From 4e6d43d003ad32a8489c5f9273e7dc2647700a9f Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Tue, 4 Mar 2014 22:08:01 +0700 Subject: [PATCH] Refactored maven directories and java packages replacing "sting" with "gatk". To reduce merge conflicts, this commit only renames files, while file modifications are in next commit. Some updates/fixes here are actually included in the next commit. = Maven updates Moved artifacts to new package names: * private/queue-private -> private/gatk-queue-private * private/gatk-private -> private/gatk-tools-private * public/gatk-package -> protected/gatk-package-distribution * public/queue-package -> protected/gatk-queue-package-distribution * protected/gatk-protected -> protected/gatk-tools-protected * public/queue-framework -> public/gatk-queue * public/gatk-framework -> public/gatk-tools-public New poms for new artifacts and packages: * private/gatk-package-internal * private/gatk-queue-package-internal * private/gatk-queue-extensions-internal * protected/gatk-queue-extensions-distribution * public/gatk-engine Updated references to StingText.properties to GATKText.properties. Updated ant-bridge.sh to use gatk.* properties instead of sting.*. = Engine updates Renaming files containing engine parts from o.b.gatk.tools to o.b.gatk.engine. Changed package references from tools to engine for CommandLineGATK, GenomeAnalysisEngine, ReadMetrics, ReadProperties, and WalkerManager. Changed package reference tools.phonehome to engine.phonehome. Renamed classes *Sting* to *GATK*, such as ReviewedGATKException. = Test updates Moved gatk example resources. Moved test engine files from tools to engine packages. Moved resources for phonehome to proper package. Moved test classes under o.b.gatk into packages: * o.b.g.utils.{BaseTest,ExampleToCopyUnitTest,GATKTextReporter,MD5DB,MD5Mismatch,TestNGTestTransformer} * o.b.g.engine.walkers.WalkerTest Updated package names in DependencyAnalyzerOutputLoaderUnitTest's data. = Queue updates Moving queue scripts to location where generated extensions can be used. Renamed *.q to *.scala, updating licenses previously missed by git hooks. Moved queue extensions to new artifact gatk-queue-extensions. Fixed import statments frequently merge-conflicting on FullProcessingPipeline.scala. = BWA Added README on how to obtain and include bwa as a library. Updated libbwa build. Fixed packaged names under bwa/java implementation. Updated contents of BWCAligner native implementation. = Other fixes Don't duplicate the resource bundle entries by both unpacking *and* appending. (partial fix) Staged engine and utils poms to build GATKText.properties, once Utils random generator dependency on GATK engine is fixed. Re-enabled custom testng listeners/reporters and moved testng dependencies to the gatk-root. Updated comments referencing Sting with GATK. Moved a couple untangled classes from gatk-tools-public to gatk-utils and gatk-engine. --- .../gatk-package-distribution}/pom.xml | 0 .../src/main/assembly/binary-dist.xml | 0 .../pom.xml | 217 +++++++++++++++++ .../gatk-queue-package-distribution}/pom.xml | 0 .../src/main/assembly/binary-dist.xml | 0 .../pom.xml | 0 .../StandardCallerArgumentCollection.java | 0 .../broadinstitute/gatk}/package-info.java | 0 .../annotator/BaseQualityRankSumTest.java | 0 .../walkers/annotator/ChromosomeCounts.java | 0 .../annotator/ClippingRankSumTest.java | 0 .../tools}/walkers/annotator/Coverage.java | 0 .../annotator/DepthPerAlleleBySample.java | 0 .../walkers/annotator/DepthPerSampleHC.java | 0 .../walkers/annotator/FisherStrand.java | 0 .../tools}/walkers/annotator/GCContent.java | 0 .../walkers/annotator/GenotypeSummaries.java | 0 .../walkers/annotator/HaplotypeScore.java | 0 .../walkers/annotator/HardyWeinberg.java | 0 .../walkers/annotator/HomopolymerRun.java | 0 .../walkers/annotator/InbreedingCoeff.java | 0 .../annotator/LikelihoodRankSumTest.java | 0 .../walkers/annotator/MVLikelihoodRatio.java | 0 .../annotator/MappingQualityRankSumTest.java | 0 .../walkers/annotator/MappingQualityZero.java | 0 .../tools}/walkers/annotator/QualByDepth.java | 0 .../walkers/annotator/RMSMappingQuality.java | 0 .../tools}/walkers/annotator/RankSumTest.java | 0 .../walkers/annotator/ReadPosRankSumTest.java | 0 .../tools}/walkers/annotator/SampleList.java | 0 .../walkers/annotator/SpanningDeletions.java | 0 .../walkers/annotator/StrandBiasBySample.java | 0 .../walkers/annotator/StrandBiasTest.java | 0 .../walkers/annotator/StrandOddsRatio.java | 0 .../annotator/TandemRepeatAnnotator.java | 0 .../TransmissionDisequilibriumTest.java | 0 .../tools}/walkers/annotator/VariantType.java | 0 .../walkers/bqsr/AnalyzeCovariates.java | 0 .../tools}/walkers/bqsr/BQSRGatherer.java | 0 .../tools}/walkers/bqsr/BaseRecalibrator.java | 0 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0 ...NPGenotypeLikelihoodsCalculationModel.java | 0 .../genotyper/UnifiedArgumentCollection.java | 0 .../walkers/genotyper/UnifiedGenotyper.java | 0 .../genotyper/UnifiedGenotypingEngine.java | 0 .../walkers/genotyper/VariantCallContext.java | 0 .../walkers/genotyper/afcalc/AFCalc.java | 0 .../genotyper/afcalc/AFCalcFactory.java | 0 .../afcalc/AFCalcPerformanceTest.java | 0 .../genotyper/afcalc/AFCalcResult.java | 0 .../genotyper/afcalc/AFCalcTestBuilder.java | 0 .../genotyper/afcalc/DiploidExactAFCalc.java | 0 .../genotyper/afcalc/ExactACcounts.java | 0 .../walkers/genotyper/afcalc/ExactACset.java | 0 .../walkers/genotyper/afcalc/ExactAFCalc.java | 0 .../genotyper/afcalc/ExactCallLogger.java | 0 .../afcalc/GeneralPloidyExactAFCalc.java | 0 .../IndependentAllelesDiploidExactAFCalc.java | 0 .../afcalc/OriginalDiploidExactAFCalc.java | 0 .../afcalc/ReferenceDiploidExactAFCalc.java | 0 .../genotyper/afcalc/StateTracker.java | 0 .../haplotypecaller/ActiveRegionTrimmer.java | 0 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.../utils/clipping/ReadClipperTestUtils.java | 0 .../utils/clipping/ReadClipperUnitTest.java | 0 .../utils/codecs/hapmap/HapMapUnitTest.java | 0 .../collections/DefaultHashMapUnitTest.java | 0 .../ExpandingArrayListUnitTest.java | 0 .../ArgumentMatchSiteUnitTest.java | 0 .../ArgumentMatchSourceUnitTest.java | 0 .../ArgumentTypeDescriptorUnitTest.java | 0 .../InvalidArgumentIntegrationTest.java | 0 .../commandline/LoggingIntegrationTest.java | 0 .../commandline/ParsingEngineUnitTest.java | 0 .../RodBindingCollectionUnitTest.java | 0 .../commandline/RodBindingUnitTest.java | 0 .../gatk}/utils/crypt/CryptUtilsUnitTest.java | 0 .../utils/crypt/GATKKeyIntegrationTest.java | 0 .../gatk}/utils/crypt/GATKKeyUnitTest.java | 0 ...chingIndexedFastaSequenceFileUnitTest.java | 0 .../utils/file/FSLockWithSharedUnitTest.java | 0 .../fragments/FragmentUtilsBenchmark.java | 0 .../fragments/FragmentUtilsUnitTest.java | 0 .../utils/haplotype/EventMapUnitTest.java | 0 .../utils/haplotype/HaplotypeUnitTest.java | 0 .../interval/IntervalIntegrationTest.java | 0 .../utils/interval/IntervalUtilsUnitTest.java | 0 .../gatk}/utils/io/IOUtilsUnitTest.java | 0 .../utils}/jna/clibrary/LibCUnitTest.java | 0 .../jna/drmaa/v1_0/JnaSessionQueueTest.java | 0 .../jna/drmaa/v1_0/LibDrmaaQueueTest.java | 0 .../jna/lsf/v7_0_6/LibBatQueueTest.java | 0 .../AlignmentStateMachineUnitTest.java | 0 .../utils/locusiterator/LIBS_position.java | 0 .../locusiterator/LocusIteratorBenchmark.java | 0 .../LocusIteratorByStateBaseTest.java | 0 .../LocusIteratorByStateUnitTest.java | 0 .../PerSampleReadStateManagerUnitTest.java | 0 .../nanoScheduler/InputProducerUnitTest.java | 0 .../nanoScheduler/MapResultUnitTest.java | 0 .../nanoScheduler/NanoSchedulerUnitTest.java | 0 .../utils/nanoScheduler/ReducerUnitTest.java | 0 .../utils/pileup/PileupElementUnitTest.java | 0 .../pileup/ReadBackedPileupUnitTest.java | 0 .../ProgressMeterDaemonUnitTest.java | 0 .../ProgressMeterDataUnitTest.java | 0 .../recalibration/EventTypeUnitTest.java | 0 .../report/ReportMarshallerUnitTest.java | 0 .../runtime/ProcessControllerUnitTest.java | 0 .../utils/runtime/RuntimeUtilsUnitTest.java | 0 .../utils/sam/AlignmentUtilsUnitTest.java | 0 .../sam/ArtificialBAMBuilderUnitTest.java | 0 ...rtificialPatternedSAMIteratorUnitTest.java | 0 .../sam/ArtificialSAMFileWriterUnitTest.java | 0 .../ArtificialSAMQueryIteratorUnitTest.java | 0 .../utils/sam/ArtificialSAMUtilsUnitTest.java | 0 ...ificialSingleSampleReadStreamUnitTest.java | 0 .../utils/sam/GATKSAMRecordUnitTest.java | 0 .../sam/MisencodedBaseQualityUnitTest.java | 0 .../gatk}/utils/sam/ReadUtilsUnitTest.java | 0 .../smithwaterman/SmithWatermanBenchmark.java | 0 .../utils/text/ListFileUtilsUnitTest.java | 0 .../text/TextFormattingUtilsUnitTest.java | 0 ...ciencyMonitoringThreadFactoryUnitTest.java | 0 .../threading/ThreadPoolMonitorUnitTest.java | 0 .../utils/variant/GATKVCFUtilsUnitTest.java | 0 .../GATKVariantContextUtilsUnitTest.java | 0 .../utils/variant/VCFIntegrationTest.java | 0 .../variant/VariantContextBenchmark.java | 0 .../test/resources/testProperties.properties | 0 public/{sting-utils => gatk-utils}/pom.xml | 0 .../gatk}/utils/help/log4j.properties | 0 .../broadinstitute/gatk}/utils/GenomeLoc.java | 0 .../gatk}/utils/HasGenomeLocation.java | 0 .../gatk}/utils/SimpleTimer.java | 0 .../gatk/utils/exceptions/GATKException.java} | 0 .../exceptions/ReviewedGATKException.java} | 0 .../gatk}/utils/package-info.java | 0 .../utils/pairhmm/libVectorLoglessPairHMM.so | Bin 1487 files changed, 561 insertions(+) rename {public/gatk-package => protected/gatk-package-distribution}/pom.xml (100%) rename {public/gatk-package => protected/gatk-package-distribution}/src/main/assembly/binary-dist.xml (100%) create mode 100644 protected/gatk-queue-extensions-distribution/pom.xml rename {public/queue-package => protected/gatk-queue-package-distribution}/pom.xml (100%) rename {public/queue-package => protected/gatk-queue-package-distribution}/src/main/assembly/binary-dist.xml (100%) rename protected/{gatk-protected => gatk-tools-protected}/pom.xml (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine}/arguments/StandardCallerArgumentCollection.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/package-info.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/BaseQualityRankSumTest.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/ChromosomeCounts.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/ClippingRankSumTest.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/Coverage.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/DepthPerAlleleBySample.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/DepthPerSampleHC.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/FisherStrand.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/GCContent.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/GenotypeSummaries.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/HaplotypeScore.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/HardyWeinberg.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/HomopolymerRun.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/InbreedingCoeff.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/LikelihoodRankSumTest.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/MVLikelihoodRatio.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/MappingQualityRankSumTest.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/MappingQualityZero.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/QualByDepth.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/RMSMappingQuality.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/RankSumTest.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/ReadPosRankSumTest.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/SampleList.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/SpanningDeletions.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/StrandBiasBySample.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/StrandBiasTest.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/StrandOddsRatio.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/TandemRepeatAnnotator.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/TransmissionDisequilibriumTest.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/VariantType.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/bqsr/AnalyzeCovariates.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/bqsr/BQSRGatherer.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/bqsr/BaseRecalibrator.java (100%) rename 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protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/AbstractStratification.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/CallableStatus.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/IntervalMetric.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/IntervalStratification.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/LocusMetric.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/LocusStratification.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/Metric.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/PluginUtils.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/SampleMetric.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/SampleStratification.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/ThresHolder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/missing/Metrics.