From bb7151192a09f3a25e1e6f658c92de8a841d697c Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Wed, 22 Oct 2014 00:40:42 +0800 Subject: [PATCH] Split all imports of tools|engine from utils, and all tools from engine. First of two commits, renaming files only. --- .../bqsr => engine/recalibration}/BQSRGatherer.java | 0 .../recalibration/BQSRReadTransformer.java | 0 .../recalibration/BaseRecalibration.java | 0 .../recalibration/QualQuantizer.java | 0 .../recalibration/QuantizationInfo.java | 0 .../recalibration/ReadCovariates.java | 0 .../{utils => engine}/recalibration/RecalDatum.java | 0 .../recalibration/RecalDatumNode.java | 0 .../{utils => engine}/recalibration/RecalUtils.java | 0 .../RecalibrationArgumentCollection.java | 0 .../recalibration/RecalibrationReport.java | 0 .../recalibration/RecalibrationTables.java | 0 .../recalibration/covariates/ContextCovariate.java | 0 .../recalibration/covariates/Covariate.java | 0 .../recalibration/covariates/CycleCovariate.java | 0 .../covariates/ExperimentalCovariate.java | 0 .../covariates/QualityScoreCovariate.java | 0 .../covariates/ReadGroupCovariate.java | 0 .../recalibration/covariates/RepeatCovariate.java | 0 .../covariates/RepeatLengthCovariate.java | 0 .../covariates/RepeatUnitAndLengthCovariate.java | 0 .../covariates/RepeatUnitCovariate.java | 0 .../recalibration/covariates/RequiredCovariate.java | 0 .../recalibration/covariates/StandardCovariate.java | 0 .../StandardCallerArgumentCollection.java | 0 .../haplotypecaller}/HaplotypeLDCalculator.java | 0 .../walkers/haplotypecaller}/LDMerger.java | 0 .../MergeVariantsAcrossHaplotypes.java | 0 ...inder.java => EmptyPathHaplotypeFinderNode.java} | 0 .../ReferenceConfidenceVariantContextMerger.java | 0 .../recalibration/ContextCovariateUnitTest.java | 0 .../recalibration/CycleCovariateUnitTest.java | 0 .../recalibration/QualQuantizerUnitTest.java | 0 .../recalibration/ReadCovariatesUnitTest.java | 0 .../recalibration/ReadGroupCovariateUnitTest.java | 0 .../recalibration/RecalDatumUnitTest.java | 0 .../recalibration/RecalUtilsUnitTest.java | 0 .../recalibration/RecalibrationReportUnitTest.java | 0 .../recalibration/RecalibrationTablesUnitTest.java | 0 .../recalibration/RecalibrationTestUtils.java | 0 .../recalibration/RepeatCovariatesUnitTest.java | 0 .../genotyper}/NanoSchedulerIntegrationTest.java | 0 .../walkers}/genotyper/ReadLikelihoodsUnitTest.java | 0 .../haplotypecaller}/ActiveRegionTestDataSet.java | 0 .../FastLoglessPairHMMUnitTest.java | 0 .../HaplotypeBaseComparatorUnitTest.java | 0 .../HaplotypeLDCalculatorUnitTest.java | 0 .../HaplotypeScoreComparatorUnitTest.java | 0 .../HaplotypeSizeAndBaseComparatorUnitTest.java | 0 .../walkers/haplotypecaller}/LDMergerUnitTest.java | 0 .../PairHMMProbabilityBugIntegrationTest.java | 0 .../variantutils}/VariantContextMergerUnitTest.java | 0 .../diffengine/DiffEngineUnitTest.java | 0 .../diffengine/DiffNodeUnitTest.java | 0 .../diffengine/DiffableReaderUnitTest.java | 0 .../diffengine/DifferenceUnitTest.java | 0 .../main/java/htsjdk/samtools/GATKBAMFileSpan.java | 0 .../src/main/java/htsjdk/samtools/GATKBin.java | 0 .../src/main/java/htsjdk/samtools/GATKChunk.java | 0 .../java/htsjdk/samtools/PicardNamespaceUtils.java | 0 .../gatk/engine/CommandLineExecutable.java | 0 .../broadinstitute/gatk/engine/CommandLineGATK.java | 0 .../broadinstitute/gatk/engine}/GATKVCFUtils.java | 0 .../gatk/engine/GenomeAnalysisEngine.java | 0 .../broadinstitute/gatk/engine/ReadProperties.java | 0 .../broadinstitute/gatk/engine}/SampleUtils.java | 0 .../broadinstitute/gatk/engine/WalkerManager.java | 0 .../gatk/engine/alignment/Aligner.java | 0 .../gatk/engine/alignment/Alignment.java | 0 .../gatk/engine/alignment/bwa/BWAAligner.java | 0 .../gatk/engine/alignment/bwa/BWAConfiguration.java | 0 .../gatk/engine/alignment/bwa/BWTFiles.java | 0 .../alignment/bwa/java/AlignerTestHarness.java | 0 .../alignment/bwa/java/AlignmentMatchSequence.java | 0 .../engine/alignment/bwa/java/AlignmentState.java | 0 .../engine/alignment/bwa/java/BWAAlignment.java | 0 .../engine/alignment/bwa/java/BWAJavaAligner.java | 0 .../gatk/engine/alignment/bwa/java/LowerBound.java | 0 .../gatk/engine/alignment/package-info.java | 0 .../engine/alignment/reference/bwt/AMBWriter.java | 0 .../engine/alignment/reference/bwt/ANNWriter.java | 0 .../gatk/engine/alignment/reference/bwt/BWT.java | 0 .../engine/alignment/reference/bwt/BWTReader.java | 0 .../bwt/BWTSupplementaryFileGenerator.java | 0 .../engine/alignment/reference/bwt/BWTWriter.java | 0 .../gatk/engine/alignment/reference/bwt/Bases.java | 0 .../gatk/engine/alignment/reference/bwt/Counts.java | 0 .../reference/bwt/CreateBWTFromReference.java | 0 .../alignment/reference/bwt/SequenceBlock.java | 0 .../engine/alignment/reference/bwt/SuffixArray.java | 0 .../alignment/reference/bwt/SuffixArrayReader.java | 0 .../alignment/reference/bwt/SuffixArrayWriter.java | 0 .../reference/packing/BasePackedInputStream.java | 0 .../reference/packing/BasePackedOutputStream.java | 0 .../reference/packing/CreatePACFromReference.java | 0 .../alignment/reference/packing/PackUtils.java | 0 .../packing/UnsignedIntPackedInputStream.java | 0 .../packing/UnsignedIntPackedOutputStream.java | 0 .../engine/arguments/DbsnpArgumentCollection.java | 0 .../engine/arguments/GATKArgumentCollection.java | 0 ...andardVariantContextInputArgumentCollection.java | 0 .../gatk/engine}/crypt/CryptUtils.java | 0 .../broadinstitute/gatk/engine}/crypt/GATKKey.java | 0 .../gatk/engine/datasources/package-info.java | 0 .../engine/datasources/providers/AllLocusView.java | 0 .../datasources/providers/CoveredLocusView.java | 0 .../IntervalOverlappingRODsFromStream.java | 0 .../providers/IntervalReferenceOrderedView.java | 0 .../providers/InvalidPositionException.java | 0 .../datasources/providers/LocusReferenceView.java | 0 .../providers/LocusShardDataProvider.java | 0 .../engine/datasources/providers/LocusView.java | 0 .../providers/ManagingReferenceOrderedView.java | 0 .../datasources/providers/RODMetaDataContainer.java | 0 .../providers/ReadBasedReferenceOrderedView.java | 0 .../datasources/providers/ReadReferenceView.java | 0 .../providers/ReadShardDataProvider.java | 0 .../gatk/engine/datasources/providers/ReadView.java | 0 .../datasources/providers/ReferenceOrderedView.java | 0 .../engine/datasources/providers/ReferenceView.java | 0 .../engine/datasources/providers/RodLocusView.java | 0 .../datasources/providers/ShardDataProvider.java | 0 .../gatk/engine/datasources/providers/View.java | 0 .../engine/datasources/providers/package-info.java | 0 .../reads/ActiveRegionShardBalancer.java | 0 .../engine/datasources/reads/BAMAccessPlan.java | 0 .../gatk/engine/datasources/reads/BAMSchedule.java | 0 .../gatk/engine/datasources/reads/BAMScheduler.java | 0 .../reads/BGZFBlockLoadingDispatcher.java | 0 .../engine/datasources/reads/BlockInputStream.java | 0 .../gatk/engine/datasources/reads/BlockLoader.java | 0 .../engine/datasources/reads/FileHandleCache.java | 0 .../gatk/engine/datasources/reads/FilePointer.java | 0 .../gatk/engine/datasources/reads/GATKBAMIndex.java | 0 .../engine/datasources/reads/GATKBAMIndexData.java | 0 .../reads/IntervalOverlapFilteringIterator.java | 0 .../engine/datasources/reads/IntervalSharder.java | 0 .../gatk/engine/datasources/reads/LocusShard.java | 0 .../datasources/reads/LocusShardBalancer.java | 0 .../gatk/engine/datasources/reads/ReadShard.java | 0 .../engine/datasources/reads/ReadShardBalancer.java | 0 .../engine/datasources/reads/SAMDataSource.java | 0 .../gatk/engine/datasources/reads/Shard.java | 0 .../engine/datasources/reads/ShardBalancer.java | 0 .../gatk/engine/datasources/reads/package-info.java | 0 .../datasources/reads/utilities/BAMFileStat.java | 0 .../datasources/reads/utilities/BAMTagRenamer.java | 0 .../reads/utilities/FindLargeShards.java | 0 .../datasources/reads/utilities/PrintBAMRegion.java | 0 .../reads/utilities/PrintBGZFBounds.java | 0 .../reads/utilities/UnzipSingleBlock.java | 0 .../datasources/reads/utilities/package-info.java | 0 .../datasources/reference/ReferenceDataSource.java | 0 .../engine/datasources/reference/package-info.java | 0 .../engine/datasources/rmd/DataStreamSegment.java | 0 .../gatk/engine/datasources/rmd/EntireStream.java | 0 .../engine/datasources/rmd/MappedStreamSegment.java | 0 .../datasources/rmd/ReferenceOrderedDataPool.java | 0 .../datasources/rmd/ReferenceOrderedDataSource.java | 0 .../gatk/engine/datasources/rmd/ResourcePool.java | 0 .../gatk/engine/datasources/rmd/package-info.java | 0 .../gatk/engine/executive/Accumulator.java | 0 .../executive/HierarchicalMicroScheduler.java | 0 .../executive/HierarchicalMicroSchedulerMBean.java | 0 .../gatk/engine/executive/LinearMicroScheduler.java | 0 .../gatk/engine/executive/MicroScheduler.java | 0 .../gatk/engine/executive/MicroSchedulerMBean.java | 0 .../gatk/engine/executive/OutputMergeTask.java | 0 .../gatk/engine/executive/ReduceTree.java | 0 .../gatk/engine/executive/ShardTraverser.java | 0 .../gatk/engine/executive/TreeReducer.java | 0 .../gatk/engine/executive/WindowMaker.java | 0 .../gatk/engine/executive/package-info.java | 0 .../gatk/engine/filters}/BAQReadTransformer.java | 0 .../gatk/engine/filters/BadCigarFilter.java | 0 .../gatk/engine/filters/BadMateFilter.java | 0 .../engine/filters/CountingFilteringIterator.java | 0 .../gatk/engine/filters/DuplicateReadFilter.java | 0 .../filters/FailsVendorQualityCheckFilter.java | 0 .../gatk/engine/filters/FilterManager.java | 0 .../gatk/engine/filters/LibraryReadFilter.java | 0 .../gatk/engine/filters/MalformedReadFilter.java | 0 .../gatk/engine/filters/MappingQualityFilter.java | 0 .../filters/MappingQualityUnavailableFilter.java | 0 .../engine/filters/MappingQualityZeroFilter.java | 0 .../gatk/engine/filters/MateSameStrandFilter.java | 0 .../gatk/engine/filters/MaxInsertSizeFilter.java | 0 .../gatk/engine/filters/MissingReadGroupFilter.java | 0 .../engine/filters/NDNCigarReadTransformer.java | 0 .../filters/NoOriginalQualityScoresFilter.java | 0 .../engine/filters/NotPrimaryAlignmentFilter.java | 0 .../gatk/engine/filters/Platform454Filter.java | 0 .../gatk/engine/filters/PlatformFilter.java | 0 .../gatk/engine/filters/PlatformUnitFilter.java | 0 .../engine/filters/PlatformUnitFilterHelper.java | 0 .../gatk/engine/filters/ReadFilter.java | 0 .../engine/filters/ReadGroupBlackListFilter.java | 0 .../gatk/engine/filters/ReadLengthFilter.java | 0 .../gatk/engine/filters/ReadNameFilter.java | 0 .../gatk/engine/filters/ReadStrandFilter.java | 0 .../filters/ReassignMappingQualityFilter.java | 0 .../filters/ReassignOneMappingQualityFilter.java | 0 .../gatk/engine/filters/SampleFilter.java | 0 .../gatk/engine/filters/SingleReadGroupFilter.java | 0 .../gatk/engine/filters/UnmappedReadFilter.java | 0 .../gatk/engine/filters/package-info.java | 0 .../gatk/engine/io}/BySampleSAMFileWriter.java | 0 .../gatk/engine/io/DirectOutputTracker.java | 0 .../gatk/engine/io/FastqFileWriter.java | 0 .../gatk/engine/io}/NWaySAMFileWriter.java | 0 .../gatk/engine/io/OutputTracker.java | 0 .../gatk/engine/io/ThreadGroupOutputTracker.java | 0 .../gatk/engine/io/storage/OutputStreamStorage.java | 0 .../engine/io/storage/SAMFileWriterStorage.java | 0 .../gatk/engine/io/storage/Storage.java | 0 .../gatk/engine/io/storage/StorageFactory.java | 0 .../io/storage/VariantContextWriterStorage.java | 0 .../stubs/OutputStreamArgumentTypeDescriptor.java | 0 .../gatk/engine/io/stubs/OutputStreamStub.java | 0 .../stubs/SAMFileReaderArgumentTypeDescriptor.java | 0 .../stubs/SAMFileWriterArgumentTypeDescriptor.java | 0 .../gatk/engine/io/stubs/SAMFileWriterStub.java | 0 .../broadinstitute/gatk/engine/io/stubs/Stub.java | 0 .../io/stubs/VCFWriterArgumentTypeDescriptor.java | 0 .../engine/io/stubs/VariantContextWriterStub.java | 0 .../gatk/engine/iterators/BoundedReadIterator.java | 0 .../gatk/engine/iterators/GenomeLocusIterator.java | 0 .../gatk/engine/iterators/IterableIterator.java | 0 .../MalformedBAMErrorReformatingIterator.java | 0 .../MisencodedBaseQualityReadTransformer.java | 0 .../gatk/engine/iterators/NullSAMIterator.java | 0 .../gatk/engine/iterators/PeekingIterator.java | 0 .../engine/iterators/PositionTrackingIterator.java | 0 .../gatk/engine/iterators/RNAReadTransformer.java | 0 .../engine/iterators/ReadFormattingIterator.java | 0 .../gatk/engine/iterators/ReadTransformer.java | 0 .../gatk/engine/iterators/ReadTransformersMode.java | 0 .../engine/iterators}/ReadTransformingIterator.java | 0 .../gatk/engine/iterators/VerifyingSamIterator.java | 0 .../gatk/engine/iterators/package-info.java | 0 .../gatk/engine/phonehome/GATKRunReport.java | 0 .../engine/phonehome/GATKRunReportException.java | 0 .../gatk/engine}/recalibration/BQSRArgumentSet.java | 0 .../gatk/engine}/recalibration/BQSRMode.java | 0 .../engine/resourcemanagement/ThreadAllocation.java | 0 .../gatk/engine/samples/Affection.java | 0 .../broadinstitute/gatk/engine/samples/Gender.java | 0 .../gatk/engine/samples}/MendelianViolation.java | 0 .../gatk/engine/samples/PedReader.java | 0 .../gatk/engine/samples/PedigreeValidationType.java | 0 .../broadinstitute/gatk/engine/samples/Sample.java | 0 .../gatk/engine/samples/SampleDB.java | 0 .../gatk/engine/samples/SampleDBBuilder.java | 0 .../broadinstitute/gatk/engine/samples/Trio.java | 0 .../traversals}/ArtificialReadsTraversal.java | 0 .../gatk/engine/traversals/TAROrderedReadCache.java | 0 .../gatk/engine/traversals/TraversalEngine.java | 0 .../engine/traversals/TraverseActiveRegions.java | 0 .../gatk/engine/traversals/TraverseDuplicates.java | 0 .../gatk/engine/traversals/TraverseLociNano.java | 0 .../gatk/engine/traversals/TraverseReadPairs.java | 0 .../gatk/engine/traversals/TraverseReadsNano.java | 0 .../gatk/engine/traversals/package-info.java | 0 .../walkers/ActiveRegionTraversalParameters.java | 0 .../gatk/engine/walkers/ActiveRegionWalker.java | 0 .../broadinstitute/gatk/engine/walkers/Allows.java | 0 .../gatk/engine/walkers/Attribution.java | 0 .../broadinstitute/gatk/engine/walkers/BAQMode.java | 0 .../org/broadinstitute/gatk/engine/walkers/By.java | 0 .../gatk/engine/walkers/DataSource.java | 0 .../gatk/engine/walkers/Downsample.java | 0 .../gatk/engine/walkers/DuplicateWalker.java | 0 .../gatk/engine/walkers/LocusWalker.java | 0 .../gatk/engine/walkers/NanoSchedulable.java | 0 .../gatk/engine/walkers/PartitionBy.java | 0 .../gatk/engine/walkers/PartitionType.java | 0 .../org/broadinstitute/gatk/engine/walkers/RMD.java | 0 .../gatk/engine/walkers/ReadFilters.java | 0 .../gatk/engine/walkers/ReadPairWalker.java | 0 .../gatk/engine/walkers/ReadWalker.java | 0 .../gatk/engine/walkers/RefWalker.java | 0 .../gatk/engine/walkers/Reference.java | 0 .../gatk/engine/walkers/RemoveProgramRecords.java | 0 .../gatk/engine/walkers/Requires.java | 0 .../gatk/engine/walkers/RodWalker.java | 0 .../gatk/engine/walkers/TreeReducible.java | 0 .../broadinstitute/gatk/engine/walkers/Walker.java | 0 .../gatk/engine/walkers/WalkerName.java | 0 .../broadinstitute/gatk/engine/walkers/Window.java | 0 .../src/main/resources/GATK_public.key | Bin .../engine/phonehome/resources/GATK_AWS_access.key | Bin .../engine/phonehome/resources/GATK_AWS_secret.key | Bin .../gatk/engine}/recalibration/BQSR.R | 0 .../htsjdk/samtools/GATKBAMFileSpanUnitTest.java | 0 .../java/htsjdk/samtools/GATKChunkUnitTest.java | 0 .../gatk/engine/CommandLineGATKUnitTest.java | 0 .../gatk/engine/EngineFeaturesIntegrationTest.java | 0 .../gatk/engine}/GATKVCFUtilsUnitTest.java | 0 .../gatk/engine/GenomeAnalysisEngineUnitTest.java | 0 .../gatk/engine/MaxRuntimeIntegrationTest.java | 0 .../gatk/engine/ReadMetricsUnitTest.java | 0 .../gatk/engine}/SampleUtilsUnitTest.java | 0 .../gatk/engine/WalkerManagerUnitTest.java | 0 .../engine/arguments}/IntervalIntegrationTest.java | 0 .../arguments}/InvalidArgumentIntegrationTest.java | 0 .../engine/arguments}/LoggingIntegrationTest.java | 0 .../gatk/engine}/crypt/CryptUtilsUnitTest.java | 0 .../gatk/engine}/crypt/GATKKeyIntegrationTest.java | 0 .../gatk/engine}/crypt/GATKKeyUnitTest.java | 0 .../datasources/providers/AllLocusViewUnitTest.java | 0 .../providers/CoveredLocusViewUnitTest.java | 0 .../IntervalReferenceOrderedViewUnitTest.java | 0 .../providers/LocusReferenceViewUnitTest.java | 0 .../datasources/providers/LocusViewTemplate.java | 0 .../providers/ReadReferenceViewUnitTest.java | 0 .../providers/ReferenceOrderedViewUnitTest.java | 0 .../providers/ReferenceViewTemplate.java | 0 .../providers/ShardDataProviderUnitTest.java | 0 .../reads/ActiveRegionShardBalancerUnitTest.java | 0 .../datasources/reads/DownsamplerBenchmark.java | 0 .../datasources/reads/FilePointerUnitTest.java | 0 .../datasources/reads/GATKBAMIndexUnitTest.java | 0 .../datasources/reads/GATKWalkerBenchmark.java | 0 .../IntervalOverlapFilteringIteratorUnitTest.java | 0 .../engine/datasources/reads/MockLocusShard.java | 0 .../datasources/reads/PicardBaselineBenchmark.java | 0 .../datasources/reads/ReadProcessingBenchmark.java | 0 .../reads/ReadShardBalancerUnitTest.java | 0 .../datasources/reads/SAMDataSourceUnitTest.java | 0 .../datasources/reads/SAMReaderIDUnitTest.java | 0 .../reads/SeekableBufferedStreamUnitTest.java | 0 .../reads/TheoreticalMinimaBenchmark.java | 0 .../ReferenceDataSourceIntegrationTest.java | 0 .../rmd/ReferenceOrderedDataPoolUnitTest.java | 0 .../rmd/ReferenceOrderedQueryDataPoolUnitTest.java | 0 .../downsampling/DownsamplingIntegrationTest.java | 0 .../DownsamplingReadsIteratorUnitTest.java | 0 .../downsampling/FractionalDownsamplerUnitTest.java | 0 .../downsampling/LevelingDownsamplerUnitTest.java | 0 .../PerSampleDownsamplingReadsIteratorUnitTest.java | 0 ...ledArtificialSingleSampleReadStreamAnalyzer.java | 0 .../downsampling/ReservoirDownsamplerUnitTest.java | 0 .../SimplePositionalDownsamplerUnitTest.java | 0 .../gatk/engine/executive/ReduceTreeUnitTest.java | 0 .../AllowNCigarMalformedReadFilterUnitTest.java | 0 .../gatk/engine/filters/BadCigarFilterUnitTest.java | 0 .../filters/BadReadGroupsIntegrationTest.java | 0 .../engine/filters/MalformedReadFilterUnitTest.java | 0 .../filters/NDNCigarReadTransformerUnitTest.java | 0 .../gatk/engine/filters/ReadFilterTest.java | 