.broadinstitute.gatk.utils.pairhmm;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.QualityUtils;
 
 import java.util.Arrays;
 
 import static java.lang.Math.log10;
-import static org.broadinstitute.sting.utils.pairhmm.PairHMMModel.*;
+import static org.broadinstitute.gatk.utils.pairhmm.PairHMMModel.*;
 
 /**
  * Util class for performing the pair HMM for local alignment. Figure 4.3 in Durbin 1998 book.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java
index 972c9fc9d..0e0ffb509 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pairhmm;
+package org.broadinstitute.gatk.utils.pairhmm;
 
 import com.google.java.contract.Requires;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java
index 55d928fc5..da29e0c42 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pairhmm;
+package org.broadinstitute.gatk.utils.pairhmm;
 
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.haplotype.Haplotype;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.haplotype.Haplotype;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import htsjdk.variant.variantcontext.Allele;
 
 import java.util.Arrays;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java
index 551be676a..1cd886581 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pairhmm;
+package org.broadinstitute.gatk.utils.pairhmm;
 
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.QualityUtils;
 
 /**
  * Helper class that implement calculations required to implement the PairHMM Finite State Automation (FSA) model.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java
index 125fee36c..29484048e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pairhmm;
+package org.broadinstitute.gatk.utils.pairhmm;
 
 import java.util.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java
index 233efd21e..d36d3551b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pileup;
+package org.broadinstitute.gatk.utils.pileup;
 
 import htsjdk.samtools.util.PeekableIterator;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java
index a8f3f7c45..4db0927bf 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pileup;
+package org.broadinstitute.gatk.utils.pileup;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.util.Arrays;
 import java.util.EnumSet;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java
index 9a2906696..7f8270984 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pileup;
+package org.broadinstitute.gatk.utils.pileup;
 
 /**
  * A filtering interface for pileup elements.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java
index 288b033cb..7d49fcce9 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pileup;
+package org.broadinstitute.gatk.utils.pileup;
 
 import org.apache.commons.collections.iterators.IteratorChain;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java
index 059c41d64..e4394f161 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pileup;
+package org.broadinstitute.gatk.utils.pileup;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.HasGenomeLocation;
-import org.broadinstitute.sting.utils.fragments.FragmentCollection;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.HasGenomeLocation;
+import org.broadinstitute.gatk.utils.fragments.FragmentCollection;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.util.Collection;
 import java.util.HashSet;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java
index 6ccf74e4e..840fbebd1 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pileup;
+package org.broadinstitute.gatk.utils.pileup;
 
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.fragments.FragmentCollection;
-import org.broadinstitute.sting.utils.fragments.FragmentUtils;
-import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.fragments.FragmentCollection;
+import org.broadinstitute.gatk.utils.fragments.FragmentUtils;
+import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseUtils;
 
 import java.util.*;
 
@@ -78,8 +78,8 @@ public class ReadBackedPileupImpl implements ReadBackedPileup {
      * pointer to pileup.  Don't go changing the data in pileup.
      */
     public ReadBackedPileupImpl(GenomeLoc loc, List pileup) {
-        if (loc == null) throw new ReviewedStingException("Illegal null genomeloc in ReadBackedPileup");
-        if (pileup == null) throw new ReviewedStingException("Illegal null pileup in ReadBackedPileup");
+        if (loc == null) throw new ReviewedGATKException("Illegal null genomeloc in ReadBackedPileup");
+        if (pileup == null) throw new ReviewedGATKException("Illegal null pileup in ReadBackedPileup");
 
         this.loc = loc;
         this.pileupElementTracker = new UnifiedPileupElementTracker(pileup);
@@ -123,10 +123,10 @@ public class ReadBackedPileupImpl implements ReadBackedPileup {
      * @return
      */
     private PileupElementTracker readsOffsets2Pileup(List reads, List offsets) {
-        if (reads == null) throw new ReviewedStingException("Illegal null read list in UnifiedReadBackedPileup");
-        if (offsets == null) throw new ReviewedStingException("Illegal null offsets list in UnifiedReadBackedPileup");
+        if (reads == null) throw new ReviewedGATKException("Illegal null read list in UnifiedReadBackedPileup");
+        if (offsets == null) throw new ReviewedGATKException("Illegal null offsets list in UnifiedReadBackedPileup");
         if (reads.size() != offsets.size())
-            throw new ReviewedStingException("Reads and offset lists have different sizes!");
+            throw new ReviewedGATKException("Reads and offset lists have different sizes!");
 
         UnifiedPileupElementTracker pileup = new UnifiedPileupElementTracker();
         for (int i = 0; i < reads.size(); i++) {
@@ -146,8 +146,8 @@ public class ReadBackedPileupImpl implements ReadBackedPileup {
      * @return
      */
     private PileupElementTracker readsOffsets2Pileup(List reads, int offset) {
-        if (reads == null) throw new ReviewedStingException("Illegal null read list in UnifiedReadBackedPileup");
-        if (offset < 0) throw new ReviewedStingException("Illegal offset < 0 UnifiedReadBackedPileup");
+        if (reads == null) throw new ReviewedGATKException("Illegal null read list in UnifiedReadBackedPileup");
+        if (offset < 0) throw new ReviewedGATKException("Illegal offset < 0 UnifiedReadBackedPileup");
 
         UnifiedPileupElementTracker pileup = new UnifiedPileupElementTracker();
         for (GATKSAMRecord read : reads) {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java
index 9d1011c8f..bee21286d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.progressmeter;
+package org.broadinstitute.gatk.utils.progressmeter;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.*;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java
index 38316e537..f1f48e6f4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.progressmeter;
+package org.broadinstitute.gatk.utils.progressmeter;
 
 /**
  * Daemon thread that periodically prints the progress of the progress meter
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java
index 5860c4f91..680403252 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.progressmeter;
+package org.broadinstitute.gatk.utils.progressmeter;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRArgumentSet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRArgumentSet.java
index 600700484..cc41bc5c6 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRArgumentSet.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRArgumentSet.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.recalibration;
+package org.broadinstitute.gatk.utils.recalibration;
 
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
+import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
 
 import java.io.File;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRMode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRMode.java
index 3bed717aa..a742ed452 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRMode.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRMode.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.recalibration;
+package org.broadinstitute.gatk.utils.recalibration;
 
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
 
 import java.lang.annotation.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java
index 0e5b59410..84ab785fd 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.recalibration;
+package org.broadinstitute.gatk.utils.recalibration;
 
 public enum EventType {
     BASE_SUBSTITUTION("M", "Base Substitution"),
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java
index 207da4d9f..0166e9847 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.output.NullOutputStream;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.io.HardThresholdingOutputStream;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.io.HardThresholdingOutputStream;
 
 import java.io.*;
 import java.util.EnumMap;
@@ -92,7 +92,7 @@ public class CapturedStreamOutput extends StreamOutput {
                     outputStream = standardStream;
                     break;
                 default:
-                    throw new ReviewedStingException("Unexpected stream location: " + location);
+                    throw new ReviewedGATKException("Unexpected stream location: " + location);
             }
             this.outputStreams.put(location, outputStream);
         }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java
index 041829501..56bfabde5 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
 import java.io.File;
 import java.util.Collections;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java
index 60af6814d..bc9229107 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
 import java.io.File;
 import java.util.Collections;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java
index da7de61fe..3955817ba 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
@@ -170,7 +170,7 @@ public class ProcessController {
             String message = String.format("Unable to start command: %s\nReason: %s",
                     StringUtils.join(builder.command(), " "),
                     e.getMessage());
-            throw new ReviewedStingException(message);
+            throw new ReviewedGATKException(message);
         }
 
         int exitCode;
@@ -208,7 +208,7 @@ public class ProcessController {
                                 inputStream = System.in;
                                 break;
                             default:
-                                throw new ReviewedStingException("Unexpected stream location: " + location);
+                                throw new ReviewedGATKException("Unexpected stream location: " + location);
                         }
                         try {
                             IOUtils.copy(inputStream, stdinStream);
@@ -219,7 +219,7 @@ public class ProcessController {
                     }
                     stdinStream.flush();
                 } catch (IOException e) {
-                    throw new ReviewedStingException("Error writing to stdin on command: " + StringUtils.join(builder.command(), " "), e);
+                    throw new ReviewedGATKException("Error writing to stdin on command: " + StringUtils.join(builder.command(), " "), e);
                 }
             }
 
@@ -228,9 +228,9 @@ public class ProcessController {
                 process.getOutputStream().close();
                 process.waitFor();
             } catch (IOException e) {
-                throw new ReviewedStingException("Unable to close stdin on command: " + StringUtils.join(builder.command(), " "), e);
+                throw new ReviewedGATKException("Unable to close stdin on command: " + StringUtils.join(builder.command(), " "), e);
             } catch (InterruptedException e) {
-                throw new ReviewedStingException("Process interrupted", e);
+                throw new ReviewedGATKException("Process interrupted", e);
             } finally {
                 while (!destroyed && stdout == null || stderr == null) {
                     synchronized (fromCapture) {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java
index a389d9bc5..9276de76f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
 public class ProcessOutput {
     private final int exitValue;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java
index 659523641..7027b9d25 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
 
 import java.io.File;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java
index 136da1369..7a982dda5 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
 import org.apache.commons.lang.StringUtils;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java
index 77ab403d3..37d66f097 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
 /**
  * Where to read/write a stream
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java
index 99120bb9c..9ce039ee0 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
 /**
  * The content of stdout or stderr.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java
index c249d059e..7e926d5d3 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMRecord;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java
index 0650523fd..db3f458f8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java
index c9a1f3fda..618128c4b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
@@ -32,10 +32,10 @@ import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
 import htsjdk.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.recalibration.EventType;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.recalibration.EventType;
 
 import java.util.*;
 
@@ -169,7 +169,7 @@ public final class AlignmentUtils {
                 case P:
                     break;
                 default:
-                    throw new ReviewedStingException("The " + ce.getOperator() + " cigar element is not currently supported");
+                    throw new ReviewedGATKException("The " + ce.getOperator() + " cigar element is not currently supported");
             }
         }
 
@@ -270,7 +270,7 @@ public final class AlignmentUtils {
                 case P:
                     break;
                 default:
-                    throw new ReviewedStingException("The " + ce.getOperator() + " cigar element is not currently supported");
+                    throw new ReviewedGATKException("The " + ce.getOperator() + " cigar element is not currently supported");
             }
 
         }
@@ -464,7 +464,7 @@ public final class AlignmentUtils {
                 case N:
                     break;
                 default:
-                    throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator());
+                    throw new ReviewedGATKException("Unsupported cigar operator: " + ce.getOperator());
             }
         }
 
@@ -526,7 +526,7 @@ public final class AlignmentUtils {
                 case P:
                     break;
                 default:
-                    throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator());
+                    throw new ReviewedGATKException("Unsupported cigar operator: " + ce.getOperator());
             }
         }
         return alignment;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java
index 0fd641d83..8233252d7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.NGSPlatform;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.NGSPlatform;
 
 import java.io.File;
 import java.io.IOException;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java
index b13273344..0821f4604 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.util.ProgressLoggerInterface;
-import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
+import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -62,12 +62,12 @@ import java.util.List;
 /**
  * @author aaron
  *         

- *         Class ArtificialStingSAMFileWriter
+ *         Class ArtificialGATKSAMFileWriter
  *         

  * generates a fake samwriter, that you can get the output reads
  * from when you're done.  
  */
-public class ArtificialStingSAMFileWriter implements StingSAMFileWriter {
+public class ArtificialGATKSAMFileWriter implements GATKSAMFileWriter {
 
     // are we closed
     private boolean closed = false;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java
index ef4e131d8..84978c1ef 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.MergingSamRecordIterator;
 import htsjdk.samtools.SamFileHeaderMerger;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIteratorAdapter;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.*;
 
@@ -48,7 +48,7 @@ public class ArtificialMultiSampleReadStream implements Iterable {
 
     public ArtificialMultiSampleReadStream( Collection perSampleArtificialReadStreams ) {
         if ( perSampleArtificialReadStreams == null || perSampleArtificialReadStreams.isEmpty() ) {
-            throw new ReviewedStingException("Can't create an ArtificialMultiSampleReadStream out of 0 ArtificialSingleSampleReadStreams");
+            throw new ReviewedGATKException("Can't create an ArtificialMultiSampleReadStream out of 0 ArtificialSingleSampleReadStreams");
         }
 
         this.perSampleArtificialReadStreams = perSampleArtificialReadStreams;
@@ -61,11 +61,11 @@ public class ArtificialMultiSampleReadStream implements Iterable {
         return mergingIterator;
     }
 
-    public StingSAMIterator getStingSAMIterator() {
+    public GATKSAMIterator getGATKSAMIterator() {
         // lazy initialization to prevent reads from being created until they're needed
         initialize();
 
-        return StingSAMIteratorAdapter.adapt(mergingIterator);
+        return GATKSAMIteratorAdapter.adapt(mergingIterator);
     }
 
     private void initialize() {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java
index 3ff92f4ae..8434e158d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialReadsTraversal.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialReadsTraversal.java
index fe894b61c..54c2b873a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialReadsTraversal.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialReadsTraversal.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
-import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.datasources.providers.ShardDataProvider;
+import org.broadinstitute.gatk.engine.traversals.TraversalEngine;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Walker;
 
 
 /*
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java
index 219948b7d..427b12e00 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.ByteArrayInputStream;
 import java.io.InputStream;
@@ -150,7 +150,7 @@ public class ArtificialSAMFileReader extends SAMFileReader {
             return new ByteArrayInputStream(byteArray);
         }
         catch( UnsupportedEncodingException ex ) {
-            throw new ReviewedStingException("Unable to build empty input stream",ex);
+            throw new ReviewedGATKException("Unable to build empty input stream",ex);
         }
     }
 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java
index 91c20a4a8..b133e9c55 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
 
 import java.util.Iterator;
 
@@ -58,7 +58,7 @@ import java.util.Iterator;
  */
 
 /** this fake iterator allows us to look at how specific piles of reads are handled */
-public class ArtificialSAMIterator implements StingSAMIterator {
+public class ArtificialSAMIterator implements GATKSAMIterator {
 
 
     protected int currentChromo = 0;
@@ -183,7 +183,7 @@ public class ArtificialSAMIterator implements StingSAMIterator {
     }
 
     public void remove() {
-        throw new UnsupportedOperationException("You've tried to remove on a StingSAMIterator (unsupported), not to mention that this is a fake iterator.");
+        throw new UnsupportedOperationException("You've tried to remove on a GATKSAMIterator (unsupported), not to mention that this is a fake iterator.");
     }
 
     /**
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java
index 88e36fd2e..fe7f7b0e7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMSequenceRecord;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.List;
 
@@ -150,7 +150,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator {
         // sanity check that we have an actual matching read next
         SAMRecord rec = this.peek();
         if (rec == null) {
-            throw new ReviewedStingException("The next read doesn't match");
+            throw new ReviewedGATKException("The next read doesn't match");
         }
         // set the seeked variable to true
         seeked = true;
@@ -189,7 +189,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator {
             super.next();
         }
         if (!super.hasNext()) {
-            throw new ReviewedStingException("Unable to find the target chromosome");
+            throw new ReviewedGATKException("Unable to find the target chromosome");
         }
         while (super.hasNext() && this.peek().getAlignmentStart() < start) {
             super.next();
@@ -197,7 +197,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator {
         // sanity check that we have an actual matching read next
         SAMRecord rec = this.peek();
         if (!matches(rec)) {
-            throw new ReviewedStingException("The next read doesn't match");
+            throw new ReviewedGATKException("The next read doesn't match");
         }
         // set the seeked variable to true
         seeked = true;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java
index 69bddd849..7fb43efab 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl;
 
 import java.io.File;
 import java.util.*;
@@ -163,7 +163,7 @@ public class ArtificialSAMUtils {
      */
     public static SAMFileHeader createEnumeratedReadGroups(SAMFileHeader header, List readGroupIDs, List sampleNames) {
         if (readGroupIDs.size() != sampleNames.size()) {
-            throw new ReviewedStingException("read group count and sample name count must be the same");
+            throw new ReviewedGATKException("read group count and sample name count must be the same");
         }
 
         List readGroups = new ArrayList();
@@ -192,7 +192,7 @@ public class ArtificialSAMUtils {
     public static GATKSAMRecord createArtificialRead(SAMFileHeader header, String name, int refIndex, int alignmentStart, int length) {
         if ((refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMENT_START) ||
                 (refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START))
-            throw new ReviewedStingException("Invalid alignment start for artificial read, start = " + alignmentStart);
+            throw new ReviewedGATKException("Invalid alignment start for artificial read, start = " + alignmentStart);
         GATKSAMRecord record = new GATKSAMRecord(header);
         record.setReadName(name);
         record.setReferenceIndex(refIndex);
@@ -230,7 +230,7 @@ public class ArtificialSAMUtils {
      */
     public static GATKSAMRecord createArtificialRead(SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual) {
         if (bases.length != qual.length) {
-            throw new ReviewedStingException("Passed in read string is different length then the quality array");
+            throw new ReviewedGATKException("Passed in read string is different length then the quality array");
         }
         GATKSAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length);
         rec.setReadBases(bases);
@@ -354,9 +354,9 @@ public class ArtificialSAMUtils {
      * @param startingChr the chromosome (reference ID) to start from
      * @param endingChr   the id to end with
      * @param readCount   the number of reads per chromosome
-     * @return StingSAMIterator representing the specified amount of fake data
+     * @return GATKSAMIterator representing the specified amount of fake data
      */
-    public static StingSAMIterator mappedReadIterator(int startingChr, int endingChr, int readCount) {
+    public static GATKSAMIterator mappedReadIterator(int startingChr, int endingChr, int readCount) {
         SAMFileHeader header = createArtificialSamHeader((endingChr - startingChr) + 1, startingChr, readCount + DEFAULT_READ_LENGTH);
 
         return new ArtificialSAMQueryIterator(startingChr, endingChr, readCount, 0, header);
@@ -369,9 +369,9 @@ public class ArtificialSAMUtils {
      * @param endingChr         the id to end with
      * @param readCount         the number of reads per chromosome
      * @param unmappedReadCount the count of unmapped reads to place at the end of the iterator, like in a sorted bam file
-     * @return StingSAMIterator representing the specified amount of fake data
+     * @return GATKSAMIterator representing the specified amount of fake data
      */
-    public static StingSAMIterator mappedAndUnmappedReadIterator(int startingChr, int endingChr, int readCount, int unmappedReadCount) {
+    public static GATKSAMIterator mappedAndUnmappedReadIterator(int startingChr, int endingChr, int readCount, int unmappedReadCount) {
         SAMFileHeader header = createArtificialSamHeader((endingChr - startingChr) + 1, startingChr, readCount + DEFAULT_READ_LENGTH);
 
         return new ArtificialSAMQueryIterator(startingChr, endingChr, readCount, unmappedReadCount, header);
@@ -383,7 +383,7 @@ public class ArtificialSAMUtils {
      * @param startingChr the chromosome (reference ID) to start from
      * @param endingChr   the id to end with
      * @param readCount   the number of reads per chromosome
-     * @return StingSAMIterator representing the specified amount of fake data
+     * @return GATKSAMIterator representing the specified amount of fake data
      */
     public static ArtificialSAMQueryIterator queryReadIterator(int startingChr, int endingChr, int readCount) {
         SAMFileHeader header = createArtificialSamHeader((endingChr - startingChr) + 1, startingChr, readCount + DEFAULT_READ_LENGTH);
@@ -398,9 +398,9 @@ public class ArtificialSAMUtils {
      * @param endingChr         the id to end with
      * @param readCount         the number of reads per chromosome
      * @param unmappedReadCount the count of unmapped reads to place at the end of the iterator, like in a sorted bam file
-     * @return StingSAMIterator representing the specified amount of fake data
+     * @return GATKSAMIterator representing the specified amount of fake data
      */
-    public static StingSAMIterator queryReadIterator(int startingChr, int endingChr, int readCount, int unmappedReadCount) {
+    public static GATKSAMIterator queryReadIterator(int startingChr, int endingChr, int readCount, int unmappedReadCount) {
         SAMFileHeader header = createArtificialSamHeader((endingChr - startingChr) + 1, startingChr, readCount + DEFAULT_READ_LENGTH);
 
         return new ArtificialSAMQueryIterator(startingChr, endingChr, readCount, unmappedReadCount, header);
@@ -412,7 +412,7 @@ public class ArtificialSAMUtils {
      * @param reads the reads
      * @return iterator for the reads
      */
-    public static StingSAMIterator createReadIterator(SAMRecord... reads) {
+    public static GATKSAMIterator createReadIterator(SAMRecord... reads) {
         return createReadIterator(Arrays.asList(reads));
     }
 