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/missing/QualifyMissingIntervals.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/BaseMismatchModel.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/ConsensusAlleleCounter.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/ErrorModel.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => 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protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/GenotypingEngine.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/GenotypingOutputMode.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/OutputMode.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/PoolGenotypePriors.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/ProbabilityVector.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedArgumentCollection.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedGenotyper.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedGenotypingEngine.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/VariantCallContext.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/AFCalc.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/AFCalcFactory.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/AFCalcPerformanceTest.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/AFCalcResult.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/AFCalcTestBuilder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/DiploidExactAFCalc.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/ExactACcounts.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/ExactACset.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/ExactAFCalc.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/ExactCallLogger.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/StateTracker.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ActiveRegionTrimmer.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/AssemblyResult.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/AssemblyResultSet.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/EventBlock.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/EventBlockFinder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeCaller.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeResolver.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeRoute.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/KMerCounter.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/Kmer.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/KmerSequence.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/KmerSequenceGraphMap.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/LocalAssemblyEngine.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReadAnchoring.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReadCost.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReadErrorCorrector.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReadSegmentComparator.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReadSegmentCost.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/RefVsAnyResult.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReferenceConfidenceMode.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReferenceConfidenceModel.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/BaseEdge.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/BaseGraph.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/BaseGraphIterator.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/BaseVertex.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/DeBruijnVertex.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/GraphUtils.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/KBestHaplotype.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/KmerSearchableGraph.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/LowWeightChainPruner.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/MultiSampleEdge.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/Path.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/Route.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/RouteFinder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/SeqGraph.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/SeqVertex.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/SharedSequenceMerger.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/TestGraph.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/VertexOrder.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/readthreading/HaplotypeGraph.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/readthreading/SequenceForKmers.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/indels/ConstrainedMateFixingManager.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/indels/HaplotypeIndelErrorModel.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/indels/IndelRealigner.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/indels/LeftAlignIndels.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/indels/PairHMMIndelErrorModel.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/indels/ReadBin.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/indels/RealignerTargetCreator.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/AllelePair.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/BaseArray.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/CardinalityCounter.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/CloneableIteratorLinkedList.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/DisjointSet.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/Haplotype.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/PhaseByTransmission.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/PhasingGraph.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/PhasingGraphEdge.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/PhasingRead.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/PhasingUtils.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/PreciseNonNegativeDouble.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/ReadBackedPhasing.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/ReadBase.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/ReadBasesAtPosition.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/phasing/SNPallelePair.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/rnaseq/OverhangFixingManager.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/rnaseq/SplitNCigarReads.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/simulatereads/SimulateReadsForVariants.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/GenotypeAndValidate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/validationsiteselector/FrequencyModeSelector.