0 .../filters/ReadGroupBlackListFilterUnitTest.java | 0 .../filters/UnsafeMalformedReadFilterUnitTest.java | 0 .../gatk/engine/io/OutputTrackerUnitTest.java | 0 .../io/stubs}/ArgumentTypeDescriptorUnitTest.java | 0 .../iterators/BoundedReadIteratorUnitTest.java | 0 .../iterators/GATKSAMIteratorAdapterUnitTest.java | 0 .../iterators}/MisencodedBaseQualityUnitTest.java | 0 .../iterators/ReadFormattingIteratorUnitTest.java | 0 .../iterators/VerifyingSamIteratorUnitTest.java | 0 .../engine/phonehome/GATKRunReportUnitTest.java | 0 .../gatk/engine/samples/PedReaderUnitTest.java | 0 .../gatk/engine/samples/SampleDBUnitTest.java | 0 .../gatk/engine/samples/SampleUnitTest.java | 0 .../engine/traversals/DummyActiveRegionWalker.java | 0 .../traversals/TAROrderedReadCacheUnitTest.java | 0 .../traversals/TraverseActiveRegionsUnitTest.java | 0 .../traversals/TraverseDuplicatesUnitTest.java | 0 .../engine/traversals/TraverseReadsUnitTest.java | 0 .../gatk/engine/walkers/WalkerTest.java | 0 .../annotator/interfaces/AnnotationHelpUtils.java} | 0 .../gatk/tools}/walkers/diffengine/DiffObjects.java | 0 .../diffengine/DiffObjectsIntegrationTest.java | 0 .../walkers/variantutils}/VCFIntegrationTest.java | 0 .../src/main/assembly/example-resources.xml | 0 .../gatk/utils/AutoFormattingTime.java | 0 .../org/broadinstitute/gatk/utils/BaseUtils.java | 0 .../org/broadinstitute/gatk/utils/BitSetUtils.java | 0 .../broadinstitute/gatk/utils/ContigComparator.java | 0 .../gatk/utils/DeprecatedToolChecks.java | 0 .../broadinstitute/gatk/utils/GenomeLocParser.java | 0 .../gatk/utils/GenomeLocSortedSet.java | 0 .../broadinstitute/gatk/utils/HeapSizeMonitor.java | 0 .../org/broadinstitute/gatk/utils/IndelUtils.java | 0 .../org/broadinstitute/gatk/utils/LRUCache.java | 0 .../gatk/utils/MRUCachingSAMSequenceDictionary.java | 0 .../org/broadinstitute/gatk/utils/MannWhitneyU.java | 0 .../org/broadinstitute/gatk/utils/MathUtils.java | 0 .../java/org/broadinstitute/gatk/utils/Median.java | 0 .../gatk/utils/MultiThreadedErrorTracker.java | 0 .../org/broadinstitute/gatk/utils/NGSPlatform.java | 0 .../org/broadinstitute/gatk/utils/PathUtils.java | 0 .../org/broadinstitute/gatk/utils/QualityUtils.java | 0 .../gatk/utils/R/RScriptExecutor.java | 0 .../gatk/utils/R/RScriptExecutorException.java | 0 .../broadinstitute/gatk/utils/R/RScriptLibrary.java | 0 .../org/broadinstitute/gatk/utils/R/RUtils.java | 0 .../gatk/utils/SequenceDictionaryUtils.java | 0 .../gatk/utils/UnvalidatingGenomeLoc.java | 0 .../java/org/broadinstitute/gatk/utils/Utils.java | 0 .../gatk/utils}/ValidationExclusion.java | 0 .../gatk/utils/activeregion/ActiveRegion.java | 0 .../utils/activeregion/ActiveRegionReadState.java | 0 .../gatk/utils/activeregion/ActivityProfile.java | 0 .../utils/activeregion/ActivityProfileState.java | 0 .../utils/activeregion/BandPassActivityProfile.java | 0 .../gatk/utils/analysis/AminoAcid.java | 0 .../gatk/utils/analysis/AminoAcidTable.java | 0 .../gatk/utils/analysis/AminoAcidUtils.java | 0 .../java/org/broadinstitute/gatk/utils/baq/BAQ.java | 0 .../gatk/utils/classloader/JVMUtils.java | 0 .../gatk/utils/classloader/PluginManager.java | 0 .../utils/classloader/ProtectedPackageSource.java | 0 .../gatk/utils/classloader/PublicPackageSource.java | 0 .../gatk/utils/clipping/ClippingOp.java | 0 .../gatk/utils/clipping/ClippingRepresentation.java | 0 .../gatk/utils/clipping/ReadClipper.java | 0 .../gatk/utils/codecs/beagle/BeagleCodec.java | 0 .../gatk/utils/codecs/beagle/BeagleFeature.java | 0 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protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/BQSRReadTransformer.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/BaseRecalibration.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/QualQuantizer.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/QuantizationInfo.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/ReadCovariates.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RecalDatum.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RecalDatumNode.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RecalUtils.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{tools/walkers/bqsr => engine/recalibration}/RecalibrationArgumentCollection.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RecalibrationReport.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RecalibrationTables.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/ContextCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/Covariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/CycleCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/ExperimentalCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/QualityScoreCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/ReadGroupCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/RepeatCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/RepeatLengthCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/RepeatUnitAndLengthCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/RepeatUnitCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/RequiredCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils => engine}/recalibration/covariates/StandardCovariate.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{engine/arguments => tools/walkers/genotyper}/StandardCallerArgumentCollection.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils/haplotype => tools/walkers/haplotypecaller}/HaplotypeLDCalculator.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils/haplotype => tools/walkers/haplotypecaller}/LDMerger.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils/haplotype => tools/walkers/haplotypecaller}/MergeVariantsAcrossHaplotypes.java (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/{EmptyPathHaplotypeFinder.java => EmptyPathHaplotypeFinderNode.java} (100%) rename protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/{utils/variant => tools/walkers/variantutils}/ReferenceConfidenceVariantContextMerger.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/ContextCovariateUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/CycleCovariateUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/QualQuantizerUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/ReadCovariatesUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/ReadGroupCovariateUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RecalDatumUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RecalUtilsUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RecalibrationReportUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RecalibrationTablesUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RecalibrationTestUtils.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => engine}/recalibration/RepeatCovariatesUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils/nanoScheduler => tools/walkers/genotyper}/NanoSchedulerIntegrationTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils => tools/walkers}/genotyper/ReadLikelihoodsUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils/pairhmm => tools/walkers/haplotypecaller}/ActiveRegionTestDataSet.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils/pairhmm => tools/walkers/haplotypecaller}/FastLoglessPairHMMUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils/haplotype => tools/walkers/haplotypecaller}/HaplotypeBaseComparatorUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils/haplotype => tools/walkers/haplotypecaller}/HaplotypeLDCalculatorUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils/haplotype => tools/walkers/haplotypecaller}/HaplotypeScoreComparatorUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils/haplotype => tools/walkers/haplotypecaller}/HaplotypeSizeAndBaseComparatorUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils/haplotype => tools/walkers/haplotypecaller}/LDMergerUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils/pairhmm => tools/walkers/haplotypecaller}/PairHMMProbabilityBugIntegrationTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{utils/variant => tools/walkers/variantutils}/VariantContextMergerUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{engine/walkers => utils}/diffengine/DiffEngineUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{engine/walkers => utils}/diffengine/DiffNodeUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{engine/walkers => utils}/diffengine/DiffableReaderUnitTest.java (100%) rename protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/{engine/walkers => utils}/diffengine/DifferenceUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/htsjdk/samtools/GATKBin.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/htsjdk/samtools/GATKChunk.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java 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gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java (100%) rename public/{gatk-tools-public => 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gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils => gatk-engine/src/main/java/org/broadinstitute/gatk/engine}/crypt/CryptUtils.