@@ -422,9 +422,9 @@ public class ArtificialSAMUtils {
      * @param reads the reads
      * @return iterator for the reads
      */
-    public static StingSAMIterator createReadIterator(List reads) {
+    public static GATKSAMIterator createReadIterator(List reads) {
         final Iterator iter = reads.iterator();
-        return new StingSAMIterator() {
+        return new GATKSAMIterator() {
             @Override public void close() {}
             @Override public Iterator iterator() { return iter; }
             @Override public boolean hasNext() { return iter.hasNext(); }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java
index 4b3b718a3..27e25d39c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIteratorAdapter;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.ArrayList;
 import java.util.Collection;
@@ -94,33 +94,33 @@ public class ArtificialSingleSampleReadStream implements Iterable {
 
     private void validateStreamParameters() {
         if ( header == null || readGroupID == null ) {
-            throw new ReviewedStingException("null SAMFileHeader or read group ID") ;
+            throw new ReviewedGATKException("null SAMFileHeader or read group ID") ;
         }
 
         if ( header.getReadGroup(readGroupID) == null ) {
-            throw new ReviewedStingException(String.format("Read group %s not found in SAMFileHeader", readGroupID));
+            throw new ReviewedGATKException(String.format("Read group %s not found in SAMFileHeader", readGroupID));
         }
 
         if ( numContigs < 0 || numStacksPerContig < 0 || minReadsPerStack < 0 || maxReadsPerStack < 0 ||
              minDistanceBetweenStacks < 0 || maxDistanceBetweenStacks < 0 || minReadLength < 0 || maxReadLength < 0 ||
              numUnmappedReads < 0 ) {
-            throw new ReviewedStingException("Read stream parameters must be >= 0");
+            throw new ReviewedGATKException("Read stream parameters must be >= 0");
         }
 
         if ( (numContigs == 0 && numStacksPerContig != 0) || (numContigs != 0 && numStacksPerContig == 0) ) {
-            throw new ReviewedStingException("numContigs and numStacksPerContig must either both be > 0, or both be 0");
+            throw new ReviewedGATKException("numContigs and numStacksPerContig must either both be > 0, or both be 0");
         }
 
         if ( minReadsPerStack > maxReadsPerStack ) {
-            throw new ReviewedStingException("minReadsPerStack > maxReadsPerStack");
+            throw new ReviewedGATKException("minReadsPerStack > maxReadsPerStack");
         }
 
         if ( minDistanceBetweenStacks > maxDistanceBetweenStacks ) {
-            throw new ReviewedStingException("minDistanceBetweenStacks > maxDistanceBetweenStacks");
+            throw new ReviewedGATKException("minDistanceBetweenStacks > maxDistanceBetweenStacks");
         }
 
         if ( minReadLength > maxReadLength ) {
-            throw new ReviewedStingException("minReadLength > maxReadLength");
+            throw new ReviewedGATKException("minReadLength > maxReadLength");
         }
     }
 
@@ -128,8 +128,8 @@ public class ArtificialSingleSampleReadStream implements Iterable {
         return makeReads().iterator();
     }
 
-    public StingSAMIterator getStingSAMIterator() {
-        return StingSAMIteratorAdapter.adapt(iterator());
+    public GATKSAMIterator getGATKSAMIterator() {
+        return GATKSAMIteratorAdapter.adapt(iterator());
     }
 
     public Collection makeReads() {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java
index c4f9c1bcd..196fa7182 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -114,7 +114,7 @@ public class ArtificialSingleSampleReadStreamAnalyzer {
 
     /**
      * Validate the stream by checking whether our collected statistics match the properties of the
-     * original stream. Throws a ReviewedStingException if the stream is invalid.
+     * original stream. Throws a ReviewedGATKException if the stream is invalid.
      *
      * Override this method if you want to check whether the stream has been transformed in some
      * way relative to the original stream.
@@ -122,72 +122,72 @@ public class ArtificialSingleSampleReadStreamAnalyzer {
     public void validate() {
         if ( (originalStream.getNumContigs() == 0 || originalStream.getNumStacksPerContig() == 0) && originalStream.getNumUnmappedReads() == 0 ) {
             if ( totalReads != 0 ) {
-                throw new ReviewedStingException("got reads from the stream, but the stream was configured to have 0 reads");
+                throw new ReviewedGATKException("got reads from the stream, but the stream was configured to have 0 reads");
             }
             return;  // no further validation needed for the 0-reads case
         }
         else if ( totalReads == 0 ) {
-            throw new ReviewedStingException("got no reads from the stream, but the stream was configured to have > 0 reads");
+            throw new ReviewedGATKException("got no reads from the stream, but the stream was configured to have > 0 reads");
         }
 
         if ( ! allSamplesMatch ) {
-            throw new ReviewedStingException("some reads had the wrong sample");
+            throw new ReviewedGATKException("some reads had the wrong sample");
         }
 
         if ( numContigs != originalStream.getNumContigs() ) {
-            throw new ReviewedStingException("number of contigs not correct");
+            throw new ReviewedGATKException("number of contigs not correct");
         }
 
         if ( stacksPerContig.size() != originalStream.getNumContigs() ) {
-            throw new ReviewedStingException(String.format("bug in analyzer code: calculated sizes for %d contigs even though there were only %d contigs",
+            throw new ReviewedGATKException(String.format("bug in analyzer code: calculated sizes for %d contigs even though there were only %d contigs",
                                                            stacksPerContig.size(), originalStream.getNumContigs()));
         }
 
         for ( int contigStackCount : stacksPerContig ) {
             if ( contigStackCount != originalStream.getNumStacksPerContig() ) {
-                throw new ReviewedStingException("contig had incorrect number of stacks");
+                throw new ReviewedGATKException("contig had incorrect number of stacks");
             }
         }
 
         if ( originalStream.getNumStacksPerContig() > 0 ) {
             if ( minReadsPerStack < originalStream.getMinReadsPerStack() ) {
-                throw new ReviewedStingException("stack had fewer than the minimum number of reads");
+                throw new ReviewedGATKException("stack had fewer than the minimum number of reads");
             }
             if ( maxReadsPerStack > originalStream.getMaxReadsPerStack() ) {
-                throw new ReviewedStingException("stack had more than the maximum number of reads");
+                throw new ReviewedGATKException("stack had more than the maximum number of reads");
             }
         }
         else if ( minReadsPerStack != null || maxReadsPerStack != null ) {
-            throw new ReviewedStingException("bug in analyzer code: reads per stack was calculated even though 0 stacks per contig was specified");
+            throw new ReviewedGATKException("bug in analyzer code: reads per stack was calculated even though 0 stacks per contig was specified");
         }
 
         if ( originalStream.getNumStacksPerContig() > 1 ) {
             if ( minDistanceBetweenStacks < originalStream.getMinDistanceBetweenStacks() ) {
-                throw new ReviewedStingException("stacks were separated by less than the minimum distance");
+                throw new ReviewedGATKException("stacks were separated by less than the minimum distance");
             }
             if ( maxDistanceBetweenStacks > originalStream.getMaxDistanceBetweenStacks() ) {
-                throw new ReviewedStingException("stacks were separated by more than the maximum distance");
+                throw new ReviewedGATKException("stacks were separated by more than the maximum distance");
             }
         }
         else if ( minDistanceBetweenStacks != null || maxDistanceBetweenStacks != null ) {
-            throw new ReviewedStingException("bug in analyzer code: distance between stacks was calculated even though numStacksPerContig was <= 1");
+            throw new ReviewedGATKException("bug in analyzer code: distance between stacks was calculated even though numStacksPerContig was <= 1");
         }
 
         if ( minReadLength < originalStream.getMinReadLength() ) {
-            throw new ReviewedStingException("read was shorter than the minimum allowed length");
+            throw new ReviewedGATKException("read was shorter than the minimum allowed length");
         }
         if ( maxReadLength > originalStream.getMaxReadLength() ) {
-            throw new ReviewedStingException("read was longer than the maximum allowed length");
+            throw new ReviewedGATKException("read was longer than the maximum allowed length");
         }
 
         if ( numUnmappedReads != originalStream.getNumUnmappedReads() ) {
-            throw new ReviewedStingException(String.format("wrong number of unmapped reads: requested %d but saw %d",
+            throw new ReviewedGATKException(String.format("wrong number of unmapped reads: requested %d but saw %d",
                                                            originalStream.getNumUnmappedReads(), numUnmappedReads));
         }
 
         if ( (originalStream.getNumContigs() == 0 || originalStream.getNumStacksPerContig() == 0) &&
              numUnmappedReads != totalReads ) {
-            throw new ReviewedStingException("stream should have consisted only of unmapped reads, but saw some mapped reads");
+            throw new ReviewedGATKException("stream should have consisted only of unmapped reads, but saw some mapped reads");
         }
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/BySampleSAMFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/BySampleSAMFileWriter.java
index 88f7e66a7..e212bd909 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/BySampleSAMFileWriter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/BySampleSAMFileWriter.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMProgramRecord;
 import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -54,7 +54,7 @@ public class BySampleSAMFileWriter extends NWaySAMFileWriter{
             for (SAMReadGroupRecord rg : toolkit.getReadsDataSource().getHeader(readerID).getReadGroups()) {
                 String sample = rg.getSample();
                 if (sampleToWriterMap.containsKey(sample) && sampleToWriterMap.get(sample) != readerID) {
-                    throw new ReviewedStingException("The same sample appears in multiple files, this input cannot be multiplexed using the BySampleSAMFileWriter, try NWaySAMFileWriter instead.");
+                    throw new ReviewedGATKException("The same sample appears in multiple files, this input cannot be multiplexed using the BySampleSAMFileWriter, try NWaySAMFileWriter instead.");
                 }
                 else {
                     sampleToWriterMap.put(sample, readerID);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java
index 31c6f6a95..fe7f3d9f9 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import com.google.java.contract.Ensures;
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
 import htsjdk.samtools.TextCigarCodec;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.smithwaterman.Parameters;
-import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment;
-import org.broadinstitute.sting.utils.smithwaterman.SmithWaterman;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.smithwaterman.Parameters;
+import org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment;
+import org.broadinstitute.gatk.utils.smithwaterman.SmithWaterman;
 
 import java.util.Arrays;
 import java.util.Stack;
@@ -164,7 +164,7 @@ public class CigarUtils {
                 case I:
                     break;
                 default:
-                    throw new ReviewedStingException("Unsupported cigar operator: " + cigarElement.getOperator());
+                    throw new ReviewedGATKException("Unsupported cigar operator: " + cigarElement.getOperator());
             }
         }
         return result;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java
index 951f79d45..6af90597d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.utils.NGSPlatform;
+import org.broadinstitute.gatk.utils.NGSPlatform;
 
 /**
  * @author ebanks
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java
index ad58a8f9c..c0f22201e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import com.google.java.contract.Ensures;
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.utils.NGSPlatform;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.recalibration.EventType;
+import org.broadinstitute.gatk.utils.NGSPlatform;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.recalibration.EventType;
 
 import java.util.*;
 
@@ -252,7 +252,7 @@ public class GATKSAMRecord extends BAMRecord {
                 setAttribute( GATKSAMRecord.BQSR_BASE_DELETION_QUALITIES, quals == null ? null : SAMUtils.phredToFastq(quals) );
                 break;
             default:
-                throw new ReviewedStingException("Unrecognized Base Recalibration type: " + errorModel );
+                throw new ReviewedGATKException("Unrecognized Base Recalibration type: " + errorModel );
         }
     }
 
@@ -265,7 +265,7 @@ public class GATKSAMRecord extends BAMRecord {
             case BASE_DELETION:
                 return getBaseDeletionQualities();
             default:
-                throw new ReviewedStingException("Unrecognized Base Recalibration type: " + errorModel );
+                throw new ReviewedGATKException("Unrecognized Base Recalibration type: " + errorModel );
         }
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java
index 642e824e1..1e5ad1e78 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMRecordFactory;
 import htsjdk.samtools.BAMRecord;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 /**
  * Factory interface implementation used to create GATKSamRecords
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityReadTransformer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityReadTransformer.java
index 20e3736f2..35146f0b8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityReadTransformer.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityReadTransformer.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
+import org.broadinstitute.gatk.engine.walkers.Walker;
+import org.broadinstitute.gatk.utils.QualityUtils;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 /**
  * Checks for and errors out (or fixes if requested) when it detects reads with base qualities that are not encoded with
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/NWaySAMFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/NWaySAMFileWriter.java
index c1e0548e1..abf70d5a4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/NWaySAMFileWriter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/NWaySAMFileWriter.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.*;
 import htsjdk.samtools.util.ProgressLoggerInterface;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.io.File;
 import java.util.Collection;
@@ -89,7 +89,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
      */
     public void setupByReader(GenomeAnalysisEngine toolkit, Map in2out, SAMFileHeader.SortOrder order,
                               boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord) {
-        if ( in2out==null ) throw new StingException("input-output bam filename map for n-way-out writing is NULL");
+        if ( in2out==null ) throw new GATKException("input-output bam filename map for n-way-out writing is NULL");
         for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
 
             String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();
@@ -100,7 +100,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
             outName = in2out.get(fName);
 
             if ( writerMap.containsKey( rid ) )
-                throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered; "+
+                throw new GATKException("nWayOut mode: Reader id for input sam file "+fName+" is already registered; "+
                         "map file likely contains multiple entries for this input file");
 
             addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5, pRecord);
@@ -133,7 +133,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
             outName = prefix+ext;
 
             if ( writerMap.containsKey( rid ) )
-                throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
+                throw new GATKException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
             addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5, pRecord);
         }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java
index 4607f9f1b..9d2a3912e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java
index 704c839f8..100749847 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.*;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.*;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.io.File;
 import java.util.*;
@@ -480,7 +480,7 @@ public class ReadUtils {
             if (allowGoalNotReached) {
                 return new Pair(CLIPPING_GOAL_NOT_REACHED, false);
             } else {
-                throw new ReviewedStingException("Somehow the requested coordinate is not covered by the read. Too many deletions?");
+                throw new ReviewedGATKException("Somehow the requested coordinate is not covered by the read. Too many deletions?");
             }
         }
         boolean goalReached = refBases == goal;
@@ -513,7 +513,7 @@ public class ReadUtils {
                     if (allowGoalNotReached) {
                         return new Pair(CLIPPING_GOAL_NOT_REACHED, false);
                     } else {
-                        throw new ReviewedStingException(String.format("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- check read with alignment start: %s  and cigar: %s", alignmentStart, cigar));
+                        throw new ReviewedGATKException(String.format("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- check read with alignment start: %s  and cigar: %s", alignmentStart, cigar));
                     }
                 }
 
@@ -534,7 +534,7 @@ public class ReadUtils {
                             if (allowGoalNotReached) {
                                 return new Pair(CLIPPING_GOAL_NOT_REACHED, false);
                             } else {
-                                throw new ReviewedStingException(String.format("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- check read with alignment start: %s  and cigar: %s", alignmentStart, cigar));
+                                throw new ReviewedGATKException(String.format("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- check read with alignment start: %s  and cigar: %s", alignmentStart, cigar));
                             }
                         }
 
@@ -570,7 +570,7 @@ public class ReadUtils {
             if (allowGoalNotReached) {
                 return new Pair(CLIPPING_GOAL_NOT_REACHED, false);
             } else {
-                throw new ReviewedStingException("Somehow the requested coordinate is not covered by the read. Alignment " + alignmentStart + " | " + cigar);
+                throw new ReviewedGATKException("Somehow the requested coordinate is not covered by the read. Alignment " + alignmentStart + " | " + cigar);
             }
         }
 
@@ -795,7 +795,7 @@ public class ReadUtils {
                     bases[i] = 'N';
                     break;
                 default:
-                    throw new ReviewedStingException("Something went wrong, this is just impossible");
+                    throw new ReviewedGATKException("Something went wrong, this is just impossible");
             }
         }
         return bases;
@@ -829,7 +829,7 @@ public class ReadUtils {
      */
     public static long getReferenceCoordinateForReadCoordinate(GATKSAMRecord read, int offset) {
         if (offset > read.getReadLength()) 
-            throw new ReviewedStingException(String.format(OFFSET_OUT_OF_BOUNDS_EXCEPTION, offset, read.getReadLength()));
+            throw new ReviewedGATKException(String.format(OFFSET_OUT_OF_BOUNDS_EXCEPTION, offset, read.getReadLength()));
 
         long location = read.getAlignmentStart();
         Iterator cigarElementIterator = read.getCigar().getCigarElements().iterator();
@@ -842,7 +842,7 @@ public class ReadUtils {
             offset -= move;
         }
         if (offset > 0 && !cigarElementIterator.hasNext()) 
-            throw new ReviewedStingException(OFFSET_NOT_ZERO_EXCEPTION);
+            throw new ReviewedGATKException(OFFSET_NOT_ZERO_EXCEPTION);
 
         return location;
     }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java
index 13bca872a..2c065bb24 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileReader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.File;
 