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/validationsiteselector/GLBasedSampleSelector.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/validationsiteselector/GTBasedSampleSelector.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/validationsiteselector/GenomeEvent.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/validationsiteselector/NullSampleSelector.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/validationsiteselector/SampleSelector.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/validationsiteselector/ValidationSiteSelector.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/ApplyRecalibration.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/GaussianMixtureModel.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/MultivariateGaussian.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/TrainingSet.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/Tranche.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/TrancheManager.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/VariantDataManager.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/VariantDatum.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/VariantRecalibrator.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/VariantRecalibratorEngine.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/CalculateGenotypePosteriors.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/CombineGVCFs.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/GenotypeGVCFs.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/PosteriorLikelihoodsUtils.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/RegenotypeVariants.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/SequenceComplexity.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/collections/CountSet.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/gga/GenotypingGivenAllelesUtils.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/gvcf/GVCFWriter.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/gvcf/HomRefBlock.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/haplotype/HaplotypeLDCalculator.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/haplotype/LDMerger.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/haplotype/MergeVariantsAcrossHaplotypes.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/haplotypeBAMWriter/ReadDestination.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/ArrayLoglessPairHMM.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/CnyPairHMM.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/DebugJNILoglessPairHMM.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/FastLoglessPairHMM.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/FlexibleHMM.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/JNILoglessPairHMM.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/LoglessPairHMM.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/VectorLoglessPairHMM.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/BQSRReadTransformer.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/BaseRecalibration.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/QualQuantizer.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/QuantizationInfo.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/ReadCovariates.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/RecalDatum.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/RecalDatumNode.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/RecalUtils.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/RecalibrationReport.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/RecalibrationTables.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/ContextCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/Covariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/CycleCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/ExperimentalCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/QualityScoreCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/ReadGroupCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/RepeatCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/RepeatLengthCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/RepeatUnitCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/RequiredCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/recalibration/covariates/StandardCovariate.java (100%) rename protected/{gatk-protected/src/main/java/org/broadinstitute/sting => gatk-tools-protected/src/main/java/org/broadinstitute/gatk}/utils/sam/ClippedGATKSAMRecord.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DiffEngineUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DiffNodeUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DiffObjectsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DiffableReaderUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DifferenceUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/WalkerTestIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/annotator/GenotypeSummariesUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/annotator/QualByDepthUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/annotator/RankSumUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/annotator/SnpEffUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/annotator/StrandOddsRatioUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/annotator/VariantAnnotatorIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/annotator/VariantOverlapAnnotatorUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/beagle/BeagleIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/bqsr/BQSRGathererUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/bqsr/BQSRIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/bqsr/ReadRecalibrationInfoUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/fasta/FastaAlternateReferenceIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/filters/VariantFiltrationIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/ArtificialReadPileupTestProvider.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedGenotyperIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/AFCalcResultUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/AFCalcUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/AssemblyResultSetUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/Civar.