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils => gatk-engine/src/main/java/org/broadinstitute/gatk/engine}/crypt/GATKKey.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java (100%) rename public/{gatk-tools-public 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gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java 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rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq => gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters}/BAQReadTransformer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam => gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io}/BySampleSAMFileWriter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam => gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io}/NWaySAMFileWriter.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileReaderArgumentTypeDescriptor.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam => gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators}/MisencodedBaseQualityReadTransformer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq => gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators}/ReadTransformingIterator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils => gatk-engine/src/main/java/org/broadinstitute/gatk/engine}/recalibration/BQSRArgumentSet.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils => gatk-engine/src/main/java/org/broadinstitute/gatk/engine}/recalibration/BQSRMode.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils => gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples}/MendelianViolation.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam => gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals}/ArtificialReadsTraversal.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/resources/GATK_public.key (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_access.key (100%) rename public/{gatk-tools-public => gatk-engine}/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_secret.key (100%) rename public/{gatk-tools-public/src/main/resources/org/broadinstitute/gatk/utils => gatk-engine/src/main/resources/org/broadinstitute/gatk/engine}/recalibration/BQSR.R (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant => gatk-engine/src/test/java/org/broadinstitute/gatk/engine}/GATKVCFUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils => gatk-engine/src/test/java/org/broadinstitute/gatk/engine}/SampleUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval => gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments}/IntervalIntegrationTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline => gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments}/InvalidArgumentIntegrationTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline => gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments}/LoggingIntegrationTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils => gatk-engine/src/test/java/org/broadinstitute/gatk/engine}/crypt/CryptUtilsUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils => gatk-engine/src/test/java/org/broadinstitute/gatk/engine}/crypt/GATKKeyIntegrationTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils => gatk-engine/src/test/java/org/broadinstitute/gatk/engine}/crypt/GATKKeyUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline => gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs}/ArgumentTypeDescriptorUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam => gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators}/MisencodedBaseQualityUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-engine}/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java (100%) rename public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/{utils/help/HelpUtils.java => tools/walkers/annotator/interfaces/AnnotationHelpUtils.java} (100%) rename public/gatk-tools-public/src/{main/java/org/broadinstitute/gatk/engine => test/java/org/broadinstitute/gatk/tools}/walkers/diffengine/DiffObjects.java (100%) rename {protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine => public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/diffengine/DiffObjectsIntegrationTest.java (100%) rename public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/{utils/variant => tools/walkers/variantutils}/VCFIntegrationTest.java (100%) rename public/{gatk-engine => gatk-utils}/src/main/assembly/example-resources.xml (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/Median.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/Utils.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/ValidationExclusion.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java 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gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline}/Multiplex.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline}/Multiplexer.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/contexts/AlignmentContext.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/contexts/AlignmentContextUtils.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/contexts/ReferenceContext.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/diffengine/BAMDiffableReader.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/diffengine/DiffElement.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/diffengine/DiffEngine.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/diffengine/DiffNode.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/diffengine/DiffValue.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/diffengine/DiffableReader.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/diffengine/Difference.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/diffengine/GATKReportDiffableReader.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/diffengine/VCFDiffableReader.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/AlleleBiasedDownsamplingUtils.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/DownsampleType.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/Downsampler.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/DownsamplingMethod.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/DownsamplingReadsIterator.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/DownsamplingUtils.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/FractionalDownsampler.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/FractionalDownsamplerFactory.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/LevelingDownsampler.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/PassThroughDownsampler.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/PerSampleDownsamplingReadsIterator.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/ReadsDownsampler.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/ReadsDownsamplerFactory.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/ReservoirDownsampler.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/ReservoirDownsamplerFactory.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/SimplePositionalDownsampler.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/downsampling/SimplePositionalDownsamplerFactory.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/genotyper/AlleleList.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/genotyper/AlleleListPermutation.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/genotyper/AlleleListUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/genotyper/IndexedAlleleList.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/genotyper/IndexedSampleList.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/genotyper/SampleList.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/genotyper/SampleListUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java (100%) rename 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gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/iterators/GATKSAMIterator.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/iterators/GATKSAMIteratorAdapter.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/iterators/PushbackIterator.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java (100%) rename public/{gatk-tools-public => 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gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java (100%) rename 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gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/RODRecordListImpl.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/RefMetaDataTracker.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/ReferenceDependentFeatureCodec.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/ReferenceOrderedDatum.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/SeekableRODIterator.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/VariantContextAdaptors.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/package-info.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/tracks/FeatureManager.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/tracks/IndexDictionaryUtils.