@@ -71,9 +71,9 @@ public class SAMFileReaderBuilder {
      */
     public SAMFileReader build() {
         if( samFile == null )
-            throw new ReviewedStingException( "Filename for output sam file must be supplied.");
+            throw new ReviewedGATKException( "Filename for output sam file must be supplied.");
         if( validationStringency == null )
-            throw new ReviewedStingException( "Header for output sam file must be supplied.");
+            throw new ReviewedGATKException( "Header for output sam file must be supplied.");
 
         SAMFileReader reader = new SAMFileReader( samFile );
         reader.setValidationStringency( validationStringency );
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java
index 9dc739812..421461996 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileWriter;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java
index 2850d559b..ee2bcec57 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java
@@ -23,4 +23,4 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
\ No newline at end of file
+package org.broadinstitute.gatk.utils.sam;
\ No newline at end of file
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java
index 1fe8f520d..c0b83d7f1 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.smithwaterman;
+package org.broadinstitute.gatk.utils.smithwaterman;
 
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
 
 import java.util.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java
index d4364afdf..685d8fffe 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.smithwaterman;
+package org.broadinstitute.gatk.utils.smithwaterman;
 
 /**
  * Holds the core Smith-Waterman alignment parameters of
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java
index 3ff0e71ac..c28d9b9db 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.smithwaterman;
+package org.broadinstitute.gatk.utils.smithwaterman;
 
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
+import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
 
 import java.util.*;
 
@@ -577,7 +577,7 @@ public class SWPairwiseAlignment implements SmithWaterman {
                     }
                     break;
                 default:
-                    throw new StingException("Unexpected Cigar element:" + e.getOperator());
+                    throw new GATKException("Unexpected Cigar element:" + e.getOperator());
             }
         }
         for ( ; i < ref.length; i++ ) bref.append((char)ref[i]);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java
index 8c832fa75..40220f45c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java
@@ -23,10 +23,10 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.smithwaterman;
+package org.broadinstitute.gatk.utils.smithwaterman;
 
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.collections.Pair;
 
 import java.util.ArrayList;
 import java.util.HashMap;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java
index 100780023..92df21804 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.smithwaterman;
+package org.broadinstitute.gatk.utils.smithwaterman;
 
 /**
  * Handy named collection of common Smith-waterman parameter sets
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java
index 88cb76a88..c4184e16e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.smithwaterman;
+package org.broadinstitute.gatk.utils.smithwaterman;
 
 import htsjdk.samtools.Cigar;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java
index dcdc980ca..d6e1bcbea 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.text;
+package org.broadinstitute.gatk.utils.text;
 
-import org.broadinstitute.sting.commandline.ParsingEngine;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.commandline.ParsingEngine;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
+import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager;
+import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java
index 5931aa897..65fb970e1 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.text;
+package org.broadinstitute.gatk.utils.text;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.IOException;
 import java.io.StringReader;
@@ -110,7 +110,7 @@ public class TextFormattingUtils {
                 bundle = new PropertyResourceBundle(new StringReader(""));
             }
             catch(IOException ioe) {
-                throw new ReviewedStingException("No resource bundle found, and unable to create an empty placeholder.",ioe);
+                throw new ReviewedGATKException("No resource bundle found, and unable to create an empty placeholder.",ioe);
             }
         }
         return bundle;
@@ -125,7 +125,7 @@ public class TextFormattingUtils {
      */
     public static List getWordStarts(String line) {
         if (line == null)
-            throw new ReviewedStingException("line is null");
+            throw new ReviewedGATKException("line is null");
         List starts = new ArrayList();
         int stop = line.length();
         for (int i = 1; i < stop; i++)
@@ -143,9 +143,9 @@ public class TextFormattingUtils {
      */
     public static String[] splitFixedWidth(String line, List columnStarts) {
         if (line == null)
-            throw new ReviewedStingException("line is null");
+            throw new ReviewedGATKException("line is null");
         if (columnStarts == null)
-            throw new ReviewedStingException("columnStarts is null");
+            throw new ReviewedGATKException("columnStarts is null");
         int startCount = columnStarts.size();
         String[] row = new String[startCount + 1];
         if (startCount == 0) {
@@ -166,7 +166,7 @@ public class TextFormattingUtils {
      */
     public static String[] splitWhiteSpace(String line) {
         if (line == null)
-            throw new ReviewedStingException("line is null");
+            throw new ReviewedGATKException("line is null");
         return line.trim().split("\\s+");
     }
 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java
index 6defd64ea..f41015612 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.text;
+package org.broadinstitute.gatk.utils.text;
 
 import java.io.*;
 import java.util.Iterator;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java
index eddefcdc4..72820832d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.gatk.utils.threading;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
 import org.apache.log4j.Priority;
-import org.broadinstitute.sting.utils.AutoFormattingTime;
+import org.broadinstitute.gatk.utils.AutoFormattingTime;
 
 import java.lang.management.ManagementFactory;
 import java.lang.management.ThreadInfo;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java
index c7eda4f5e..6c840869a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.gatk.utils.threading;
 
 import java.util.concurrent.ThreadFactory;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java
index ab289a671..cee91a435 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.gatk.utils.threading;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
 import org.apache.log4j.Priority;
-import org.broadinstitute.sting.utils.AutoFormattingTime;
+import org.broadinstitute.gatk.utils.AutoFormattingTime;
 
 import java.lang.management.ManagementFactory;
 import java.lang.management.ThreadInfo;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java
index ed03ebce4..b8dea067b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.gatk.utils.threading;
 
 import java.lang.reflect.Array;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java
index b6af76662..92618709e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.gatk.utils.threading;
 
 import org.apache.log4j.Logger;
 /**
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java
index 6a2218d43..83093ba98 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java
@@ -23,4 +23,4 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.gatk.utils.threading;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java
index 3f00d9fe5..f142da261 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.variant;
+package org.broadinstitute.gatk.utils.variant;
 
-import org.broadinstitute.sting.commandline.EnumerationArgumentDefault;
+import org.broadinstitute.gatk.utils.commandline.EnumerationArgumentDefault;
 
 /**
  * Choose the Tribble indexing strategy
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtils.java
index bfef5eeee..6baa7b654 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.variant;
+package org.broadinstitute.gatk.utils.variant;
 
 import htsjdk.samtools.SAMSequenceDictionary;
 import org.apache.log4j.Logger;
@@ -39,12 +39,12 @@ import htsjdk.tribble.index.tabix.TabixFormat;
 import htsjdk.tribble.index.tabix.TabixIndexCreator;
 import htsjdk.tribble.readers.LineIterator;
 import htsjdk.tribble.readers.PositionalBufferedStream;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
-import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor;
+import org.broadinstitute.gatk.utils.collections.Pair;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.*;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
index be3eb1028..e746566ee 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.variant;
+package org.broadinstitute.gatk.utils.variant;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
@@ -31,9 +31,9 @@ import org.apache.commons.lang.ArrayUtils;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.TribbleException;
 import htsjdk.tribble.util.popgen.HardyWeinbergCalculation;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.*;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.vcf.VCFConstants;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java
index 4418ca104..0b1543bf9 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.variant;
+package org.broadinstitute.gatk.utils.variant;
 
 /**
  * Homo sapiens genome constants.
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java
index e38ec4a38..85681c40f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.wiggle;
+package org.broadinstitute.gatk.utils.wiggle;
 
 /**
  * A class for defining the header values for a wiggle graph file (see UCSC). The optional fields are:
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java
index 83d3795f3..af9268bb6 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.wiggle;
+package org.broadinstitute.gatk.utils.wiggle;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.io.*;
 
@@ -101,7 +101,7 @@ public class WiggleWriter {
             write(wWriter,String.format("%d\t%s",loc.getStart(),dataPoint.toString()));
         } else {
             // todo -- maybe allow this to open a new file for the new chromosome?
-            throw new ReviewedStingException("Attempting to write multiple contigs into wiggle file, first contig was "+firstLoc.getContig()+" most recent "+loc.getContig());
+            throw new ReviewedGATKException("Attempting to write multiple contigs into wiggle file, first contig was "+firstLoc.getContig()+" most recent "+loc.getContig());
         }
     }
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java
index ca7333779..dc3e99653 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk;
+package org.broadinstitute.gatk.engine;
 
 import htsjdk.samtools.SAMFileReader;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
index 850bafc0c..dc1b66039 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk;
+package org.broadinstitute.gatk.engine;
 
 import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMReadGroupRecord;
@@ -31,28 +31,28 @@ import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.tribble.readers.LineIterator;
-import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
-import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.walkers.ReadFilters;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.qc.ErrorThrowing;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.commandline.*;
+import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource;
+import org.broadinstitute.gatk.engine.filters.MappingQualityUnavailableFilter;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack;
+import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder;
+import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature;
+import org.broadinstitute.gatk.engine.walkers.ReadFilters;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.tools.walkers.qc.ErrorThrowing;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.vcf.VCFCodec;
@@ -138,7 +138,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
             for ( final String args : Arrays.asList("", " -nt 2", " -nct 2") ) {
                 new EngineErrorHandlingTestProvider(NullPointerException.class, failArg + args);
                 new EngineErrorHandlingTestProvider(UserException.class, failArg + args);
-                new EngineErrorHandlingTestProvider(ReviewedStingException.class, failArg + args);
+                new EngineErrorHandlingTestProvider(ReviewedGATKException.class, failArg + args);
             }
         }
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java
index 995a7ccb4..161bb41d1 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java
@@ -23,21 +23,21 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk;
+package org.broadinstitute.gatk.engine;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.qc.CountReads;
-import org.broadinstitute.sting.gatk.walkers.readutils.PrintReads;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
+import org.broadinstitute.gatk.engine.walkers.Walker;
+import org.broadinstitute.gatk.tools.walkers.qc.CountReads;
+import org.broadinstitute.gatk.tools.walkers.readutils.PrintReads;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.GenomeLocSortedSet;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java
index 5b3f1e790..27b6c1ca3 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk;
+package org.broadinstitute.gatk.engine;
 
-import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.utils.SimpleTimer;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.LocusWalker;
+import org.broadinstitute.gatk.utils.SimpleTimer;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java
index aeb7735b7..47081b264 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java
@@ -23,35 +23,35 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk;
+package org.broadinstitute.gatk.engine;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
-import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
-import org.broadinstitute.sting.gatk.datasources.reads.*;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.executive.WindowMaker;
-import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
-import org.broadinstitute.sting.gatk.traversals.*;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
-import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.sam.*;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.datasources.providers.LocusShardDataProvider;
+import org.broadinstitute.gatk.engine.datasources.providers.ReadShardDataProvider;
+import org.broadinstitute.gatk.engine.datasources.reads.*;
+import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.gatk.engine.executive.WindowMaker;
+import org.broadinstitute.gatk.engine.filters.ReadFilter;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation;
+import org.broadinstitute.gatk.engine.traversals.*;
+import org.broadinstitute.gatk.engine.walkers.*;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.GenomeLocSortedSet;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.activeregion.ActiveRegion;
+import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.interval.IntervalMergingRule;
+import org.broadinstitute.gatk.utils.sam.*;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java
index 52ef0d913..62348ef19 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk;
+package org.broadinstitute.gatk.engine;
 
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.qc.CountLoci;
-import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.commandline.Hidden;
+import org.broadinstitute.gatk.engine.walkers.Walker;
+import org.broadinstitute.gatk.tools.walkers.qc.CountLoci;
+import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java
index 0c6edbbd4..f9d9dfe53 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.providers;
+package org.broadinstitute.gatk.engine.datasources.providers;
 
 
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
 
 import java.util.List;
 /**
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java
index 5bf073fe3..8914a4876 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.providers;
+package org.broadinstitute.gatk.engine.datasources.providers;
 
 
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
 
 import java.util.List;
 /**
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java
index bd32eb511..29ccbd644 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.providers;
+package org.broadinstitute.gatk.engine.datasources.providers;
 
 import htsjdk.samtools.util.PeekableIterator;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.tribble.BasicFeature;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.refdata.RODRecordListImpl;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.engine.refdata.RODRecordListImpl;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature;
+import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java
index 6ff28f982..5eb9c7ac7 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.providers;
+package org.broadinstitute.gatk.engine.datasources.providers;
 
-import org.broadinstitute.sting.gatk.datasources.reads.Shard;
+import org.broadinstitute.gatk.engine.datasources.reads.Shard;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard;
-import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard;
+import org.broadinstitute.gatk.engine.iterators.GenomeLocusIterator;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
 
 import htsjdk.samtools.reference.ReferenceSequence;
 import htsjdk.samtools.util.StringUtil;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java
index ff609142d..650b14690 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java
@@ -23,23 +23,23 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.providers;
+package org.broadinstitute.gatk.engine.datasources.providers;
 
 import htsjdk.samtools.reference.ReferenceSequence;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.executive.WindowMaker;
-import org.broadinstitute.sting.gatk.datasources.reads.LocusShard;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
+import org.broadinstitute.gatk.engine.datasources.reads.Shard;
+import org.broadinstitute.gatk.engine.executive.WindowMaker;
+import org.broadinstitute.gatk.engine.datasources.reads.LocusShard;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
+import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -371,7 +371,7 @@ public abstract class LocusViewTemplate extends BaseTest {
     }
 
     /** A simple iterator which iterates over a list of reads. */
-    protected class SAMRecordIterator implements StingSAMIterator {
+    protected class SAMRecordIterator implements GATKSAMIterator {
         private Iterator backingIterator = null;
 
         public SAMRecordIterator(SAMRecord... reads) {
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java
index 04d30172f..8bf4f4103 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.providers;
+package org.broadinstitute.gatk.engine.datasources.providers;
 
 import org.testng.Assert;
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLoc;
 
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java
index 804786d7b..fdec85870 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java
@@ -23,23 +23,23 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.providers;
+package org.broadinstitute.gatk.engine.datasources.providers;
 
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard;
+import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder;
+import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet;
 import org.testng.Assert;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.codecs.table.TableFeature;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.datasources.reads.Shard;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.codecs.table.TableFeature;
+import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet.RMDStorageType;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java
index 310424024..bffd23da1 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.providers;
+package org.broadinstitute.gatk.engine.datasources.providers;
 
 import htsjdk.samtools.SAMSequenceRecord;
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java
index f14eb9316..251eec49a 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.providers;
+package org.broadinstitute.gatk.engine.datasources.providers;
 
 import org.testng.Assert;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.testng.annotations.BeforeMethod;
 
 
 import org.testng.annotations.Test;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 
 import java.util.Collection;
 import java.util.Collections;
@@ -93,7 +93,7 @@ public class ShardDataProviderUnitTest extends BaseTest {
     /**
      * Try adding a view which conflicts with some other view that's already been registered.
      */
-    @Test(expectedExceptions= ReviewedStingException.class)
+    @Test(expectedExceptions= ReviewedGATKException.class)
     public void testAddViewWithExistingConflict() {
         View initial = new ConflictingTestView( provider );
         View conflictsWithInitial = new TestView( provider );
@@ -102,7 +102,7 @@ public class ShardDataProviderUnitTest extends BaseTest {
     /**
      * Try adding a view which has a conflict with a previously registered view.
      */
-    @Test(expectedExceptions= ReviewedStingException.class)
+    @Test(expectedExceptions= ReviewedGATKException.class)
     public void testAddViewWithNewConflict() {
         View conflictsWithInitial = new TestView( provider );
         View initial = new ConflictingTestView( provider );
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java
index 77096a6ea..f1ee6ab78 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileSpan;
 import htsjdk.samtools.SAMSequenceRecord;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.interval.IntervalMergingRule;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java
index 25c71d570..27c287c9c 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java
@@ -23,13 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import com.google.caliper.Param;
-import org.broadinstitute.sting.gatk.WalkerManager;
-import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.qc.CountLoci;
+import org.broadinstitute.gatk.engine.WalkerManager;
+import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod;
+import org.broadinstitute.gatk.engine.walkers.LocusWalker;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java
index 2a2a36710..e35f1d592 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.GATKBAMFileSpan;
 import htsjdk.samtools.GATKChunk;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.interval.IntervalMergingRule;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java
index e4405bd20..289a10cf1 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMSequenceDictionary;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java
index f61b7a208..30eaeb6a1 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java
@@ -23,23 +23,23 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import com.google.caliper.Param;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.qc.CountLoci;
-import org.broadinstitute.sting.gatk.walkers.qc.CountReads;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.filters.ReadFilter;
+import org.broadinstitute.gatk.engine.filters.UnmappedReadFilter;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.engine.walkers.Walker;
+import org.broadinstitute.gatk.tools.walkers.qc.CountLoci;
+import org.broadinstitute.gatk.tools.walkers.qc.CountReads;
+import org.broadinstitute.gatk.utils.classloader.JVMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.io.File;
 import java.util.Collections;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java
index 3db6b0ac9..90ac7549e 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMSequenceRecord;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -123,7 +123,7 @@ public class IntervalOverlapFilteringIteratorUnitTest {
         Assert.assertEquals(actual, expected);
     }
 
-    @Test(expectedExceptions = ReviewedStingException.class)
+    @Test(expectedExceptions = ReviewedGATKException.class)
     public void testMappedAndUnmapped() {
         new IntervalOverlapFilteringIterator(
                 ArtificialSAMUtils.createReadIterator(testReads),
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java
index 68a137c6a..eb3c89493 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
-import org.broadinstitute.sting.gatk.datasources.reads.LocusShard;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.gatk.engine.datasources.reads.LocusShard;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
+import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
 
 import java.util.List;
 import java.util.Collections;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java
index 04a1f9fc1..f96a35a79 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import com.google.caliper.Param;
 import com.google.caliper.SimpleBenchmark;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java
index 4200b7b1e..71fc81aeb 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import com.google.caliper.Param;
 import com.google.caliper.SimpleBenchmark;
@@ -31,7 +31,7 @@ import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMFileWriter;
 import htsjdk.samtools.SAMFileWriterFactory;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.File;
 import java.io.IOException;
@@ -58,7 +58,7 @@ public abstract class ReadProcessingBenchmark extends SimpleBenchmark {
             tempFile = File.createTempFile("testfile_"+getMaxReads(),".bam");
         }
         catch(IOException ex) {
-            throw new ReviewedStingException("Unable to create temporary BAM",ex);
+            throw new ReviewedGATKException("Unable to create temporary BAM",ex);
         }
         SAMFileWriterFactory factory = new SAMFileWriterFactory();
         factory.setCreateIndex(true);
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java
index f48459c1e..747082508 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java
@@ -23,20 +23,20 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
-import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
-import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.ArtificialSingleSampleReadStream;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
+import org.broadinstitute.gatk.engine.downsampling.DownsampleType;
+import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod;
+import org.broadinstitute.gatk.engine.filters.ReadFilter;
+import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStream;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 import org.testng.Assert;
@@ -160,7 +160,7 @@ public class ReadShardBalancerUnitTest extends BaseTest {
                 testBAMFile.deleteOnExit();
             }
             catch ( IOException e ) {
-                throw new ReviewedStingException(String.format("Failed to create temp bam file for test %s. %s", this, e.getMessage()));
+                throw new ReviewedGATKException(String.format("Failed to create temp bam file for test %s. %s", this, e.getMessage()));
             }
 