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/CivarUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/KmerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/PathUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/RouteUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/indels/ConstrainedMateFixingManagerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/indels/IndelRealignerIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/indels/IndelRealignerLargeScaleTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/indels/IndelRealignerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/indels/PairHMMIndelErrorModelUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/indels/ReadBinUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/indels/RealignerTargetCreatorIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/indels/RealignerTargetCreatorLargeScaleTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/phasing/PhaseByTransmissionIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/phasing/ReadBackedPhasingIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/rnaseq/OverhangFixingManagerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/rnaseq/SplitNCigarReadsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/validation/ValidationAmpliconsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/validation/ValidationSiteSelectorIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/varianteval/VariantEvalIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/varianteval/VariantEvalWalkerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/VariantDataManagerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/CombineGVCFsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/CombineVariantsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/CombineVariantsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/ConcordanceMetricsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/GenotypeConcordanceIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/GenotypeGVCFsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/LiftoverVariantsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/RegenotypeVariantsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/SelectVariantsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/SelectVariantsParallelIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/VCFStreamingIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/ValidateVariantsIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/VariantsToTableIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/VariantsToVCFIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/ContigComparatorUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/RandomDNA.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/collections/CountSetUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/genotyper/DiploidGenotypeUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/genotyper/MostLikelyAlleleUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/gvcf/GVCFWriterUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/gvcf/HomRefBlockUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/haplotype/HaplotypeBaseComparatorUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/haplotype/HaplotypeLDCalculatorUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/haplotype/HaplotypeScoreComparatorUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/haplotype/LDMergerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/nanoScheduler/NanoSchedulerIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/pairhmm/ActiveRegionTestDataSet.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/pairhmm/CnyPairHMMUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/pairhmm/FastLoglessPairHMMUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/pairhmm/PairHMMEmpiricalBenchmark.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/pairhmm/PairHMMModelUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/pairhmm/PairHMMSyntheticBenchmark.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/pairhmm/PairHMMTestData.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/pairhmm/PairHMMUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/ContextCovariateUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/CycleCovariateUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/QualQuantizerUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/ReadCovariatesUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/ReadGroupCovariateUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/RecalDatumUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/RecalUtilsUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/RecalibrationReportUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/RecalibrationTablesUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/RecalibrationTestUtils.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/recalibration/RepeatCovariatesUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java (100%) rename protected/{gatk-protected/src/test/java/org/broadinstitute/sting => gatk-tools-protected/src/test/java/org/broadinstitute/gatk}/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java (100%) rename public/c/bwa/{org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp => org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.cpp} (100%) rename public/c/bwa/{org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h => org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.h} (100%) create mode 100644 public/gatk-engine/pom.xml rename public/{gatk-framework => gatk-engine}/src/main/assembly/example-resources.xml (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-engine/src/main/java/org/broadinstitute/gatk/engine}/ReadMetrics.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-engine/src/main/java/org/broadinstitute/gatk/engine}/package-info.java (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleBAM.bam (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleBAM.bam.bai (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleBAM.simple.bai (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleBAM.simple.bam (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleDBSNP.vcf (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleDBSNP.vcf.idx (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA-3contigs.fasta (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA-combined.fasta (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA-windows.fasta (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.dict (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.fasta (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.fasta.amb (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.fasta.ann (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.fasta.bwt (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.fasta.fai (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.fasta.pac (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.fasta.rbwt (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.fasta.rpac (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.fasta.rsa (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleFASTA.fasta.sa (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleGATKReport.eval (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleGATKReportv1.tbl (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleGATKReportv2.tbl (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleGRP.grp (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleINTERVAL.intervals (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleNORG.bam (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/exampleNORG.bam.bai (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/forAlleleFractionSimulation.vcf (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/forAlleleFractionSimulation.vcf.idx (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/forSimulation.vcf (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/forSimulation.vcf.idx (100%) rename public/{gatk-framework => gatk-engine}/src/test/resources/testfile.sam (100%) rename public/{gatk-queue-extgen => gatk-queue-extensions-generator}/pom.xml (100%) rename public/{gatk-queue-extgen/src/main/java/org/broadinstitute/sting => gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk}/queue/extensions/gatk/ArgumentDefinitionField.java (100%) rename public/{gatk-queue-extgen/src/main/java/org/broadinstitute/sting => gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk}/queue/extensions/gatk/ArgumentField.java (100%) rename public/{gatk-queue-extgen/src/main/java/org/broadinstitute/sting => gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk}/queue/extensions/gatk/GATKExtensionsGenerator.java (100%) rename public/{gatk-queue-extgen/src/main/java/org/broadinstitute/sting => gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk}/queue/extensions/gatk/ReadFilterField.java (100%) create mode 100644 public/gatk-queue-extensions-public/pom.xml rename public/{queue-framework => gatk-queue-extensions-public}/src/main/assembly/example-resources.xml (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/CNV/xhmmCNVpipeline.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/GATKResourcesBundle.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/examples/ExampleCountLoci.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/examples/ExampleCountReads.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/examples/ExampleCustomWalker.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/examples/ExamplePrintReads.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/examples/ExampleReadFilter.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/examples/ExampleRetryMemoryLimit.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/examples/ExampleUnifiedGenotyper.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/examples/HelloWorld.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/lib/ChunkVCF.scala (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala} (100%) rename public/{queue-framework/src/main/qscripts/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk}/queue/qscripts/lib/VcfToPed.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/cancer/MuTect.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/BamGatherFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/CatVariantsGatherer.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/ContigScatterFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/DistributedScatterFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting/queue/util => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk}/DoC/package.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/GATKIntervals.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/GATKScatterFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/IntervalScatterFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/LocusScatterFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/ReadScatterFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/TaggedFile.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/VcfGatherFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/AddOrReplaceReadGroups.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/CalculateHsMetrics.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/CollectGcBiasMetrics.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/CollectMultipleMetrics.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/FastqToSam.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/MarkDuplicates.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/MergeSamFiles.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/PicardBamFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/PicardMetricsFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/ReorderSam.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/RevertSam.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/SamToFastq.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/SortSam.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/picard/ValidateSamFile.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/samtools/SamtoolsCommandLineFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/samtools/SamtoolsIndexFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/samtools/SamtoolsMergeFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk}/queue/extensions/snpeff/SnpEff.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk}/queue/extensions/gatk/GATKIntervalsUnitTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk}/queue/pipeline/examples/ExampleCountLociQueueTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk}/queue/pipeline/examples/ExampleCountReadsQueueTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk}/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk}/queue/pipeline/examples/ExampleReadFilterQueueTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk}/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk}/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk}/queue/pipeline/examples/HelloWorldQueueTest.scala (100%) rename public/{queue-framework => gatk-queue}/pom.xml (100%) rename public/{queue-framework/src/main/java/org/broadinstitute/sting => gatk-queue/src/main/java/org/broadinstitute/gatk}/queue/QueueVersion.java (100%) rename public/{queue-framework/src/main/java/org/broadinstitute/sting => gatk-queue/src/main/java/org/broadinstitute/gatk}/queue/package-info.java (100%) rename public/{queue-framework/src/main/resources/org/broadinstitute/sting => gatk-queue/src/main/resources/org/broadinstitute/gatk}/queue/util/queueJobReport.R (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/QCommandLine.