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/tracks/RMDTrack.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/tracks/RMDTrackBuilder.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/utils/FeatureToGATKFeatureIterator.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/utils/FlashBackIterator.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/utils/GATKFeature.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/utils/LocationAwareSeekableRODIterator.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/utils/RMDTriplet.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/refdata/utils/RODRecordList.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/report/GATKReport.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/report/GATKReportColumn.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine => gatk-utils/src/main/java/org/broadinstitute/gatk/utils}/report/GATKReportColumnFormat.java (100%) rename 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gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java (100%) rename 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gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators => gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam}/GATKSAMRecordIterator.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java (100%) rename public/{gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads => gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam}/SAMReaderID.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java (100%) rename 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public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine => gatk-utils/src/test/java/org/broadinstitute/gatk/utils}/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine => gatk-utils/src/test/java/org/broadinstitute/gatk/utils}/refdata/RefMetaDataTrackerUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine => gatk-utils/src/test/java/org/broadinstitute/gatk/utils}/refdata/tracks/FeatureManagerUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine => gatk-utils/src/test/java/org/broadinstitute/gatk/utils}/refdata/tracks/RMDTrackBuilderUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine => gatk-utils/src/test/java/org/broadinstitute/gatk/utils}/refdata/utils/CheckableCloseableTribbleIterator.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine => gatk-utils/src/test/java/org/broadinstitute/gatk/utils}/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine => gatk-utils/src/test/java/org/broadinstitute/gatk/utils}/refdata/utils/FlashBackIteratorUnitTest.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine => gatk-utils/src/test/java/org/broadinstitute/gatk/utils}/refdata/utils/TestFeatureReader.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine => gatk-utils/src/test/java/org/broadinstitute/gatk/utils}/refdata/utils/TestRMDTrackBuilder.java (100%) rename public/{gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine => gatk-utils/src/test/java/org/broadinstitute/gatk/utils}/report/GATKReportUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleBAM.bam (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleBAM.bam.bai (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleBAM.simple.bai (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleBAM.simple.bam (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleDBSNP.vcf (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleDBSNP.vcf.idx (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA-3contigs.fasta (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA-combined.fasta (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA-windows.fasta (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.dict (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.fasta (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.fasta.amb (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.fasta.ann (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.fasta.bwt (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.fasta.fai (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.fasta.pac (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.fasta.rbwt (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.fasta.rpac (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.fasta.rsa (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleFASTA.fasta.sa (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleGATKReport.eval (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleGATKReportv1.tbl (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleGATKReportv2.tbl (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleGRP.grp (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleINTERVAL.intervals (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleNORG.bam (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/exampleNORG.bam.bai (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/forAlleleFractionSimulation.vcf (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/forAlleleFractionSimulation.vcf.idx (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/forLongInsert.vcf (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/forLongInsert.vcf.idx (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/forSimulation.vcf (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/forSimulation.vcf.idx (100%) rename public/{gatk-tools-public => gatk-utils}/src/test/resources/testProperties.properties (100%) rename public/{gatk-engine => gatk-utils}/src/test/resources/testfile.sam (100%) 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/engine/recalibration/BQSRGatherer.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGatherer.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java 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/engine/recalibration/BQSRReadTransformer.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRReadTransformer.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java 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/engine/recalibration/BaseRecalibration.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BaseRecalibration.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java 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/engine/recalibration/QualQuantizer.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizer.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java 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/engine/recalibration/QuantizationInfo.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QuantizationInfo.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java 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/engine/recalibration/ReadCovariates.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariates.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java 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/engine/recalibration/RecalDatum.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatum.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java 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/engine/recalibration/RecalDatumNode.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumNode.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java 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/engine/recalibration/RecalUtils.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalUtils.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java 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/engine/recalibration/RecalibrationArgumentCollection.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationArgumentCollection.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java 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/engine/recalibration/RecalibrationReport.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReport.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java 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/engine/recalibration/RecalibrationTables.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTables.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java 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/engine/recalibration/covariates/ContextCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ContextCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java 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/engine/recalibration/covariates/Covariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/Covariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java 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/engine/recalibration/covariates/CycleCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/CycleCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java 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/engine/recalibration/covariates/ExperimentalCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ExperimentalCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java 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/engine/recalibration/covariates/QualityScoreCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/QualityScoreCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java 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/engine/recalibration/covariates/ReadGroupCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ReadGroupCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java 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/engine/recalibration/covariates/RepeatCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java 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/engine/recalibration/covariates/RepeatLengthCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatLengthCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java 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/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java 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/engine/recalibration/covariates/RepeatUnitCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java 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/engine/recalibration/covariates/RequiredCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RequiredCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java 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/engine/recalibration/covariates/StandardCovariate.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/StandardCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java 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/tools/walkers/genotyper/StandardCallerArgumentCollection.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardCallerArgumentCollection.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java 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/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java 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/tools/walkers/haplotypecaller/LDMerger.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/LDMerger.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java 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/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/MergeVariantsAcrossHaplotypes.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java 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/EmptyPathHaplotypeFinderNode.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/ReferenceConfidenceVariantContextMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java similarity index 100% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/ReferenceConfidenceVariantContextMerger.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java 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/engine/recalibration/ContextCovariateUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ContextCovariateUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java 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/engine/recalibration/CycleCovariateUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/CycleCovariateUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java 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/engine/recalibration/QualQuantizerUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java 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/engine/recalibration/ReadCovariatesUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariatesUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java 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/engine/recalibration/ReadGroupCovariateUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadGroupCovariateUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java 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/engine/recalibration/RecalDatumUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumUnitTest.java 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/engine/recalibration/RecalUtilsUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalUtilsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java 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/engine/recalibration/RecalibrationReportUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReportUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java 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/engine/recalibration/RecalibrationTablesUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTablesUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java 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/engine/recalibration/RecalibrationTestUtils.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTestUtils.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java 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/engine/recalibration/RepeatCovariatesUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RepeatCovariatesUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java 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/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoodsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java 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/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/ActiveRegionTestDataSet.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java 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/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMMUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java 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/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java 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/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java 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/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java 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/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java 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/tools/walkers/haplotypecaller/LDMergerUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/LDMergerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java 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/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextMergerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java 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/utils/diffengine/DiffEngineUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngineUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java 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/utils/diffengine/DiffNodeUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNodeUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java 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/utils/diffengine/DiffableReaderUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReaderUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java 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/utils/diffengine/DifferenceUnitTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DifferenceUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java diff --git a/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java b/public/gatk-engine/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java similarity index 100% rename from public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java rename to public/gatk-engine/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java diff --git a/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBin.java b/public/gatk-engine/src/main/java/htsjdk/samtools/GATKBin.java similarity index 100% rename from public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBin.java rename to public/gatk-engine/src/main/java/htsjdk/samtools/GATKBin.java diff --git a/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKChunk.java b/public/gatk-engine/src/main/java/htsjdk/samtools/GATKChunk.java similarity index 100% rename from public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKChunk.java rename to public/gatk-engine/src/main/java/htsjdk/samtools/GATKChunk.java diff --git a/public/gatk-tools-public/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java b/public/gatk-engine/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java rename to public/gatk-engine/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtils.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/SampleUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/SampleUtils.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/CryptUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/CryptUtils.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/GATKKey.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/GATKKey.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQReadTransformer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/BySampleSAMFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/BySampleSAMFileWriter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/NWaySAMFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/NWaySAMFileWriter.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileReaderArgumentTypeDescriptor.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileReaderArgumentTypeDescriptor.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileReaderArgumentTypeDescriptor.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileReaderArgumentTypeDescriptor.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityReadTransformer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/ReadTransformingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/ReadTransformingIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRArgumentSet.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRArgumentSet.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRMode.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRMode.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MendelianViolation.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MendelianViolation.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialReadsTraversal.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialReadsTraversal.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java diff --git a/public/gatk-tools-public/src/main/resources/GATK_public.key b/public/gatk-engine/src/main/resources/GATK_public.key similarity index 100% rename from public/gatk-tools-public/src/main/resources/GATK_public.key rename to public/gatk-engine/src/main/resources/GATK_public.key diff --git a/public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_access.key b/public/gatk-engine/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_access.key similarity index 100% rename from public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_access.key rename to public/gatk-engine/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_access.key diff --git a/public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_secret.key b/public/gatk-engine/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_secret.key similarity index 100% rename from public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_secret.key rename to public/gatk-engine/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_secret.key diff --git a/public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/utils/recalibration/BQSR.R b/public/gatk-engine/src/main/resources/org/broadinstitute/gatk/engine/recalibration/BQSR.R similarity index 100% rename from public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/utils/recalibration/BQSR.R rename to public/gatk-engine/src/main/resources/org/broadinstitute/gatk/engine/recalibration/BQSR.R diff --git a/public/gatk-tools-public/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java b/public/gatk-engine/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java rename to public/gatk-engine/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java b/public/gatk-engine/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java rename to public/gatk-engine/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtilsUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SampleUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SampleUtilsUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalIntegrationTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/InvalidArgumentIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/InvalidArgumentIntegrationTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/LoggingIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/LoggingIntegrationTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/CryptUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/CryptUtilsUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyIntegrationTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptorUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java rename to public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java 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/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjects.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjects.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjectsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java similarity index 100% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjectsIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java 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/tools/walkers/variantutils/VCFIntegrationTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VCFIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java diff --git a/public/gatk-engine/src/main/assembly/example-resources.xml b/public/gatk-utils/src/main/assembly/example-resources.xml similarity index 100% rename from public/gatk-engine/src/main/assembly/example-resources.xml rename to public/gatk-utils/src/main/assembly/example-resources.xml diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/Median.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/Median.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/Utils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/Utils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/ValidationExclusion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/ValidationExclusion.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Multiplex.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Multiplex.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Multiplexer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Multiplexer.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContext.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContext.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContextUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/ReferenceContext.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/ReferenceContext.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/BAMDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/BAMDiffableReader.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffElement.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffElement.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngine.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNode.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNode.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffValue.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReader.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/Difference.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/Difference.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/GATKReportDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/GATKReportDiffableReader.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/VCFDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/VCFDiffableReader.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsampleType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsampleType.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/Downsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/Downsampler.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingMethod.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingMethod.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsampler.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerFactory.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsampler.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PassThroughDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PassThroughDownsampler.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsampler.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsamplerFactory.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsampler.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerFactory.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsampler.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerFactory.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleList.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListPermutation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListPermutation.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleList.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleList.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleList.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapter.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PushbackIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PushbackIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup2/Notes b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup2/Notes similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup2/Notes rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup2/Notes diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RODRecordListImpl.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RODRecordListImpl.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTracker.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceDependentFeatureCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceDependentFeatureCodec.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceOrderedDatum.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceOrderedDatum.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/SeekableRODIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/SeekableRODIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/VariantContextAdaptors.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/VariantContextAdaptors.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/package-info.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManager.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/IndexDictionaryUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrack.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrack.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilder.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/GATKFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/GATKFeature.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/LocationAwareSeekableRODIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/LocationAwareSeekableRODIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RMDTriplet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RMDTriplet.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RODRecordList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RODRecordList.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReport.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReport.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumn.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumn.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumnFormat.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumnFormat.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportDataType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportDataType.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportGatherer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportGatherer.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportTable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportTable.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportVersion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportVersion.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/GATKSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/GATKSAMFileWriter.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMRecordIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMRecordIterator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderID.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderID.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCountConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCountConstants.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java similarity index 100% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTrackerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTrackerUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManagerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManagerUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/CheckableCloseableTribbleIterator.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/CheckableCloseableTribbleIterator.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIteratorUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestFeatureReader.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestFeatureReader.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestRMDTrackBuilder.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestRMDTrackBuilder.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/report/GATKReportUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/report/GATKReportUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java similarity index 100% rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java diff --git a/public/gatk-engine/src/test/resources/exampleBAM.bam b/public/gatk-utils/src/test/resources/exampleBAM.bam similarity index 100% rename from public/gatk-engine/src/test/resources/exampleBAM.bam rename to public/gatk-utils/src/test/resources/exampleBAM.bam diff --git a/public/gatk-engine/src/test/resources/exampleBAM.bam.bai b/public/gatk-utils/src/test/resources/exampleBAM.bam.bai similarity index 100% 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a/public/gatk-engine/src/test/resources/exampleFASTA-windows.fasta b/public/gatk-utils/src/test/resources/exampleFASTA-windows.fasta similarity index 100% rename from public/gatk-engine/src/test/resources/exampleFASTA-windows.fasta rename to public/gatk-utils/src/test/resources/exampleFASTA-windows.fasta diff --git a/public/gatk-engine/src/test/resources/exampleFASTA.dict b/public/gatk-utils/src/test/resources/exampleFASTA.dict similarity index 100% rename from public/gatk-engine/src/test/resources/exampleFASTA.dict rename to public/gatk-utils/src/test/resources/exampleFASTA.dict diff --git a/public/gatk-engine/src/test/resources/exampleFASTA.fasta b/public/gatk-utils/src/test/resources/exampleFASTA.fasta similarity index 100% rename from public/gatk-engine/src/test/resources/exampleFASTA.fasta rename to public/gatk-utils/src/test/resources/exampleFASTA.fasta diff --git a/public/gatk-engine/src/test/resources/exampleFASTA.fasta.amb 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public/gatk-engine/src/test/resources/exampleFASTA.fasta.fai rename to public/gatk-utils/src/test/resources/exampleFASTA.fasta.fai diff --git a/public/gatk-engine/src/test/resources/exampleFASTA.fasta.pac b/public/gatk-utils/src/test/resources/exampleFASTA.fasta.pac similarity index 100% rename from public/gatk-engine/src/test/resources/exampleFASTA.fasta.pac rename to public/gatk-utils/src/test/resources/exampleFASTA.fasta.pac diff --git a/public/gatk-engine/src/test/resources/exampleFASTA.fasta.rbwt b/public/gatk-utils/src/test/resources/exampleFASTA.fasta.rbwt similarity index 100% rename from public/gatk-engine/src/test/resources/exampleFASTA.fasta.rbwt rename to public/gatk-utils/src/test/resources/exampleFASTA.fasta.rbwt diff --git a/public/gatk-engine/src/test/resources/exampleFASTA.fasta.rpac b/public/gatk-utils/src/test/resources/exampleFASTA.fasta.rpac similarity index 100% rename from public/gatk-engine/src/test/resources/exampleFASTA.fasta.rpac rename to 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a/public/gatk-engine/src/test/resources/exampleGATKReportv1.tbl b/public/gatk-utils/src/test/resources/exampleGATKReportv1.tbl similarity index 100% rename from public/gatk-engine/src/test/resources/exampleGATKReportv1.tbl rename to public/gatk-utils/src/test/resources/exampleGATKReportv1.tbl diff --git a/public/gatk-engine/src/test/resources/exampleGATKReportv2.tbl b/public/gatk-utils/src/test/resources/exampleGATKReportv2.tbl similarity index 100% rename from public/gatk-engine/src/test/resources/exampleGATKReportv2.tbl rename to public/gatk-utils/src/test/resources/exampleGATKReportv2.tbl diff --git a/public/gatk-engine/src/test/resources/exampleGRP.grp b/public/gatk-utils/src/test/resources/exampleGRP.grp similarity index 100% rename from public/gatk-engine/src/test/resources/exampleGRP.grp rename to public/gatk-utils/src/test/resources/exampleGRP.grp diff --git a/public/gatk-engine/src/test/resources/exampleINTERVAL.intervals b/public/gatk-utils/src/test/resources/exampleINTERVAL.intervals similarity index 100% rename from public/gatk-engine/src/test/resources/exampleINTERVAL.intervals rename to public/gatk-utils/src/test/resources/exampleINTERVAL.intervals diff --git a/public/gatk-engine/src/test/resources/exampleNORG.bam b/public/gatk-utils/src/test/resources/exampleNORG.bam similarity index 100% rename from public/gatk-engine/src/test/resources/exampleNORG.bam rename to public/gatk-utils/src/test/resources/exampleNORG.bam diff --git a/public/gatk-engine/src/test/resources/exampleNORG.bam.bai b/public/gatk-utils/src/test/resources/exampleNORG.bam.bai similarity index 100% rename from public/gatk-engine/src/test/resources/exampleNORG.bam.bai rename to public/gatk-utils/src/test/resources/exampleNORG.bam.bai diff --git a/public/gatk-engine/src/test/resources/forAlleleFractionSimulation.vcf b/public/gatk-utils/src/test/resources/forAlleleFractionSimulation.vcf similarity index 100% rename from public/gatk-engine/src/test/resources/forAlleleFractionSimulation.vcf rename to public/gatk-utils/src/test/resources/forAlleleFractionSimulation.vcf diff --git a/public/gatk-engine/src/test/resources/forAlleleFractionSimulation.vcf.idx b/public/gatk-utils/src/test/resources/forAlleleFractionSimulation.vcf.idx similarity index 100% rename from public/gatk-engine/src/test/resources/forAlleleFractionSimulation.vcf.idx rename to public/gatk-utils/src/test/resources/forAlleleFractionSimulation.vcf.idx diff --git a/public/gatk-engine/src/test/resources/forLongInsert.vcf b/public/gatk-utils/src/test/resources/forLongInsert.vcf similarity index 100% rename from public/gatk-engine/src/test/resources/forLongInsert.vcf rename to public/gatk-utils/src/test/resources/forLongInsert.vcf diff --git a/public/gatk-engine/src/test/resources/forLongInsert.vcf.idx b/public/gatk-utils/src/test/resources/forLongInsert.vcf.idx similarity index 100% rename from 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