             SAMFileWriter bamWriter = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(header, true, testBAMFile);
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java
index 70a6adc15..e3d871707 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
+import org.broadinstitute.gatk.engine.filters.ReadFilter;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
+import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.interval.IntervalMergingRule;
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -123,7 +123,7 @@ public class SAMDataSourceUnitTest extends BaseTest {
                 GenomeLoc firstLocus = sh.getGenomeLocs().get(0), lastLocus = sh.getGenomeLocs().get(sh.getGenomeLocs().size()-1);
                 logger.debug("Start : " + firstLocus.getStart() + " stop : " + lastLocus.getStop() + " contig " + firstLocus.getContig());
                 logger.debug("count = " + count);
-                StingSAMIterator datum = data.seek(sh);
+                GATKSAMIterator datum = data.seek(sh);
 
                 // for the first couple of shards make sure we can see the reads
                 if (count < 5) {
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java
index a594573e5..982b1aad7 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.Tags;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.Tags;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java
index 89989d834..c24a21a63 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import htsjdk.samtools.seekablestream.SeekableBufferedStream;
 import htsjdk.samtools.seekablestream.SeekableFileStream;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java
index 4a9f9e587..aa66f179f 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reads;
+package org.broadinstitute.gatk.engine.datasources.reads;
 
 import com.google.caliper.Param;
 import htsjdk.samtools.Cigar;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java
index 00d0dd051..8ffbb7d39 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.reference;
+package org.broadinstitute.gatk.engine.datasources.reference;
 
 import junit.framework.Assert;
-import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.Test;
 
 import java.io.File;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
index 6ef702a3b..baa2af098 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
@@ -23,19 +23,19 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.rmd;
+package org.broadinstitute.gatk.engine.datasources.rmd;
 
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder;
 import org.testng.Assert;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.codecs.table.TableFeature;
-import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.codecs.table.TableFeature;
+import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator;
+import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet;
+import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet.RMDStorageType;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 
 import static org.testng.Assert.assertTrue;
 import org.testng.annotations.BeforeMethod;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java
index 0a71486b2..6c403cd83 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.datasources.rmd;
+package org.broadinstitute.gatk.engine.datasources.rmd;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.refdata.utils.*;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.refdata.utils.*;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java
index bdfd0f4dc..2d86f73c4 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.downsampling;
+package org.broadinstitute.gatk.engine.downsampling;
 
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
 import htsjdk.samtools.SAMFileHeader;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java
index 85f9169da..2f171de0b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.downsampling;
+package org.broadinstitute.gatk.engine.downsampling;
 
-import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.Test;
 
 public class DownsamplingIntegrationTest extends WalkerTest {
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java
index bdd2cdcc4..19eec62cf 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.downsampling;
+package org.broadinstitute.gatk.engine.downsampling;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.ArtificialSingleSampleReadStream;
-import org.broadinstitute.sting.utils.sam.ArtificialSingleSampleReadStreamAnalyzer;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStream;
+import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStreamAnalyzer;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -68,7 +68,7 @@ public class DownsamplingReadsIteratorUnitTest extends BaseTest {
 
         public void run() {
             streamAnalyzer = new PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer(stream, targetCoverage);
-            downsamplingIter = new DownsamplingReadsIterator(stream.getStingSAMIterator(), new SimplePositionalDownsampler(targetCoverage));
+            downsamplingIter = new DownsamplingReadsIterator(stream.getGATKSAMIterator(), new SimplePositionalDownsampler(targetCoverage));
 
             streamAnalyzer.analyze(downsamplingIter);
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java
index 2f90e3aef..918537439 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.downsampling;
+package org.broadinstitute.gatk.engine.downsampling;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 import org.testng.Assert;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java
index 07a8a7975..2544b72fd 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.downsampling;
+package org.broadinstitute.gatk.engine.downsampling;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
 import org.testng.annotations.Test;
 import org.testng.annotations.DataProvider;
 import org.testng.Assert;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java
index c6103e7a1..2606a01d3 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java
@@ -23,21 +23,21 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.downsampling;
+package org.broadinstitute.gatk.engine.downsampling;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.sam.ArtificialMultiSampleReadStream;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.ArtificialSingleSampleReadStream;
-import org.broadinstitute.sting.utils.sam.ArtificialSingleSampleReadStreamAnalyzer;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
+import org.broadinstitute.gatk.engine.iterators.VerifyingSamIterator;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.sam.ArtificialMultiSampleReadStream;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStream;
+import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStreamAnalyzer;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -215,7 +215,7 @@ public class PerSampleDownsamplingReadsIteratorUnitTest extends BaseTest {
         }
 
         public void run() {
-            StingSAMIterator downsamplingIter = new PerSampleDownsamplingReadsIterator(mergedReadStream.getStingSAMIterator(), downsamplerFactory);
+            GATKSAMIterator downsamplingIter = new PerSampleDownsamplingReadsIterator(mergedReadStream.getGATKSAMIterator(), downsamplerFactory);
 
             if ( verifySortedness ) {
                 downsamplingIter = new VerifyingSamIterator(downsamplingIter);
@@ -230,7 +230,7 @@ public class PerSampleDownsamplingReadsIteratorUnitTest extends BaseTest {
                     analyzer.update(read);
                 }
                 else {
-                    throw new ReviewedStingException("bug: stream analyzer for sample " + sampleName + " not found");
+                    throw new ReviewedGATKException("bug: stream analyzer for sample " + sampleName + " not found");
                 }
             }
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java
index f4fad8e02..b8a57e791 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.downsampling;
+package org.broadinstitute.gatk.engine.downsampling;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.sam.ArtificialSingleSampleReadStream;
-import org.broadinstitute.sting.utils.sam.ArtificialSingleSampleReadStreamAnalyzer;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStream;
+import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStreamAnalyzer;
 
 /**
  * Class for analyzing an artificial read stream that has been positionally downsampled, and verifying
@@ -51,30 +51,30 @@ public class PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer ext
     public void validate() {
         if ( (originalStream.getNumContigs() == 0 || originalStream.getNumStacksPerContig() == 0) && originalStream.getNumUnmappedReads() == 0 ) {
             if ( totalReads != 0 ) {
-                throw new ReviewedStingException("got reads from the stream, but the stream was configured to have 0 reads");
+                throw new ReviewedGATKException("got reads from the stream, but the stream was configured to have 0 reads");
             }
             return;  // no further validation needed for the 0-reads case
         }
         else if ( totalReads == 0 ) {
-            throw new ReviewedStingException("got no reads from the stream, but the stream was configured to have > 0 reads");
+            throw new ReviewedGATKException("got no reads from the stream, but the stream was configured to have > 0 reads");
         }
 
         if ( ! allSamplesMatch ) {
-            throw new ReviewedStingException("some reads had the wrong sample");
+            throw new ReviewedGATKException("some reads had the wrong sample");
         }
 
         if ( numContigs != originalStream.getNumContigs() ) {
-            throw new ReviewedStingException("number of contigs not correct");
+            throw new ReviewedGATKException("number of contigs not correct");
         }
 
         if ( stacksPerContig.size() != originalStream.getNumContigs() ) {
-            throw new ReviewedStingException(String.format("bug in analyzer code: calculated sizes for %d contigs even though there were only %d contigs",
+            throw new ReviewedGATKException(String.format("bug in analyzer code: calculated sizes for %d contigs even though there were only %d contigs",
                                                            stacksPerContig.size(), originalStream.getNumContigs()));
         }
 
         for ( int contigStackCount : stacksPerContig ) {
             if ( contigStackCount != originalStream.getNumStacksPerContig() ) {
-                throw new ReviewedStingException("contig had incorrect number of stacks");
+                throw new ReviewedGATKException("contig had incorrect number of stacks");
             }
         }
 
@@ -85,43 +85,43 @@ public class PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer ext
             int stackMaximumAfterDownsampling = targetCoverage;
 
             if ( minReadsPerStack < stackMinimumAfterDownsampling ) {
-                throw new ReviewedStingException("stack had fewer than the minimum number of reads after downsampling");
+                throw new ReviewedGATKException("stack had fewer than the minimum number of reads after downsampling");
             }
             if ( maxReadsPerStack > stackMaximumAfterDownsampling ) {
-                throw new ReviewedStingException("stack had more than the maximum number of reads after downsampling");
+                throw new ReviewedGATKException("stack had more than the maximum number of reads after downsampling");
             }
         }
         else if ( minReadsPerStack != null || maxReadsPerStack != null ) {
-            throw new ReviewedStingException("bug in analyzer code: reads per stack was calculated even though 0 stacks per contig was specified");
+            throw new ReviewedGATKException("bug in analyzer code: reads per stack was calculated even though 0 stacks per contig was specified");
         }
 
         if ( originalStream.getNumStacksPerContig() > 1 ) {
             if ( minDistanceBetweenStacks < originalStream.getMinDistanceBetweenStacks() ) {
-                throw new ReviewedStingException("stacks were separated by less than the minimum distance");
+                throw new ReviewedGATKException("stacks were separated by less than the minimum distance");
             }
             if ( maxDistanceBetweenStacks > originalStream.getMaxDistanceBetweenStacks() ) {
-                throw new ReviewedStingException("stacks were separated by more than the maximum distance");
+                throw new ReviewedGATKException("stacks were separated by more than the maximum distance");
             }
         }
         else if ( minDistanceBetweenStacks != null || maxDistanceBetweenStacks != null ) {
-            throw new ReviewedStingException("bug in analyzer code: distance between stacks was calculated even though numStacksPerContig was <= 1");
+            throw new ReviewedGATKException("bug in analyzer code: distance between stacks was calculated even though numStacksPerContig was <= 1");
         }
 
         if ( minReadLength < originalStream.getMinReadLength() ) {
-            throw new ReviewedStingException("read was shorter than the minimum allowed length");
+            throw new ReviewedGATKException("read was shorter than the minimum allowed length");
         }
         if ( maxReadLength > originalStream.getMaxReadLength() ) {
-            throw new ReviewedStingException("read was longer than the maximum allowed length");
+            throw new ReviewedGATKException("read was longer than the maximum allowed length");
         }
 
         if ( numUnmappedReads != originalStream.getNumUnmappedReads() ) {
-            throw new ReviewedStingException(String.format("wrong number of unmapped reads: requested %d but saw %d",
+            throw new ReviewedGATKException(String.format("wrong number of unmapped reads: requested %d but saw %d",
                                                            originalStream.getNumUnmappedReads(), numUnmappedReads));
         }
 
         if ( (originalStream.getNumContigs() == 0 || originalStream.getNumStacksPerContig() == 0) &&
              numUnmappedReads != totalReads ) {
-            throw new ReviewedStingException("stream should have consisted only of unmapped reads, but saw some mapped reads");
+            throw new ReviewedGATKException("stream should have consisted only of unmapped reads, but saw some mapped reads");
         }
     }
 }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java
index ff1cfc63b..4e6f157f1 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.downsampling;
+package org.broadinstitute.gatk.engine.downsampling;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 import org.testng.Assert;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java
index 26839af4b..e04c347b3 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.downsampling;
+package org.broadinstitute.gatk.engine.downsampling;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 import org.testng.Assert;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java
index cc8965642..50f21a62e 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.executive;
+package org.broadinstitute.gatk.engine.executive;
 
 
 import org.testng.Assert;
@@ -31,7 +31,7 @@ import org.testng.annotations.AfterMethod;
 import org.testng.annotations.Test;
 import org.testng.annotations.BeforeMethod;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 
 import java.util.concurrent.Callable;
 import java.util.concurrent.Future;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java
index 728061b48..7a0122085 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.filters;
+package org.broadinstitute.gatk.engine.filters;
 
 
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
+import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java
index 403aa85a7..bdb194c6b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.filters;
+package org.broadinstitute.gatk.engine.filters;
 
 import htsjdk.samtools.Cigar;
-import org.broadinstitute.sting.utils.clipping.ReadClipperTestUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.clipping.ReadClipperTestUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java
index 12d875a4d..3ff8ed4dc 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.filters;
+package org.broadinstitute.gatk.engine.filters;
 
-import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.Test;
 
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java
index 43f51dcf0..d25db50e0 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java
@@ -23,23 +23,23 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.filters;
+package org.broadinstitute.gatk.engine.filters;
 
 
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.TextCigarCodec;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.exceptions.UserException.UnsupportedCigarOperatorException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException.UnsupportedCigarOperatorException;
 
 import java.lang.annotation.*;
 import java.lang.reflect.Method;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java
index 667082eb2..beb4123fe 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.filters;
+package org.broadinstitute.gatk.engine.filters;
 
 import htsjdk.samtools.Cigar;
-import org.broadinstitute.sting.utils.sam.CigarUtils;
+import org.broadinstitute.gatk.utils.sam.CigarUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java
index 0511b06dd..9a003d51d 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.filters;
+package org.broadinstitute.gatk.engine.filters;
 
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
-import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
+import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod;
+import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java
index 5c7c5b5ed..3a0fc6ebd 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.filters;
+package org.broadinstitute.gatk.engine.filters;
 
 import org.testng.Assert;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.annotations.Test;
 
 import htsjdk.samtools.SAMRecord;
@@ -39,18 +39,18 @@ import java.util.Collections;
 
 public class ReadGroupBlackListFilterUnitTest extends ReadFilterTest {
 
-    @Test(expectedExceptions=ReviewedStingException.class)
+    @Test(expectedExceptions=ReviewedGATKException.class)
     public void testBadFilter() {
         List badFilters = Collections.singletonList("bad");
         new ReadGroupBlackListFilter(badFilters);
     }
-    @Test(expectedExceptions=ReviewedStingException.class)
+    @Test(expectedExceptions=ReviewedGATKException.class)
     public void testBadFilterTag() {
         List badFilters = Collections.singletonList("bad:filter");
         new ReadGroupBlackListFilter(badFilters);
     }
 
-    @Test(expectedExceptions=ReviewedStingException.class)
+    @Test(expectedExceptions=ReviewedGATKException.class)
     public void testBadFilterFile() {
         List badFilters = Collections.singletonList("/foo/bar/rgbl.txt");
         new ReadGroupBlackListFilter(badFilters);
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java
index 30e2f0f1b..a00f0a0ba 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.filters;
+package org.broadinstitute.gatk.engine.filters;
 
 
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
+import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
 
 import java.util.Collections;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java
index 436101934..7c3aca2d1 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.gatk.engine.iterators;
 
 import static org.testng.Assert.fail;
 
@@ -31,11 +31,11 @@ import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
 
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 
 import org.testng.annotations.BeforeMethod;
 
@@ -118,7 +118,7 @@ public class BoundedReadIteratorUnitTest extends BaseTest {
     }
 }
 
-class testIterator implements StingSAMIterator {
+class testIterator implements GATKSAMIterator {
     SAMFileHeader header;
     testIterator() {
         header = ArtificialSAMUtils.createArtificialSamHeader(1,1,2000);
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java
index 0c109ba15..6cbd4fd1b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.gatk.engine.iterators;
 
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import static org.testng.Assert.assertEquals;
 import org.testng.annotations.Test;
 
@@ -55,11 +55,11 @@ import java.util.Iterator;
  * @version 1.0
  * @date May 13, 2009
  * 

- * Class StingSAMIteratorTest
+ * Class GATKSAMIteratorTest
  * 

- * Tests the StingSAMIteratorAdapter class.
+ * Tests the GATKSAMIteratorAdapter class.
  */
-public class StingSAMIteratorAdapterUnitTest extends BaseTest {
+public class GATKSAMIteratorAdapterUnitTest extends BaseTest {
 
     class MyTestIterator implements Iterator {
 
@@ -122,7 +122,7 @@ public class StingSAMIteratorAdapterUnitTest extends BaseTest {
         final int COUNT = 100;
         MyTestIterator it = new MyTestIterator();
 
-        StingSAMIterator samIt = StingSAMIteratorAdapter.adapt(it);
+        GATKSAMIterator samIt = GATKSAMIteratorAdapter.adapt(it);
         int countCheck = 0;
         while (samIt.hasNext()) {
             samIt.next();
@@ -141,7 +141,7 @@ public class StingSAMIteratorAdapterUnitTest extends BaseTest {
 
         MyTestCloseableIterator it = new MyTestCloseableIterator();
 
-        StingSAMIterator samIt = StingSAMIteratorAdapter.adapt(it);
+        GATKSAMIterator samIt = GATKSAMIteratorAdapter.adapt(it);
 
         int countCheck = 0;
         while (samIt.hasNext()) {
@@ -158,7 +158,7 @@ public class StingSAMIteratorAdapterUnitTest extends BaseTest {
 
         MyTestCloseableIterator it = new MyTestCloseableIterator();
         
-        StingSAMIterator samIt = StingSAMIteratorAdapter.adapt(it);
+        GATKSAMIterator samIt = GATKSAMIteratorAdapter.adapt(it);
 
 
         int countCheck = 0;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java
index 686142575..c926d066c 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.gatk.engine.iterators;
 
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
@@ -41,7 +41,7 @@ public class ReadFormattingIteratorUnitTest extends BaseTest {
         final Cigar unconsolidatedCigar = TextCigarCodec.getSingleton().decode("3M0M5M0M");
         final SAMRecord unconsolidatedRead = ArtificialSAMUtils.createArtificialRead(unconsolidatedCigar);
 
-        final StingSAMIterator readIterator = StingSAMIteratorAdapter.adapt(Arrays.asList(unconsolidatedRead).iterator());
+        final GATKSAMIterator readIterator = GATKSAMIteratorAdapter.adapt(Arrays.asList(unconsolidatedRead).iterator());
         final ReadFormattingIterator formattingIterator = new ReadFormattingIterator(readIterator, false, (byte)-1);
         final SAMRecord postIterationRead = formattingIterator.next();
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java
index 1c684403a..371f94f00 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.gatk.engine.iterators;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -64,7 +64,7 @@ public class VerifyingSamIteratorUnitTest {
         SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read2",getContig(0).getSequenceIndex(),2,10);
         List reads = Arrays.asList(read1,read2);
 
-        VerifyingSamIterator iterator = new VerifyingSamIterator(StingSAMIteratorAdapter.adapt(reads.iterator()));
+        VerifyingSamIterator iterator = new VerifyingSamIterator(GATKSAMIteratorAdapter.adapt(reads.iterator()));
 
         Assert.assertTrue(iterator.hasNext(),"Insufficient reads");
         Assert.assertSame(iterator.next(),read1,"Incorrect read in read 1 position");
@@ -79,7 +79,7 @@ public class VerifyingSamIteratorUnitTest {
         SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read2",getContig(1).getSequenceIndex(),1,10);
         List reads = Arrays.asList(read1,read2);
 
-        VerifyingSamIterator iterator = new VerifyingSamIterator(StingSAMIteratorAdapter.adapt(reads.iterator()));
+        VerifyingSamIterator iterator = new VerifyingSamIterator(GATKSAMIteratorAdapter.adapt(reads.iterator()));
 
         Assert.assertTrue(iterator.hasNext(),"Insufficient reads");
         Assert.assertSame(iterator.next(),read1,"Incorrect read in read 1 position");
@@ -94,7 +94,7 @@ public class VerifyingSamIteratorUnitTest {
         SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read2",getContig(0).getSequenceIndex(),1,10);
         List reads = Arrays.asList(read1,read2);
 
-        VerifyingSamIterator iterator = new VerifyingSamIterator(StingSAMIteratorAdapter.adapt(reads.iterator()));
+        VerifyingSamIterator iterator = new VerifyingSamIterator(GATKSAMIteratorAdapter.adapt(reads.iterator()));
 
         Assert.assertTrue(iterator.hasNext(),"Insufficient reads");
         Assert.assertSame(iterator.next(),read1,"Incorrect read in read 1 position");
@@ -112,7 +112,7 @@ public class VerifyingSamIteratorUnitTest {
         read1.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
         List reads = Arrays.asList(read1,read2);
 
-        VerifyingSamIterator iterator = new VerifyingSamIterator(StingSAMIteratorAdapter.adapt(reads.iterator()));
+        VerifyingSamIterator iterator = new VerifyingSamIterator(GATKSAMIteratorAdapter.adapt(reads.iterator()));
 
         Assert.assertTrue(iterator.hasNext(),"Insufficient reads");
         Assert.assertSame(iterator.next(),read1,"Incorrect read in read 1 position");
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java
index e62020215..d7b9b3dda 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java
@@ -23,24 +23,24 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.phonehome;
+package org.broadinstitute.gatk.engine.phonehome;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.qc.CountLoci;
-import org.broadinstitute.sting.gatk.walkers.qc.CountRODs;
-import org.broadinstitute.sting.gatk.walkers.qc.CountReads;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
-import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker;
+import org.broadinstitute.gatk.engine.walkers.Walker;
+import org.broadinstitute.gatk.tools.walkers.qc.CountLoci;
+import org.broadinstitute.gatk.tools.walkers.qc.CountRODs;
+import org.broadinstitute.gatk.tools.walkers.qc.CountReads;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.activeregion.ActiveRegion;
+import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.jets3t.service.S3Service;
 import org.jets3t.service.S3ServiceException;
 import org.jets3t.service.ServiceException;
@@ -116,7 +116,7 @@ public class GATKRunReportUnitTest extends BaseTest {
 
         final Exception noException = null;
         final Exception javaException = new IllegalArgumentException("javaException");
-        final Exception stingException = new ReviewedStingException("StingException");
+        final Exception stingException = new ReviewedGATKException("GATKException");
         final Exception userException = new UserException("userException");
 
         final GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTrackerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTrackerUnitTest.java
index 112f869de..f25ab8d58 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTrackerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTrackerUnitTest.java
@@ -23,21 +23,21 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.refdata;
+package org.broadinstitute.gatk.engine.refdata;
 
 import htsjdk.samtools.SAMFileHeader;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.codecs.table.TableFeature;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.utils.codecs.table.TableFeature;
+import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature;
+import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManagerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManagerUnitTest.java
index ac17ec8ed..ec3b470f8 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManagerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManagerUnitTest.java
@@ -23,20 +23,20 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.refdata.tracks;
+package org.broadinstitute.gatk.engine.refdata.tracks;
 
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.FeatureCodec;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.codecs.table.BedTableCodec;
-import org.broadinstitute.sting.utils.codecs.table.TableFeature;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.codecs.table.BedTableCodec;
+import org.broadinstitute.gatk.utils.codecs.table.TableFeature;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
 import htsjdk.variant.vcf.VCF3Codec;
 import htsjdk.variant.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import htsjdk.variant.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java
index 5f399c9a6..ec12f7df8 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.refdata.tracks;
+package org.broadinstitute.gatk.engine.refdata.tracks;
 
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
@@ -31,11 +31,11 @@ import htsjdk.tribble.Tribble;
 import htsjdk.tribble.index.Index;
 import htsjdk.tribble.util.LittleEndianOutputStream;
 import htsjdk.variant.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.Assert;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 
 import org.testng.annotations.BeforeMethod;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/CheckableCloseableTribbleIterator.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/CheckableCloseableTribbleIterator.java
index 80978171e..e77c0797e 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/CheckableCloseableTribbleIterator.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/CheckableCloseableTribbleIterator.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.refdata.utils;
+package org.broadinstitute.gatk.engine.refdata.utils;
 
 import htsjdk.tribble.CloseableTribbleIterator;
 import htsjdk.tribble.Feature;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java
index ef5e66640..d95c320cb 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.refdata.utils;
+package org.broadinstitute.gatk.engine.refdata.utils;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
 import htsjdk.variant.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIteratorUnitTest.java
index a7d30e8cc..7aa07ef58 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIteratorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIteratorUnitTest.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.refdata.utils;
+package org.broadinstitute.gatk.engine.refdata.utils;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMSequenceDictionary;
 import org.testng.Assert;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 
 import org.testng.annotations.BeforeMethod;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestFeatureReader.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestFeatureReader.java
index f8c1ccb00..90b5e7a35 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestFeatureReader.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestFeatureReader.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.refdata.utils;
+package org.broadinstitute.gatk.engine.refdata.utils;
 
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.FeatureCodec;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestRMDTrackBuilder.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestRMDTrackBuilder.java
index d6cdc144f..17179f3ba 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestRMDTrackBuilder.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestRMDTrackBuilder.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.refdata.utils;
+package org.broadinstitute.gatk.engine.refdata.utils;
 
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.tribble.FeatureCodec;
 import htsjdk.tribble.Tribble;
 import htsjdk.tribble.index.Index;
-import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
-import org.broadinstitute.sting.gatk.refdata.tracks.IndexDictionaryUtils;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager;
+import org.broadinstitute.gatk.engine.refdata.tracks.IndexDictionaryUtils;
+import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack;
+import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
 
 import java.io.File;
 import java.io.IOException;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/report/GATKReportUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/report/GATKReportUnitTest.java
index b746a283d..c28e901d2 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/report/GATKReportUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/report/GATKReportUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.report;
+package org.broadinstitute.gatk.engine.report;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java
index 696eeefcc..cd6014bcd 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.samples;
+package org.broadinstitute.gatk.engine.samples;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java
index a632be407..fc934ef06 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.samples;
+package org.broadinstitute.gatk.engine.samples;
 
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java
index 227d365de..b1b09db01 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.samples;
+package org.broadinstitute.gatk.engine.samples;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java
index e2cad88a1..e1d81b587 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.traversals;
+package org.broadinstitute.gatk.engine.traversals;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
-import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocSortedSet;
+import org.broadinstitute.gatk.utils.activeregion.ActiveRegion;
+import org.broadinstitute.gatk.utils.activeregion.ActiveRegionReadState;
+import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState;
 
 import java.util.*;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java
index e7adc4bea..8206eb506 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java
@@ -23,13 +23,13 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.traversals;
+package org.broadinstitute.gatk.engine.traversals;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.sam.ArtificialBAMBuilder;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.sam.ArtificialBAMBuilder;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java
index f1ca2562c..42c458f91 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java
@@ -23,33 +23,33 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.traversals;
+package org.broadinstitute.gatk.engine.traversals;
 
 import com.google.java.contract.PreconditionError;
 import htsjdk.samtools.*;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.datasources.reads.*;
-import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
-import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
-import org.broadinstitute.sting.utils.sam.*;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
+import org.broadinstitute.gatk.engine.datasources.reads.*;
+import org.broadinstitute.gatk.engine.filters.ReadFilter;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
+import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation;
+import org.broadinstitute.gatk.engine.walkers.Walker;
+import org.broadinstitute.gatk.utils.GenomeLocSortedSet;
+import org.broadinstitute.gatk.utils.SampleUtils;
+import org.broadinstitute.gatk.utils.activeregion.ActiveRegionReadState;
+import org.broadinstitute.gatk.utils.interval.IntervalMergingRule;
+import org.broadinstitute.gatk.utils.interval.IntervalUtils;
+import org.broadinstitute.gatk.utils.sam.*;
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.executive.WindowMaker;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.datasources.providers.LocusShardDataProvider;
+import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.gatk.engine.executive.WindowMaker;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.activeregion.ActiveRegion;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -57,7 +57,6 @@ import org.testng.annotations.Test;
 
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.*;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java
index 9cb14275a..a332be127 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.traversals;
+package org.broadinstitute.gatk.engine.traversals;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
 import org.testng.Assert;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 
 import org.testng.annotations.BeforeMethod;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java
index 1b73ddd02..70336a26d 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.traversals;
+package org.broadinstitute.gatk.engine.traversals;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
-import org.broadinstitute.sting.gatk.datasources.reads.*;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.qc.CountReads;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.datasources.providers.ReadShardDataProvider;
+import org.broadinstitute.gatk.engine.datasources.reads.*;
+import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation;
+import org.broadinstitute.gatk.engine.walkers.ReadWalker;
+import org.broadinstitute.gatk.tools.walkers.qc.CountReads;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java
index f40504fc4..3e5468002 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting;
+package org.broadinstitute.gatk.engine.walkers;
 
 import org.apache.commons.lang.StringUtils;
 import htsjdk.tribble.Tribble;
@@ -31,17 +31,20 @@ import htsjdk.tribble.index.Index;
 import htsjdk.tribble.index.IndexFactory;
 import htsjdk.tribble.index.tabix.TabixFormat;
 import htsjdk.tribble.util.TabixUtils;
-import org.broadinstitute.sting.gatk.CommandLineExecutable;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.MD5DB;
+import org.broadinstitute.gatk.utils.MD5Mismatch;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.classloader.JVMUtils;
+import org.broadinstitute.gatk.engine.CommandLineExecutable;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.phonehome.GATKRunReport;
 import htsjdk.variant.bcf2.BCF2Utils;
-import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.collections.Pair;
 import htsjdk.variant.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
 import org.testng.Assert;
 import org.testng.annotations.AfterSuite;
 import org.testng.annotations.BeforeMethod;
@@ -98,7 +101,7 @@ public class WalkerTest extends BaseTest {
         if ( indexFile.exists() ) {
             if ( resultFile.getAbsolutePath().contains(".vcf") ) {
                 // todo -- currently we only understand VCF files! Blow up since we can't test them
-                throw new StingException("Found an index created for file " + resultFile + " but we can only validate VCF files.  Extend this code!");
+                throw new GATKException("Found an index created for file " + resultFile + " but we can only validate VCF files.  Extend this code!");
             }
 
             System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
@@ -253,7 +256,7 @@ public class WalkerTest extends BaseTest {
         }
 
         public Class getExpectedException() {
-            if ( ! expectsException() ) throw new ReviewedStingException("Tried to get expection for walker test that doesn't expect one");
+            if ( ! expectsException() ) throw new ReviewedGATKException("Tried to get expection for walker test that doesn't expect one");
             return expectedException;
         }
 
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 cfa3da8c8..849267317 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
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.tools;
+package org.broadinstitute.gatk.tools;
 
 import org.apache.commons.lang.StringUtils;
 import htsjdk.tribble.AbstractFeatureReader;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.MD5DB;
-import org.broadinstitute.sting.MD5Mismatch;
-import org.broadinstitute.sting.utils.runtime.ProcessController;
-import org.broadinstitute.sting.utils.runtime.ProcessSettings;
-import org.broadinstitute.sting.utils.runtime.RuntimeUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.MD5DB;
+import org.broadinstitute.gatk.utils.MD5Mismatch;
+import org.broadinstitute.gatk.utils.runtime.ProcessController;
+import org.broadinstitute.gatk.utils.runtime.ProcessSettings;
+import org.broadinstitute.gatk.utils.runtime.RuntimeUtils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
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 604c0e377..68451ef49 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.gatk.tools.walkers;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
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 bfabe2bc1..16e47cda5 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.CNV;
+package org.broadinstitute.gatk.tools.walkers.CNV;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
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 24a274cee..ec10d7d02 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
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
 /**
  * Created with IntelliJ IDEA.
@@ -34,7 +34,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
  */
 
 
-import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff.EffectType;
+import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff.EffectType;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
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 5392e8037..b7d85ab58 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.coverage;
+package org.broadinstitute.gatk.tools.walkers.coverage;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
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 d3d3c2b38..ccfd743ee 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.coverage;
+package org.broadinstitute.gatk.tools.walkers.coverage;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
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 8afb7e2e8..af74beec6 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.coverage;
+package org.broadinstitute.gatk.tools.walkers.coverage;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.io.File;
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 ebaec3396..5b3f8595a 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.coverage;
+package org.broadinstitute.gatk.tools.walkers.coverage;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.io.File;
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 0971cb90b..eae4decad 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
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
 import org.testng.annotations.Test;
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 
 import java.util.Collections;
 
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 8f5541c41..e79edfdde 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
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 a813fada2..69e623e5e 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
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.Test;
 
 /**
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 e8a69cfc9..7a8868198 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
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 6141a484c..38154bd6d 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.qc;
+package org.broadinstitute.gatk.tools.walkers.qc;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
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 b3d583ef1..29f4621f0 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.readutils;
+package org.broadinstitute.gatk.tools.walkers.readutils;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.io.File;
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 adc7ad765..5f8be81a1 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.readutils;
+package org.broadinstitute.gatk.tools.walkers.readutils;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
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 63c0f2db7..956d70f61 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.readutils;
+package org.broadinstitute.gatk.tools.walkers.readutils;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.util.ArrayList;
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 bbf365769..53b6d42d6 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
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.readutils;
+package org.broadinstitute.gatk.tools.walkers.readutils;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.sam.ArtificialReadsTraversal;
-import org.broadinstitute.sting.utils.sam.ArtificialStingSAMFileWriter;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.utils.sam.ArtificialReadsTraversal;
+import org.broadinstitute.gatk.utils.sam.ArtificialGATKSAMFileWriter;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -84,16 +84,16 @@ public class PrintReadsUnitTest extends BaseTest {
     private ReferenceContext bases = null;
     //private ReferenceContext ref = new ReferenceContext()
 
-    org.broadinstitute.sting.gatk.walkers.readutils.PrintReads walker;
-    ArtificialStingSAMFileWriter writer;
+    org.broadinstitute.gatk.tools.walkers.readutils.PrintReads walker;
+    ArtificialGATKSAMFileWriter writer;
 
     @BeforeMethod
     public void before() {
         trav = new ArtificialReadsTraversal();
         readTotal = ( ( trav.endingChr - trav.startingChr ) + 1 ) * trav.readsPerChr + trav.unMappedReads;
 
-        walker = new org.broadinstitute.sting.gatk.walkers.readutils.PrintReads();
-        writer = new ArtificialStingSAMFileWriter();
+        walker = new org.broadinstitute.gatk.tools.walkers.readutils.PrintReads();
+        writer = new ArtificialGATKSAMFileWriter();
         walker.initialize();
     }
 
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 3b184ae3b..65ca2e7f7 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.readutils;
+package org.broadinstitute.gatk.tools.walkers.readutils;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
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 eae6d31b3..847c8f1c6 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
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
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 2a8104b61..117f50714 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
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.Utils;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java
index 8bedfb547..22e9517c8 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.AutoFormattingTime;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.AutoFormattingTime;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
index c2c28e0f1..28462ea98 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting;
+package org.broadinstitute.gatk.utils;
 
 import org.apache.log4j.AppenderSkeleton;
 import org.apache.log4j.Level;
@@ -32,12 +32,12 @@ import org.apache.log4j.PatternLayout;
 import org.apache.log4j.spi.LoggingEvent;
 import htsjdk.tribble.readers.LineIterator;
 import htsjdk.tribble.readers.PositionalBufferedStream;
-import org.broadinstitute.sting.commandline.CommandLineUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.crypt.CryptUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.io.IOUtils;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.commandline.CommandLineUtils;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.crypt.CryptUtils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.io.IOUtils;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
 import htsjdk.variant.bcf2.BCF2Codec;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
@@ -82,7 +82,7 @@ import java.util.*;
  */
 @SuppressWarnings("unchecked")
 public abstract class BaseTest {
-    /** our log, which we want to capture anything from org.broadinstitute.sting */
+    /** our log, which we want to capture anything from org.broadinstitute.gatk */
     public static final Logger logger = CommandLineUtils.getStingLogger();
 
     public static final String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
@@ -292,7 +292,7 @@ public abstract class BaseTest {
             file.deleteOnExit();
             return file;
         } catch (IOException ex) {
-            throw new ReviewedStingException("Cannot create temp file: " + ex.getMessage(), ex);
+            throw new ReviewedGATKException("Cannot create temp file: " + ex.getMessage(), ex);
         }
     }
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java
index 4b25d1d97..45e84974d 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java
@@ -23,10 +23,10 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java
index 7afe7343d..87a5914a3 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java
index 409c5d97f..87aa4944a 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting;
+package org.broadinstitute.gatk.utils;
 
 
 // the imports for unit testing.
@@ -33,23 +33,17 @@ import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
-import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
-import org.broadinstitute.sting.utils.sam.ArtificialBAMBuilder;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.gatk.utils.sam.ArtificialBAMBuilder;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
-import htsjdk.variant.vcf.VCFCodec;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java
index 58f0024db..957ccd2f9 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting;
+package org.broadinstitute.gatk.utils;
 
 import org.testng.reporters.TextReporter;
 
@@ -34,8 +34,8 @@ import org.testng.reporters.TextReporter;
  * @author hanna
  * @version 0.1
  */
-public class StingTextReporter extends TextReporter {
-    public StingTextReporter() {
-        super("Ant suite",2);
+public class GATKTextReporter extends TextReporter {
+    public GATKTextReporter() {
+        super("GATK test suite",2);
     }
 }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java
index bd6adb7c7..98044882d 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java
@@ -23,12 +23,12 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import com.google.caliper.Param;
 import com.google.caliper.SimpleBenchmark;
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 
 import java.io.File;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java
index 21a4f09e6..d413633b6 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 
 import htsjdk.samtools.SAMFileHeader;
@@ -31,12 +31,12 @@ import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
 import htsjdk.tribble.BasicFeature;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
@@ -111,7 +111,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
         assertEquals(0, "chr1".compareTo(genomeLocParser.getContigInfo("chr1").getSequenceName())); // should be in the reference
     }
 
-    @Test(expectedExceptions=ReviewedStingException.class)
+    @Test(expectedExceptions=ReviewedGATKException.class)
     public void testParseBadString() {
         genomeLocParser.parseGenomeLoc("Bad:0-1");
     }
@@ -206,7 +206,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
         assertEquals(loc.getStart(), 1);
     }
 
-    @Test(expectedExceptions=ReviewedStingException.class)
+    @Test(expectedExceptions=ReviewedGATKException.class)
     public void testGenomeLocParseOnlyBadChrome() {
         GenomeLoc loc = genomeLocParser.parseGenomeLoc("chr12");
         assertEquals(loc.getContigIndex(), 0);
@@ -214,7 +214,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
         assertEquals(loc.getStart(), 1);
     }
 
-    @Test(expectedExceptions=ReviewedStingException.class)
+    @Test(expectedExceptions=ReviewedGATKException.class)
     public void testGenomeLocBad() {
         GenomeLoc loc = genomeLocParser.parseGenomeLoc("chr1:1-");
         assertEquals(loc.getContigIndex(), 0);
@@ -252,7 +252,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
         assertTrue(!genomeLocParser.isValidGenomeLoc("chr1",2,1)); // stop < start
     }
 
-    @Test(expectedExceptions = ReviewedStingException.class)
+    @Test(expectedExceptions = ReviewedGATKException.class)
     public void testValidateGenomeLoc() {
         // bad contig index
         genomeLocParser.validateGenomeLoc("chr1", 1, 1, 2, false);
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java
index 2801ac7ba..655312056 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java
index 42def9fb7..ae86ca5a5 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 
 // the imports for unit testing.
@@ -31,12 +31,12 @@ package org.broadinstitute.sting.utils;
 
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.interval.IntervalMergingRule;
+import org.broadinstitute.gatk.utils.interval.IntervalUtils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -324,7 +324,7 @@ public class GenomeLocUnitTest extends BaseTest {
         testMerge(test.locs);
     }
 
-    @Test(expectedExceptions = ReviewedStingException.class)
+    @Test(expectedExceptions = ReviewedGATKException.class)
     public void testNotContiguousLocs() {
         final List locs = new ArrayList(1);
         locs.add(loc1);
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
index 4c0f8b11a..81c532434 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
@@ -23,13 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting;
+package org.broadinstitute.gatk.utils;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.walkers.diffengine.DiffEngine;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.walkers.diffengine.DiffEngine;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.*;
 import java.util.Arrays;
@@ -71,7 +70,7 @@ public class MD5DB {
             md5MismatchStream = new PrintStream(new FileOutputStream(MD5MismatchesFile));
             md5MismatchStream.printf("%s\t%s\t%s%n", "expected", "observed", "test");
         } catch ( FileNotFoundException e ) {
-            throw new ReviewedStingException("Failed to open md5 mismatch file", e);
+            throw new ReviewedGATKException("Failed to open md5 mismatch file", e);
         }
 
     }
@@ -101,7 +100,7 @@ public class MD5DB {
                 // within the same working directory, and another GATK instance may have come along and created the
                 // directory between the calls to exists() and mkdir() above.
                 if ( ! dir.exists() ) {
-                    throw new ReviewedStingException("Infrastructure failure: failed to create md5 directory " + LOCAL_MD5_DB_DIR);
+                    throw new ReviewedGATKException("Infrastructure failure: failed to create md5 directory " + LOCAL_MD5_DB_DIR);
                 }
             }
         }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java
index 56acedaf0..11064d109 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting;
+package org.broadinstitute.gatk.utils;
 
 import java.util.Collections;
 import java.util.List;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java
index f94f5178b..000984ea7 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java
@@ -23,18 +23,18 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -83,13 +83,13 @@ public class MRUCachingSAMSequencingDictionaryUnitTest extends BaseTest {
         }
     }
 
-    @Test(expectedExceptions = ReviewedStingException.class)
+    @Test(expectedExceptions = ReviewedGATKException.class)
     public void testBadGetSequence() {
         final MRUCachingSAMSequenceDictionary caching = new MRUCachingSAMSequenceDictionary(dict);
         caching.getSequence("notInDictionary");
     }
 
-    @Test(expectedExceptions = ReviewedStingException.class)
+    @Test(expectedExceptions = ReviewedGATKException.class)
     public void testBadGetSequenceIndex() {
         final MRUCachingSAMSequenceDictionary caching = new MRUCachingSAMSequenceDictionary(dict);
         caching.getSequence(dict.getSequences().size());
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java
index 312e4d5b1..c148dc92b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.collections.Pair;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java
index 1bcf38d10..4e2fd31d4 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import cern.jet.random.Normal;
 import org.apache.commons.lang.ArrayUtils;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java
index ce32e4ef8..21f3d898b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 
 // the imports for unit testing.
 
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java
index f07d38f72..7bdc653ab 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 
 // the imports for unit testing.
@@ -32,10 +32,10 @@ package org.broadinstitute.sting.utils;
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java
index 066d5905a..00cc0dc20 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -54,7 +54,7 @@ public class PathUtilsUnitTest extends BaseTest {
 
         try {
             PathUtils.refreshVolume(new File(filename));
-        } catch (ReviewedStingException e) {
+        } catch (ReviewedGATKException e) {
             result = false;
         }
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java
index c8cbeeaf2..86b436bd9 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 /**
  * Created by IntelliJ IDEA.
@@ -31,7 +31,7 @@ package org.broadinstitute.sting.utils;
  * Date: 3/21/12
  */
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java
index 4d68fb255..7a56b99de 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.R;
+package org.broadinstitute.gatk.utils.R;
 
 import org.apache.commons.io.FileUtils;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.io.IOUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.io.IOUtils;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java
index 08d1ccc34..b89686cbe 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.R;
+package org.broadinstitute.gatk.utils.R;
 
 import org.apache.commons.io.FileUtils;
 import org.testng.Assert;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java
index 7b1419e14..51ab6f79c 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.R;
+package org.broadinstitute.gatk.utils.R;
 
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SampleUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SampleUtilsUnitTest.java
index 2377d221c..6112d8dfe 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SampleUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SampleUtilsUnitTest.java
@@ -24,13 +24,13 @@
 */
 
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import org.apache.commons.io.FileUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.io.IOUtils;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.io.IOUtils;
 import org.testng.Assert;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java
index 36c95fd0d..6ccb0c976 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java
@@ -23,20 +23,20 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 import org.testng.Assert;
 
-import static org.broadinstitute.sting.utils.SequenceDictionaryUtils.*;
-import static org.broadinstitute.sting.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility.*;
+import static org.broadinstitute.gatk.utils.SequenceDictionaryUtils.*;
+import static org.broadinstitute.gatk.utils.SequenceDictionaryUtils.SequenceDictionaryCompatibility.*;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java
index 85b79a00f..85aec815e 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java
index ae7e41dfe..e804e70d9 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting;
+package org.broadinstitute.gatk.utils;
 
 import org.apache.log4j.Logger;
 import org.testng.IAnnotationTransformer;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java
index 9bcbee7aa..9c4027995 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import org.apache.commons.io.FileUtils;
-import org.broadinstitute.sting.utils.io.IOUtils;
+import org.broadinstitute.gatk.utils.io.IOUtils;
 import org.testng.Assert;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java
index bf94f85ae..7cfce8d37 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.activeregion;
+package org.broadinstitute.gatk.utils.activeregion;
 
 
 // the imports for unit testing.
@@ -31,13 +31,13 @@ package org.broadinstitute.sting.utils.activeregion;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.GenomeLocSortedSet;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java
index 76e04b1f6..75e9d9a37 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.activeregion;
+package org.broadinstitute.gatk.utils.activeregion;
 
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java
index 0c6d7a199..d450312e8 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java
@@ -23,19 +23,19 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.activeregion;
+package org.broadinstitute.gatk.utils.activeregion;
 
 
 // the imports for unit testing.
 
 
 import htsjdk.samtools.reference.ReferenceSequenceFile;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java
index 615b5552e..abf599a50 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.activeregion;
+package org.broadinstitute.gatk.utils.activeregion;
 
 
 // the imports for unit testing.
@@ -32,13 +32,13 @@ package org.broadinstitute.sting.utils.activeregion;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import org.apache.commons.lang.ArrayUtils;
 import htsjdk.tribble.readers.LineIterator;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFCodec;
 import htsjdk.variant.vcf.VCFHeader;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java
index 054d0d5e7..7ea26ee07 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.baq;
+package org.broadinstitute.gatk.utils.baq;
 
 
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.BeforeMethod;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.Utils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java
index 6ffd47f37..c232e1c12 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.classloader;
+package org.broadinstitute.gatk.utils.classloader;
 
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java
index 295d0137c..8ce0a9ebe 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.clipping;
+package org.broadinstitute.gatk.utils.clipping;
 
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
 import htsjdk.samtools.TextCigarCodec;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.CigarUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.CigarUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 
 import java.util.LinkedList;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java
index 7e9ba843e..400e9846b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.clipping;
+package org.broadinstitute.gatk.utils.clipping;
 
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.sam.CigarUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.sam.CigarUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java
index 9f5eb5fb8..0ff50d726 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.codecs.hapmap;
+package org.broadinstitute.gatk.utils.codecs.hapmap;
 
 import htsjdk.tribble.annotation.Strand;
 import htsjdk.tribble.readers.LineIterator;
 import htsjdk.tribble.readers.LineIteratorImpl;
 import htsjdk.tribble.readers.LineReaderUtil;
 import htsjdk.tribble.readers.PositionalBufferedStream;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java
index 176b462fc..a87aebacc 100755
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.collections;
+package org.broadinstitute.gatk.utils.collections;
 
 
 // the imports for unit testing.
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java
index 27ff5db0c..7f9d80861 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.collections;
+package org.broadinstitute.gatk.utils.collections;
 
 
 // the imports for unit testing.
@@ -33,7 +33,7 @@ import org.testng.Assert;
 import org.testng.annotations.Test;
 import org.testng.annotations.BeforeMethod;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 
 import java.util.Arrays;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java
index bb8c5be94..b1ba78416 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import org.testng.Assert;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java
index 070ca6e57..8837f4b5d 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptorUnitTest.java
index 908722909..a23c5c53e 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptorUnitTest.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import htsjdk.variant.variantcontext.VariantContext;
 import it.unimi.dsi.fastutil.objects.ObjectArrayList;
 import htsjdk.samtools.SAMFileWriter;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.io.stubs.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.io.stubs.*;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
@@ -166,7 +166,7 @@ public class ArgumentTypeDescriptorUnitTest extends BaseTest {
                 Assert.assertEquals(!provided, outputIsStdout(argumentSource.getOut()));
 
         } catch (Exception e) {
-            throw new ReviewedStingException(e.getMessage());
+            throw new ReviewedGATKException(e.getMessage());
         }
     }
 
@@ -186,14 +186,14 @@ public class ArgumentTypeDescriptorUnitTest extends BaseTest {
                     new Tags(),
                     "variantTest");
             if (!(result instanceof RodBindingCollection))
-                throw new ReviewedStingException("getRodBindingsCollection did not return a RodBindingCollection");
+                throw new ReviewedGATKException("getRodBindingsCollection did not return a RodBindingCollection");
             RodBindingCollection rbc = (RodBindingCollection) result;
 
             Assert.assertEquals(rbc.getType(), VariantContext.class);
             Assert.assertEquals(rbc.getRodBindings().size(), 1);
 
         } catch (IOException e) {
-            throw new ReviewedStingException(e.getMessage(), e);
+            throw new ReviewedGATKException(e.getMessage(), e);
         }
 
         //The same file, now with an extra blank line
@@ -207,14 +207,14 @@ public class ArgumentTypeDescriptorUnitTest extends BaseTest {
                     new Tags(),
                     "variantTest");
             if (!(result instanceof RodBindingCollection))
-                throw new ReviewedStingException("getRodBindingsCollection did not return a RodBindingCollection");
+                throw new ReviewedGATKException("getRodBindingsCollection did not return a RodBindingCollection");
             RodBindingCollection rbc = (RodBindingCollection) result;
 
             Assert.assertEquals(rbc.getType(), VariantContext.class);
             Assert.assertEquals(rbc.getRodBindings().size(), 1);
 
         } catch (IOException e) {
-            throw new ReviewedStingException(e.getMessage(), e);
+            throw new ReviewedGATKException(e.getMessage(), e);
         }
     }
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/InvalidArgumentIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/InvalidArgumentIntegrationTest.java
index f264cd46e..8ab2159d6 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/InvalidArgumentIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/InvalidArgumentIntegrationTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import org.testng.annotations.Test;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/LoggingIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/LoggingIntegrationTest.java
index fdf0ae0ea..d690f681c 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/LoggingIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/LoggingIntegrationTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import java.io.File;
 import java.io.IOException;
@@ -36,11 +36,11 @@ import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.MD5DB;
-import org.broadinstitute.sting.MD5Mismatch;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.utils.runtime.*;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.MD5DB;
+import org.broadinstitute.gatk.utils.MD5Mismatch;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.utils.runtime.*;
 
 public class LoggingIntegrationTest {
     private final MD5DB md5db = new MD5DB();
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java
index daa0651e7..35c6ac17b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
 import org.apache.commons.io.FileUtils;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import htsjdk.variant.variantcontext.VariantContext;
 import org.testng.Assert;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -379,7 +379,7 @@ public class ParsingEngineUnitTest extends BaseTest {
         parsingEngine.validate();
     }
 
-    @Test(expectedExceptions= ReviewedStingException.class)
+    @Test(expectedExceptions= ReviewedGATKException.class)
     public void duplicateLongNameTest() {
         parsingEngine.addArgumentSource( DuplicateLongNameProvider.class );
     }
@@ -392,7 +392,7 @@ public class ParsingEngineUnitTest extends BaseTest {
         public Integer bar;
     }
 
-    @Test(expectedExceptions= ReviewedStingException.class)
+    @Test(expectedExceptions= ReviewedGATKException.class)
     public void duplicateShortNameTest() {
         parsingEngine.addArgumentSource( DuplicateShortNameProvider.class );
     }
@@ -620,7 +620,7 @@ public class ParsingEngineUnitTest extends BaseTest {
         RequiredArgProvider rap = new RequiredArgProvider();
     }
 
-    @Test(expectedExceptions= ReviewedStingException.class)
+    @Test(expectedExceptions= ReviewedGATKException.class)
     public void multipleArgumentCollectionTest() {
         parsingEngine.addArgumentSource( MultipleArgumentCollectionProvider.class );
     }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java
index a5217cf73..b6e67a961 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import htsjdk.variant.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java
index 9ca0bde78..bffb1d2cf 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.commandline;
+package org.broadinstitute.gatk.utils.commandline;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import htsjdk.variant.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/CryptUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/CryptUtilsUnitTest.java
index a2fdef51b..c44bfdc03 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/CryptUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/CryptUtilsUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.crypt;
+package org.broadinstitute.gatk.utils.crypt;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.SkipException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -59,7 +59,7 @@ public class CryptUtilsUnitTest extends BaseTest {
         };
     }
 
-    @Test( dataProvider = "InvalidKeyPairSettings", expectedExceptions = ReviewedStingException.class )
+    @Test( dataProvider = "InvalidKeyPairSettings", expectedExceptions = ReviewedGATKException.class )
     public void testGenerateKeyPairWithInvalidSettings( int keyLength, String encryptionAlgorithm, String randomNumberGenerationAlgorithm ) {
         KeyPair keyPair = CryptUtils.generateKeyPair(keyLength, encryptionAlgorithm, randomNumberGenerationAlgorithm);
     }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyIntegrationTest.java
index ca7314ca9..9cafd61a7 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyIntegrationTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.crypt;
+package org.broadinstitute.gatk.utils.crypt;
 
-import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.engine.phonehome.GATKRunReport;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyUnitTest.java
index e8a5894e1..5fd6475ce 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.crypt;
+package org.broadinstitute.gatk.utils.crypt;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.SkipException;
 import org.testng.annotations.Test;
 import org.testng.Assert;
@@ -70,7 +70,7 @@ public class GATKKeyUnitTest extends BaseTest {
         Assert.assertTrue(key.isValid());
     }
 
-    @Test( expectedExceptions = ReviewedStingException.class )
+    @Test( expectedExceptions = ReviewedGATKException.class )
     public void testKeyPairMismatch() {
         KeyPair firstKeyPair = CryptUtils.generateKeyPair();
         KeyPair secondKeyPair = CryptUtils.generateKeyPair();
@@ -80,7 +80,7 @@ public class GATKKeyUnitTest extends BaseTest {
         GATKKey key = new GATKKey(firstKeyPair.getPrivate(), secondKeyPair.getPublic(), "foo@bar.com");
     }
 
-    @Test( expectedExceptions = ReviewedStingException.class )
+    @Test( expectedExceptions = ReviewedGATKException.class )
     public void testEncryptionAlgorithmMismatch() {
         KeyPair keyPair = CryptUtils.generateKeyPair(CryptUtils.DEFAULT_KEY_LENGTH, "DSA", CryptUtils.DEFAULT_RANDOM_NUMBER_GENERATION_ALGORITHM);
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
index 89f5733c2..3e877b900 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.fasta;
+package org.broadinstitute.gatk.utils.fasta;
 
 
 // the imports for unit testing.
@@ -34,8 +34,8 @@ import htsjdk.samtools.reference.ReferenceSequence;
 import htsjdk.samtools.SAMSequenceRecord;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Priority;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java
index 5c0eec252..63d98a277 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.file;
+package org.broadinstitute.gatk.utils.file;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.Test;
 
 import java.io.File;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java
index 563ff5a66..f388d14ef 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.fragments;
+package org.broadinstitute.gatk.utils.fragments;
 
 import com.google.caliper.Param;
 import com.google.caliper.SimpleBenchmark;
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java
index 01205a48e..f9f9ba441 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java
@@ -23,19 +23,19 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.fragments;
+package org.broadinstitute.gatk.utils.fragments;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.TextCigarCodec;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
-import org.broadinstitute.sting.utils.recalibration.EventType;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.gatk.utils.recalibration.EventType;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.BeforeTest;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java
index cf6c4515b..3870182fe 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.haplotype;
+package org.broadinstitute.gatk.utils.haplotype;
 
 import htsjdk.samtools.TextCigarCodec;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.UnvalidatingGenomeLoc;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java
index 5e057e77a..b0087dc05 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.haplotype;
+package org.broadinstitute.gatk.utils.haplotype;
 
 
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
 import htsjdk.samtools.TextCigarCodec;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc;
-import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.UnvalidatingGenomeLoc;
+import org.broadinstitute.gatk.utils.haplotype.Haplotype;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalIntegrationTest.java
index 69466d163..8d8f7d261 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalIntegrationTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.interval;
+package org.broadinstitute.gatk.utils.interval;
 
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.io.File;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java
index 4f8c15b5e..b991087bd 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.interval;
+package org.broadinstitute.gatk.utils.interval;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
@@ -32,16 +32,16 @@ import htsjdk.samtools.util.IntervalList;
 import htsjdk.samtools.SAMFileHeader;
 import org.apache.commons.io.FileUtils;
 import htsjdk.tribble.Feature;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.IntervalBinding;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
-import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.IntervalBinding;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
+import org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.GenomeLocSortedSet;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java
index 7eca44ee6..13a2e8a1d 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.io;
+package org.broadinstitute.gatk.utils.io;
 
 import org.apache.commons.io.FileUtils;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -35,9 +35,9 @@ import java.util.Arrays;
 import java.util.List;
 import java.util.Random;
 
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -212,8 +212,8 @@ public class IOUtilsUnitTest extends BaseTest {
     public void testMissingRelativeFile() throws IOException {
         File temp = createTempFile("temp.", ".properties");
         try {
-            // Looking for /org/broadinstitute/sting/utils/file/StingText.properties
-            IOUtils.writeResource(new Resource("StingText.properties", IOUtils.class), temp);
+            // Looking for /org/broadinstitute/gatk/utils/file/GATKText.properties
+            IOUtils.writeResource(new Resource("GATKText.properties", IOUtils.class), temp);
         } finally {
             FileUtils.deleteQuietly(temp);
         }
@@ -288,12 +288,12 @@ public class IOUtilsUnitTest extends BaseTest {
         IOUtils.readFileIntoByteArray(nonExistentFile);
     }
 
-    @Test( expectedExceptions = ReviewedStingException.class )
+    @Test( expectedExceptions = ReviewedGATKException.class )
     public void testReadNullStreamIntoByteArray() {
         IOUtils.readStreamIntoByteArray(null);
     }
 
-    @Test( expectedExceptions = ReviewedStingException.class )
+    @Test( expectedExceptions = ReviewedGATKException.class )
     public void testReadStreamIntoByteArrayInvalidBufferSize() throws Exception {
         IOUtils.readStreamIntoByteArray(new FileInputStream(createTempFile("testReadStreamIntoByteArrayInvalidBufferSize", "tmp")),
                                         -1);
@@ -304,12 +304,12 @@ public class IOUtilsUnitTest extends BaseTest {
         IOUtils.writeByteArrayToFile(new byte[]{0}, new File("/dev/foo/bar"));
     }
 
-    @Test( expectedExceptions = ReviewedStingException.class )
+    @Test( expectedExceptions = ReviewedGATKException.class )
     public void testWriteNullByteArrayToFile() {
         IOUtils.writeByteArrayToFile(null, createTempFile("testWriteNullByteArrayToFile", "tmp"));
     }
 
-    @Test( expectedExceptions = ReviewedStingException.class )
+    @Test( expectedExceptions = ReviewedGATKException.class )
     public void testWriteByteArrayToNullStream() {
         IOUtils.writeByteArrayToStream(new byte[]{0}, null);
     }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java
index dc234a8b8..f695d899b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.clibrary;
+package org.broadinstitute.gatk.utils.jna.clibrary;
 
 import com.sun.jna.NativeLong;
 import com.sun.jna.ptr.NativeLongByReference;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java
index 1562ab93e..e683f4be8 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.drmaa.v1_0;
+package org.broadinstitute.gatk.utils.jna.drmaa.v1_0;
 
 import org.apache.commons.io.FileUtils;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.ggf.drmaa.*;
 import org.testng.Assert;
 import org.testng.SkipException;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java
index 3d861f078..accc0febb 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.drmaa.v1_0;
+package org.broadinstitute.gatk.utils.jna.drmaa.v1_0;
 
 import com.sun.jna.Memory;
 import com.sun.jna.NativeLong;
@@ -32,7 +32,7 @@ import com.sun.jna.StringArray;
 import com.sun.jna.ptr.IntByReference;
 import com.sun.jna.ptr.PointerByReference;
 import org.apache.commons.io.FileUtils;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.SkipException;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java
index d7ac75695..4af2bf7c7 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java
@@ -23,18 +23,18 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.jna.lsf.v7_0_6;
+package org.broadinstitute.gatk.utils.jna.lsf.v7_0_6;
 
 import com.sun.jna.*;
 import com.sun.jna.ptr.IntByReference;
 import org.apache.commons.io.FileUtils;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.gatk.utils.Utils;
 import org.testng.Assert;
 import org.testng.SkipException;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.*;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.*;
 
 import java.io.File;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java
index 7cb148b61..d8c39d3df 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java
index ed5178a3e..92680a7ea 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java
index 54ed88ebb..1f02a68e5 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import com.google.caliper.Param;
 import com.google.caliper.SimpleBenchmark;
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.QualityUtils;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.util.LinkedList;
 import java.util.List;
@@ -71,8 +71,8 @@ public class LocusIteratorBenchmark extends SimpleBenchmark {
 
 //    public void timeOriginalLIBS(int rep) {
 //        for ( int i = 0; i < rep; i++ ) {
-//            final org.broadinstitute.sting.utils.locusiterator.old.LocusIteratorByState libs =
-//                    new org.broadinstitute.sting.utils.locusiterator.old.LocusIteratorByState(
+//            final org.broadinstitute.gatk.utils.locusiterator.old.LocusIteratorByState libs =
+//                    new org.broadinstitute.gatk.utils.locusiterator.old.LocusIteratorByState(
 //                            new LocusIteratorByStateBaseTest.FakeCloseableIterator(reads.iterator()),
 //                            LocusIteratorByStateBaseTest.createTestReadProperties(),
 //                            genomeLocParser,
@@ -86,8 +86,8 @@ public class LocusIteratorBenchmark extends SimpleBenchmark {
 //
 //    public void timeLegacyLIBS(int rep) {
 //        for ( int i = 0; i < rep; i++ ) {
-//            final org.broadinstitute.sting.utils.locusiterator.legacy.LegacyLocusIteratorByState libs =
-//                    new org.broadinstitute.sting.utils.locusiterator.legacy.LegacyLocusIteratorByState(
+//            final org.broadinstitute.gatk.utils.locusiterator.legacy.LegacyLocusIteratorByState libs =
+//                    new org.broadinstitute.gatk.utils.locusiterator.legacy.LegacyLocusIteratorByState(
 //                            new LocusIteratorByStateBaseTest.FakeCloseableIterator(reads.iterator()),
 //                            LocusIteratorByStateBaseTest.createTestReadProperties(),
 //                            genomeLocParser,
@@ -101,8 +101,8 @@ public class LocusIteratorBenchmark extends SimpleBenchmark {
 
     public void timeNewLIBS(int rep) {
         for ( int i = 0; i < rep; i++ ) {
-            final org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState libs =
-                    new org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState(
+            final org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState libs =
+                    new org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState(
                             new LocusIteratorByStateBaseTest.FakeCloseableIterator(reads.iterator()),
                             LocusIteratorByStateBaseTest.createTestReadProperties(),
                             genomeLocParser,
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java
index 5875c1f22..c32325e73 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java
@@ -23,22 +23,22 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import htsjdk.samtools.*;
 import htsjdk.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.ReadProperties;
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
-import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.ReadProperties;
+import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
+import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod;
+import org.broadinstitute.gatk.engine.filters.ReadFilter;
+import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.QualityUtils;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java
index 02ffb921e..08cbecaf8 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java
@@ -23,24 +23,24 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import htsjdk.samtools.CigarOperator;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.gatk.ReadProperties;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
-import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
-import org.broadinstitute.sting.utils.NGSPlatform;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.ArtificialBAMBuilder;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.engine.ReadProperties;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.downsampling.DownsampleType;
+import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod;
+import org.broadinstitute.gatk.utils.NGSPlatform;
+import org.broadinstitute.gatk.utils.QualityUtils;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.sam.ArtificialBAMBuilder;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java
index e39a751c4..4a760b5d6 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.locusiterator;
+package org.broadinstitute.gatk.utils.locusiterator;
 
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java
index d62ea220f..d99a07966 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java
index 0fbbbe6af..93105cdfb 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java
index b734ecc96..72636f01b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
 import org.apache.log4j.BasicConfigurator;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.SimpleTimer;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.SimpleTimer;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
@@ -274,9 +274,9 @@ public class NanoSchedulerUnitTest extends BaseTest {
         executeTestErrorThrowingInput(10, new NullPointerException(), exampleTest, false);
     }
 
-    @Test(enabled = true, expectedExceptions = ReviewedStingException.class, timeOut = EXCEPTION_THROWING_TEST_TIMEOUT)
+    @Test(enabled = true, expectedExceptions = ReviewedGATKException.class, timeOut = EXCEPTION_THROWING_TEST_TIMEOUT)
     public void testInputErrorIsThrown_RSE() throws InterruptedException {
-        executeTestErrorThrowingInput(10, new ReviewedStingException("test"), exampleTest, false);
+        executeTestErrorThrowingInput(10, new ReviewedGATKException("test"), exampleTest, false);
     }
 
     @Test(enabled = true, expectedExceptions = NullPointerException.class, dataProvider = "NanoSchedulerInputExceptionTest", timeOut = EXCEPTION_THROWING_TEST_TIMEOUT, invocationCount = 1)
@@ -284,7 +284,7 @@ public class NanoSchedulerUnitTest extends BaseTest {
         executeTestErrorThrowingInput(nElementsBeforeError, new NullPointerException(), test, addDelays);
     }
 
-    @Test(enabled = true, expectedExceptions = ReviewedStingException.class, dataProvider = "NanoSchedulerInputExceptionTest", timeOut = EXCEPTION_THROWING_TEST_TIMEOUT, invocationCount = 1)
+    @Test(enabled = true, expectedExceptions = ReviewedGATKException.class, dataProvider = "NanoSchedulerInputExceptionTest", timeOut = EXCEPTION_THROWING_TEST_TIMEOUT, invocationCount = 1)
     public void testInputErrorDoesntDeadlock(final int nElementsBeforeError, final NanoSchedulerBasicTest test, final boolean addDelays ) throws InterruptedException {
         executeTestErrorThrowingInput(nElementsBeforeError, new Error(), test, addDelays);
     }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java
index 0e6d8db55..987d13f2a 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.nanoScheduler;
+package org.broadinstitute.gatk.utils.nanoScheduler;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.MultiThreadedErrorTracker;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.MultiThreadedErrorTracker;
+import org.broadinstitute.gatk.utils.Utils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java
index a7ccda392..90d235f99 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pileup;
+package org.broadinstitute.gatk.utils.pileup;
 
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.locusiterator.AlignmentStateMachine;
-import org.broadinstitute.sting.utils.locusiterator.LIBS_position;
-import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByStateBaseTest;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.locusiterator.AlignmentStateMachine;
+import org.broadinstitute.gatk.utils.locusiterator.LIBS_position;
+import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByStateBaseTest;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java
index c83f7ba9f..9b3b3b8c3 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java
@@ -23,17 +23,17 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.pileup;
+package org.broadinstitute.gatk.utils.pileup;
 
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java
index 2ede67a3c..9d549ea21 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.progressmeter;
+package org.broadinstitute.gatk.utils.progressmeter;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.GenomeLocSortedSet;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java
index d0b9b5da9..0c97377c3 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.progressmeter;
+package org.broadinstitute.gatk.utils.progressmeter;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.AutoFormattingTime;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.AutoFormattingTime;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java
index 318955c77..7749fb2c3 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.recalibration;
+package org.broadinstitute.gatk.utils.recalibration;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java
index 3791c1c3f..ebeb1581d 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.report;
+package org.broadinstitute.gatk.utils.report;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.annotations.Test;
 
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java
index ed3345b5a..4fa7ef5de 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang.StringUtils;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.io.IOUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.io.IOUtils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -88,7 +88,7 @@ public class ProcessControllerUnitTest extends BaseTest {
             job = new ProcessSettings(new String[] {"no_such_command"});
             try {
                 controller.exec(job);
-            } catch (ReviewedStingException e) {
+            } catch (ReviewedGATKException e) {
                 /* Was supposed to throw an exception */
             }
 
@@ -392,7 +392,7 @@ public class ProcessControllerUnitTest extends BaseTest {
         }
     }
 
-    @Test(expectedExceptions = ReviewedStingException.class)
+    @Test(expectedExceptions = ReviewedGATKException.class)
     public void testUnableToStart() {
         ProcessSettings job = new ProcessSettings(new String[]{"no_such_command"});
         new ProcessController().exec(job);
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java
index 24b5cd889..95737748d 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.runtime;
+package org.broadinstitute.gatk.utils.runtime;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java
index fca18e62c..feb065ad6 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.*;
 import org.apache.commons.lang.ArrayUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java
index b45394f7c..b7042a6aa 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMRecord;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java
index 409ba3553..fe5fba7ee 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import static org.testng.Assert.assertTrue;
 import static org.testng.Assert.fail;
 import org.testng.annotations.BeforeMethod;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java
index 3df3d027f..d52762402 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMFileHeader;
 
@@ -65,14 +65,14 @@ import java.util.List;
 /**
  * @author aaron
  *         

- *         Class ArtificialStingSAMFileWriter
+ *         Class ArtificialGATKSAMFileWriter
  *         

- *         Test out the ArtificialStingSAMFileWriter class
+ *         Test out the ArtificialGATKSAMFileWriter class
  */
 public class ArtificialSAMFileWriterUnitTest extends BaseTest {
 
     /** the artificial sam writer */
-    private ArtificialStingSAMFileWriter writer;
+    private ArtificialGATKSAMFileWriter writer;
     private SAMFileHeader header;
     private final int startChr = 1;
     private final int numChr = 2;
@@ -80,7 +80,7 @@ public class ArtificialSAMFileWriterUnitTest extends BaseTest {
 
     @BeforeMethod
     public void before() {
-        writer = new ArtificialStingSAMFileWriter();
+        writer = new ArtificialGATKSAMFileWriter();
         header = ArtificialSAMUtils.createArtificialSamHeader(numChr, startChr, chrSize);
     }
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java
index 643e7e760..32409c60b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java
@@ -23,9 +23,9 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import static org.testng.Assert.assertEquals;
 import org.testng.annotations.Test;
 import htsjdk.samtools.SAMRecord;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java
index 8a45890cf..48ad2129d 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 import static org.testng.Assert.fail;
@@ -45,7 +45,7 @@ public class ArtificialSAMUtilsUnitTest extends BaseTest {
 
     @Test
     public void basicReadIteratorTest() {
-        StingSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 100);
+        GATKSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 100);
         int count = 0;
         while (iter.hasNext()) {
             SAMRecord rec = iter.next();
@@ -56,7 +56,7 @@ public class ArtificialSAMUtilsUnitTest extends BaseTest {
 
     @Test
     public void tenPerChromosome() {
-        StingSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 10);
+        GATKSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 10);
         int count = 0;
         while (iter.hasNext()) {
             SAMRecord rec = iter.next();
@@ -69,7 +69,7 @@ public class ArtificialSAMUtilsUnitTest extends BaseTest {
 
     @Test
     public void onePerChromosome() {
-        StingSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 1);
+        GATKSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 1);
         int count = 0;
         while (iter.hasNext()) {
             SAMRecord rec = iter.next();
@@ -82,7 +82,7 @@ public class ArtificialSAMUtilsUnitTest extends BaseTest {
 
     @Test
     public void basicUnmappedIteratorTest() {
-        StingSAMIterator iter = ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 100, 100, 1000);
+        GATKSAMIterator iter = ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 100, 100, 1000);
         int count = 0;
         for (int x = 0; x < (100* 100); x++ ) {
             if (!iter.hasNext()) {
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java
index 8dbcb496c..271a75ad9 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java
@@ -23,16 +23,16 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.testng.annotations.Test;
 import org.testng.annotations.DataProvider;
 
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 
 public class ArtificialSingleSampleReadStreamUnitTest extends BaseTest {
 
@@ -155,7 +155,7 @@ public class ArtificialSingleSampleReadStreamUnitTest extends BaseTest {
     }
 
     @Test(dataProvider = "ArtificialSingleSampleReadStreamInvalidArgumentsTestDataProvider",
-          expectedExceptions = ReviewedStingException.class)
+          expectedExceptions = ReviewedGATKException.class)
     public void testInvalidArguments( String testName,
                                       SAMFileHeader header,
                                       String readGroupID,
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java
index efdda7f68..e703c52fb 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityUnitTest.java
index 8dd72ace1..207e01ab9 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java
index 01fe15e6a..c7ceea10a 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java
@@ -23,15 +23,15 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.sam;
+package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.BaseUtils;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java
index ee8f411bf..bc5aa488c 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java
@@ -23,11 +23,11 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.smithwaterman;
+package org.broadinstitute.gatk.utils.smithwaterman;
 
 import com.google.caliper.Param;
 import com.google.caliper.SimpleBenchmark;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.gatk.utils.Utils;
 
 /**
  * Caliper microbenchmark of parsing a VCF file
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java
index 9b8dc0cfb..1c9607e3c 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java
@@ -23,13 +23,13 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.text;
+package org.broadinstitute.gatk.utils.text;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.ParsingEngine;
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.commandline.ParsingEngine;
+import org.broadinstitute.gatk.utils.commandline.Tags;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java
index 8582e4b80..54573103a 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.text;
+package org.broadinstitute.gatk.utils.text;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
@@ -34,7 +34,7 @@ import java.util.Arrays;
 import java.util.Collections;
 
 public class TextFormattingUtilsUnitTest extends BaseTest {
-    @Test(expectedExceptions = ReviewedStingException.class)
+    @Test(expectedExceptions = ReviewedGATKException.class)
     public void testSplitWhiteSpaceNullLine() {
         TextFormattingUtils.splitWhiteSpace(null);
     }
@@ -49,7 +49,7 @@ public class TextFormattingUtilsUnitTest extends BaseTest {
         Assert.assertEquals(TextFormattingUtils.splitWhiteSpace("\tfoo\tbar\tbaz\t"), new String[]{"foo", "bar", "baz"});
     }
 
-    @Test(expectedExceptions = ReviewedStingException.class)
+    @Test(expectedExceptions = ReviewedGATKException.class)
     public void testGetWordStartsNullLine() {
         TextFormattingUtils.getWordStarts(null);
     }
@@ -64,12 +64,12 @@ public class TextFormattingUtilsUnitTest extends BaseTest {
         Assert.assertEquals(TextFormattingUtils.getWordStarts("\tfoo\tbar\tbaz\t"), Arrays.asList(1, 5, 9));
     }
 
-    @Test(expectedExceptions = ReviewedStingException.class)
+    @Test(expectedExceptions = ReviewedGATKException.class)
     public void testSplitFixedWidthNullLine() {
         TextFormattingUtils.splitFixedWidth(null, Collections.emptyList());
     }
 
-    @Test(expectedExceptions = ReviewedStingException.class)
+    @Test(expectedExceptions = ReviewedGATKException.class)
     public void testSplitFixedWidthNullColumnStarts() {
         TextFormattingUtils.splitFixedWidth("foo bar baz", null);
     }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java
index 748d2dd9c..0c988131e 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.gatk.utils.threading;
 
 import org.apache.log4j.Priority;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.Utils;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -110,9 +110,9 @@ public class EfficiencyMonitoringThreadFactoryUnitTest extends BaseTest {
                 case WAITING_FOR_IO:
                     // TODO -- implement me
                     // shouldn't ever get here, throw an exception
-                    throw new ReviewedStingException("WAITING_FOR_IO testing currently not implemented, until we figure out how to force a system call block");
+                    throw new ReviewedGATKException("WAITING_FOR_IO testing currently not implemented, until we figure out how to force a system call block");
                 default:
-                    throw new ReviewedStingException("Unexpected thread test state " + stateToImplement);
+                    throw new ReviewedGATKException("Unexpected thread test state " + stateToImplement);
             }
         }
     }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java
index fbe7ee95a..a73cb26f9 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java
@@ -23,10 +23,10 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.gatk.utils.threading;
 
 import org.testng.annotations.Test;
-import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.gatk.utils.BaseTest;
 
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors; 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtilsUnitTest.java
index 377817a16..ab547b7c1 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtilsUnitTest.java
@@ -23,19 +23,19 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.variant;
+package org.broadinstitute.gatk.utils.variant;
 
 import htsjdk.tribble.index.DynamicIndexCreator;
 import htsjdk.tribble.index.IndexCreator;
 import htsjdk.tribble.index.interval.IntervalIndexCreator;
 import htsjdk.tribble.index.linear.LinearIndexCreator;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
+import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
+import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.engine.walkers.RodWalker;
+import org.broadinstitute.gatk.engine.walkers.Walker;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
 import org.testng.Assert;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java
index f3dd98044..53ac7b7b1 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java
@@ -23,14 +23,14 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.variant;
+package org.broadinstitute.gatk.utils.variant;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.*;
+import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import htsjdk.variant.variantcontext.*;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VCFIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VCFIntegrationTest.java
index 688663abf..4a087025a 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VCFIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VCFIntegrationTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.variant;
+package org.broadinstitute.gatk.utils.variant;
 
 import htsjdk.tribble.AbstractFeatureReader;
 import htsjdk.tribble.Tribble;
@@ -35,8 +35,8 @@ import htsjdk.tribble.index.interval.IntervalTreeIndex;
 import htsjdk.tribble.index.linear.LinearIndex;
 import htsjdk.tribble.index.tabix.TabixIndex;
 import htsjdk.tribble.util.TabixUtils;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import htsjdk.variant.vcf.VCFCodec;
 import org.testng.Assert;
 import org.testng.TestException;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java
index dcb7a3862..7c1b2028f 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.variant;
+package org.broadinstitute.gatk.utils.variant;
 
 import com.google.caliper.Param;
 import com.google.caliper.SimpleBenchmark;
diff --git a/public/gatk-utils/pom.xml b/public/gatk-utils/pom.xml
index ab4b7e1b7..8cf3ef1f3 100644
--- a/public/gatk-utils/pom.xml
+++ b/public/gatk-utils/pom.xml
@@ -3,19 +3,19 @@
     4.0.0
 
     
-        org.broadinstitute.sting
-        sting-aggregator
+        org.broadinstitute.gatk
+        gatk-aggregator
         3.2-SNAPSHOT
         ../..
     
 
-    sting-utils
+    gatk-utils
     jar
-    Sting Utils
+    GATK Utils
 
     
-        ${project.basedir}/../..
-        org/broadinstitute/sting/utils/R
+        ${project.basedir}/../..
+        org/broadinstitute/gatk/utils/R
         gsalib.tar.gz
     
 
@@ -107,11 +107,6 @@
             tar.gz
         
 
-        
-            org.testng
-            testng
-            test
-        
         
             com.google.caliper
             caliper
@@ -146,6 +141,80 @@
                     
                 
             
+            
+                org.apache.maven.plugins
+                maven-resources-plugin
+                
+                    
+                        copy-resource-bundle-log4j
+                        prepare-package
+                    
+                
+            
+            
+            
+                org.apache.maven.plugins
+                maven-invoker-plugin
+                
+                    
+                        package-unittests
+                    
+                    
+                        package-integrationtests
+                    
+                    
+                        package-largescaletests
+                    
+                    
+                        package-knowledgebasetests
+                    
+                    
+                        package-queuetests
+                    
+                
+            
         
     
+
+    
+        
+            private-testdata
+            
+                
+                    ${basedir}/../../private/pom.xml
+                
+            
+            
+                
+                    
+                    
+                        com.pyx4j
+                        maven-junction-plugin
+                        
+                            
+                                link-private-testdata
+                                process-test-resources
+                            
+                            
+                                unlink-private-testdata
+                                clean
+                            
+                        
+                    
+                
+            
+        
+    
 
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 d71144f07..101796bc0 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
@@ -23,12 +23,12 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.Serializable;
 import java.util.*;
@@ -165,15 +165,15 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome
             "that != null",
             "isUnmapped(this) == isUnmapped(that)"})
     @Ensures("result != null")
-    public GenomeLoc merge( GenomeLoc that ) throws ReviewedStingException {
+    public GenomeLoc merge( GenomeLoc that ) throws ReviewedGATKException {
         if(GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) {
             if(! GenomeLoc.isUnmapped(this) || !GenomeLoc.isUnmapped(that))
-                throw new ReviewedStingException("Tried to merge a mapped and an unmapped genome loc");
+                throw new ReviewedGATKException("Tried to merge a mapped and an unmapped genome loc");
             return UNMAPPED;
         }
 
         if (!(this.contiguousP(that))) {
-            throw new ReviewedStingException("The two genome loc's need to be contiguous");
+            throw new ReviewedGATKException("The two genome loc's need to be contiguous");
         }
 
         return new GenomeLoc(getContig(), this.contigIndex,
@@ -187,13 +187,13 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome
      */
     @Requires({"that != null", "isUnmapped(this) == isUnmapped(that)"})
     @Ensures("result != null")
-    public GenomeLoc endpointSpan(GenomeLoc that) throws ReviewedStingException {
+    public GenomeLoc endpointSpan(GenomeLoc that) throws ReviewedGATKException {
         if(GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) {
-            throw new ReviewedStingException("Cannot get endpoint span for unmerged genome locs");
+            throw new ReviewedGATKException("Cannot get endpoint span for unmerged genome locs");
         }
 
         if ( ! this.getContig().equals(that.getContig()) ) {
-            throw new ReviewedStingException("Cannot get endpoint span for genome locs on different contigs");
+            throw new ReviewedGATKException("Cannot get endpoint span for genome locs on different contigs");
         }
 
         return new GenomeLoc(getContig(),this.contigIndex,Math.min(getStart(),that.getStart()),Math.max(getStop(),that.getStop()));
@@ -206,7 +206,7 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome
      */
     public GenomeLoc[] split(final int splitPoint) {
         if(splitPoint < getStart() || splitPoint > getStop())
-            throw new ReviewedStingException(String.format("Unable to split contig %s at split point %d; split point is not contained in region.",this,splitPoint));
+            throw new ReviewedGATKException(String.format("Unable to split contig %s at split point %d; split point is not contained in region.",this,splitPoint));
         return new GenomeLoc[] { new GenomeLoc(getContig(),contigIndex,getStart(),splitPoint-1), new GenomeLoc(getContig(),contigIndex,splitPoint,getStop()) };
     }
 
@@ -214,15 +214,15 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome
 
     @Requires("that != null")
     @Ensures("result != null")
-    public GenomeLoc intersect( GenomeLoc that ) throws ReviewedStingException {
+    public GenomeLoc intersect( GenomeLoc that ) throws ReviewedGATKException {
         if(GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) {
             if(! GenomeLoc.isUnmapped(this) || !GenomeLoc.isUnmapped(that))
-                throw new ReviewedStingException("Tried to intersect a mapped and an unmapped genome loc");
+                throw new ReviewedGATKException("Tried to intersect a mapped and an unmapped genome loc");
             return UNMAPPED;
         }
 
         if (!(this.overlapsP(that))) {
-            throw new ReviewedStingException("GenomeLoc::intersect(): The two genome loc's need to overlap");
+            throw new ReviewedGATKException("GenomeLoc::intersect(): The two genome loc's need to overlap");
         }
 
         return new GenomeLoc(getContig(), this.contigIndex,
@@ -234,12 +234,12 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome
     public final List subtract( final GenomeLoc that ) {
         if(GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) {
             if(! GenomeLoc.isUnmapped(this) || !GenomeLoc.isUnmapped(that))
-                throw new ReviewedStingException("Tried to intersect a mapped and an unmapped genome loc");
+                throw new ReviewedGATKException("Tried to intersect a mapped and an unmapped genome loc");
             return Arrays.asList(UNMAPPED);
         }
 
         if (!(this.overlapsP(that))) {
-            throw new ReviewedStingException("GenomeLoc::minus(): The two genome loc's need to overlap");
+            throw new ReviewedGATKException("GenomeLoc::minus(): The two genome loc's need to overlap");
         }
 
         if (equals(that)) {
@@ -587,11 +587,11 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome
     @Requires("a != null && b != null")
     public static  GenomeLoc merge(final T a, final T b) {
         if ( isUnmapped(a) || isUnmapped(b) ) {
-            throw new ReviewedStingException("Tried to merge unmapped genome locs");
+            throw new ReviewedGATKException("Tried to merge unmapped genome locs");
         }
 
         if ( !(a.contiguousP(b)) ) {
-            throw new ReviewedStingException("The two genome locs need to be contiguous");
+            throw new ReviewedGATKException("The two genome locs need to be contiguous");
         }
 
         return new GenomeLoc(a.getContig(), a.contigIndex, Math.min(a.getStart(), b.getStart()), Math.max(a.getStop(), b.getStop()));
@@ -609,12 +609,12 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome
 
         for ( GenomeLoc loc : sortedLocs ) {
             if ( loc.isUnmapped() )
-                throw new ReviewedStingException("Tried to merge unmapped genome locs");
+                throw new ReviewedGATKException("Tried to merge unmapped genome locs");
 
             if ( result == null )
                 result = loc;
             else if ( !result.contiguousP(loc) )
-                throw new ReviewedStingException("The genome locs need to be contiguous");
+                throw new ReviewedGATKException("The genome locs need to be contiguous");
             else
                 result = merge(result, loc);
         }
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 f5dafb2ca..d080d5bc0 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
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 import com.google.java.contract.Ensures;
 
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 59516f196..39d6fa67b 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
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.gatk.utils;
 
 
 import com.google.java.contract.Ensures;
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 e51820869..0eb0941ec 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
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.exceptions;
+package org.broadinstitute.gatk.utils.exceptions;
 
 /**
  *
@@ -47,17 +47,17 @@ package org.broadinstitute.sting.utils.exceptions;
  * @version 1.0
  * @date Apr 6, 2009
  * 

- * Class StingException
+ * Class GATKException
  * 

  * This exception allows us to filter out exceptions that come from core GATK code, and those that
  * are not homegrown..
  */
-public class StingException extends RuntimeException {
-    public StingException(String msg) {
+public class GATKException extends RuntimeException {
+    public GATKException(String msg) {
         super(msg);
     }
 
-    public StingException(String message, Throwable throwable) {
+    public GATKException(String message, Throwable throwable) {
         super(message, throwable);
     }
 }
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 5709da37d..56dfc6936 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
@@ -23,19 +23,19 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils.exceptions;
+package org.broadinstitute.gatk.utils.exceptions;
 
 /**
- * A trivial extension around StingException to mark exceptions that have been reviewed for correctness,
- * completeness, etc.  By using this exception you are saying "this is the right error message".  StingException
+ * A trivial extension around GATKException to mark exceptions that have been reviewed for correctness,
+ * completeness, etc.  By using this exception you are saying "this is the right error message".  GATKException
  * is now just a catch all for lazy users.
  */
-public class ReviewedStingException extends StingException {
-    public ReviewedStingException(String msg) {
+public class ReviewedGATKException extends GATKException {
+    public ReviewedGATKException(String msg) {
         super(msg);
     }
 
-    public ReviewedStingException(String message, Throwable throwable) {
+    public ReviewedGATKException(String message, Throwable throwable) {
         super(message, throwable);
     }
 }
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 195699256..8a42dffda 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
@@ -23,4 +23,4 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.utils;
\ No newline at end of file
+package org.broadinstitute.gatk.utils;
\ No newline at end of file
diff --git a/public/gsalib/pom.xml b/public/gsalib/pom.xml
index 4f42a5c15..5a05101a6 100644
--- a/public/gsalib/pom.xml
+++ b/public/gsalib/pom.xml
@@ -3,19 +3,19 @@
     4.0.0
 
     
-        org.broadinstitute.sting
-        sting-aggregator
+        org.broadinstitute.gatk
+        gatk-aggregator
         3.2-SNAPSHOT
         ../..
     
 
     gsalib
     pom
-    Sting GSALib
+    GATK GSALib
 
     
-        ${project.basedir}/../..
-        org/broadinstitute/sting/utils/R
+        ${project.basedir}/../..
+        org/broadinstitute/gatk/utils/R
         gsalib.tar.gz
     
 
@@ -30,7 +30,7 @@
                         
                             single
                         
-                        ${sting.generate-resources.phase}
+                        ${gatk.generate-resources.phase}
                         
                             false
                             
diff --git a/public/java/config/log4j.properties b/public/java/config/log4j.properties
index 26e6a018c..480646fe5 100644
--- a/public/java/config/log4j.properties
+++ b/public/java/config/log4j.properties
@@ -1,4 +1,4 @@
-log4j.logger.org.broadinstitute.sting.gatk.walkers.Walker=INFO, walker
+log4j.logger.org.broadinstitute.gatk.tools.walkers.Walker=INFO, walker
 
 # use this to append walker data to the console only
 log4j.appender.walker=org.apache.log4j.ConsoleAppender
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index 077bd6cba..df043d0b9 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -3,65 +3,51 @@
     4.0.0
 
     
 
     
-        org.broadinstitute.sting
-        sting-root
+        org.broadinstitute.gatk
+        gatk-root
         3.2-SNAPSHOT
-        ../sting-root
+        ../gatk-root
     
 
-    sting-package-tests
+    gatk-package-tests
     pom
-    Sting Package Tests
+    GATK Package Tests
 
     
-        ${project.basedir}/../..
-        true
-        true
-        true
-        true
-        true
+        ${project.basedir}/../..
+        true
+        true
+        true
+        true
+        true
     
 
     
     
         
             ${project.groupId}
-            ${sting.packagetests.artifactId}
+            ${gatk.packagetests.artifactId}
             ${project.version}
         
 
-        
-        
-            com.sun
-            tools
-        
-
-        
-            com.google.code.cofoja
-            cofoja
-        
-
         
 
-        
-            org.testng
-            testng
-            test
-        
-
+        
         
             com.google.caliper
             caliper
@@ -90,7 +75,7 @@
     
 
     
-        ${sting.packagetests.basedir}/target
+        ${gatk.packagetests.basedir}/target
     
 
     
@@ -110,13 +95,13 @@
                         org.apache.maven.plugins
                         maven-surefire-plugin
                         
-                            ${sting.packagetests.basedir}
-                            ${sting.packagetests.basedir}
+                            ${gatk.packagetests.basedir}
+                            ${gatk.packagetests.basedir}
                             ${project.build.outputDirectory}/ignored_by_package_test
-                            ${sting.packagetests.testClasses}
+                            ${gatk.packagetests.testClasses}
                             
                             
-                                ${sting.basedir}/public/gatk-framework/target/gatk-framework-${project.version}-tests.jar
+                                ${gatk.basedir}/public/gatk-tools-public/target/gatk-tools-public-${project.version}-tests.jar
                             
                         
                         
@@ -126,7 +111,7 @@
                                     test
                                 
                                 
-                                    ${sting.packageunittests.skipped}
+                                    ${gatk.packageunittests.skipped}
                                 
                             
                         
@@ -151,13 +136,13 @@
                         org.apache.maven.plugins
                         maven-failsafe-plugin
                         
-                            ${sting.packagetests.basedir}
-                            ${sting.packagetests.basedir}
+                            ${gatk.packagetests.basedir}
+                            ${gatk.packagetests.basedir}
                             ${project.build.outputDirectory}/ignored_by_package_test
-                            ${sting.packagetests.testClasses}
+                            ${gatk.packagetests.testClasses}
                             
                             
-                                ${sting.basedir}/public/gatk-framework/target/gatk-framework-${project.version}-tests.jar
+                                ${gatk.basedir}/public/gatk-framework/target/gatk-framework-${project.version}-tests.jar
                             
                         
                         
@@ -168,7 +153,7 @@
                                 
                                 
                                 
-                                    ${sting.packageintegrationtests.skipped}
+                                    ${gatk.packageintegrationtests.skipped}
                                 
                             
                             
@@ -178,7 +163,7 @@
                                 
                                 
                                 
-                                    ${sting.packagequeuetests.skipped}
+                                    ${gatk.packagequeuetests.skipped}
                                 
                             
                             
@@ -188,7 +173,7 @@
                                 
                                 
                                 
-                                    ${sting.packagelargescaletests.skipped}
+                                    ${gatk.packagelargescaletests.skipped}
                                 
                             
                             
@@ -198,7 +183,7 @@
                                 
                                 
                                 
-                                    ${sting.packageknowledgebasetests.skipped}
+                                    ${gatk.packageknowledgebasetests.skipped}
                                 
                             
                         
diff --git a/public/pom.xml b/public/pom.xml
index 70d57f808..dc145957d 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -3,28 +3,28 @@
     4.0.0
 
     
-        org.broadinstitute.sting
-        sting-root
+        org.broadinstitute.gatk
+        gatk-root
         3.2-SNAPSHOT
-        sting-root
+        gatk-root
     
 
-    sting-public
+    gatk-aggregator-public
     pom
-    Sting Public
+    GATK Aggregator Public
 
     
-        sting-root
+        gatk-root
         gsalib
-        sting-utils
-        gatk-framework
-        gatk-package
-        
+        gatk-utils
+        gatk-engine
+        gatk-tools-public
+        external-example
         
     
 
     
-        ${project.basedir}/..
+        ${project.basedir}/..
     
 
     
@@ -37,9 +37,9 @@
                 
             
             
-                gatk-queue-extgen
-                queue-framework
-                queue-package
+                gatk-queue
+                gatk-queue-extensions-generator
+                gatk-queue-extensions-public
             
         
     
diff --git a/public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.pom b/public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.pom
index 0b8c2db4d..17cade88e 100644
--- a/public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.pom
+++ b/public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.pom
@@ -17,7 +17,7 @@
             snappy-java
             1.0.3-rc3
         
-        
+        
         
             com.google.code.cofoja
             cofoja