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/QCommandPlugin.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/QException.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/QScript.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/QScriptManager.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/QSettings.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/CommandLineJobManager.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/CommandLineJobRunner.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/CommandLinePluginManager.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/FunctionEdge.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/InProcessJobManager.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/InProcessRunner.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/JobManager.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/JobRunInfo.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/JobRunner.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/MappingEdge.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/QEdge.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/QGraph.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/QGraphSettings.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/QNode.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/QStatusMessenger.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/RunnerStatus.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/drmaa/DrmaaJobManager.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/drmaa/DrmaaJobRunner.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/gridengine/GridEngineJobManager.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/gridengine/GridEngineJobRunner.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/lsf/Lsf706JobManager.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/lsf/Lsf706JobRunner.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/pbsengine/PbsEngineJobManager.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/pbsengine/PbsEngineJobRunner.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/shell/ShellJobManager.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/engine/shell/ShellJobRunner.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/CommandLineFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/InProcessFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/JavaCommandLineFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/ListWriterFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/QFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/RetryMemoryLimit.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/scattergather/CloneFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/scattergather/ConcatenateLogsFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/scattergather/GatherFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/scattergather/GathererFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/scattergather/ScatterFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/scattergather/ScatterGatherableFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/function/scattergather/SimpleTextGatherFunction.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/library/clf/vcf/VCFExtractIntervals.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/library/clf/vcf/VCFExtractSamples.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/library/ipf/SortByRef.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/library/ipf/vcf/VCFExtractIntervals.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/library/ipf/vcf/VCFExtractSamples.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/library/ipf/vcf/VCFExtractSites.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/library/ipf/vcf/VCFSimpleMerge.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/ClassFieldCache.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/CollectionUtils.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/EmailMessage.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/EmailSettings.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/Logging.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/PrimitiveOptionConversions.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/QJobReport.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/QJobsReporter.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/QScriptUtils.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/ReflectionUtils.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/RemoteFile.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/RemoteFileConverter.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/Retry.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/RetryException.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/ScalaCompoundArgumentTypeDescriptor.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/ShellUtils.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/StringFileConversions.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/SystemUtils.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/TextFormatUtils.scala (100%) rename public/{queue-framework/src/main/scala/org/broadinstitute/sting => gatk-queue/src/main/scala/org/broadinstitute/gatk}/queue/util/VCF_BAM_utilities.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue/src/test/scala/org/broadinstitute/gatk}/queue/function/CommandLineFunctionUnitTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue/src/test/scala/org/broadinstitute/gatk}/queue/pipeline/QueueTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue/src/test/scala/org/broadinstitute/gatk}/queue/pipeline/QueueTestEvalSpec.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue/src/test/scala/org/broadinstitute/gatk}/queue/pipeline/QueueTestSpec.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue/src/test/scala/org/broadinstitute/gatk}/queue/util/ShellUtilsUnitTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue/src/test/scala/org/broadinstitute/gatk}/queue/util/StringFileConversionsUnitTest.scala (100%) rename public/{queue-framework/src/test/scala/org/broadinstitute/sting => gatk-queue/src/test/scala/org/broadinstitute/gatk}/queue/util/SystemUtilsUnitTest.scala (100%) rename public/{sting-root => gatk-root}/pom.xml (100%) rename public/{gatk-framework => gatk-tools-public}/pom.xml (100%) rename public/{gatk-framework => gatk-tools-public}/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java (100%) rename public/{gatk-framework => gatk-tools-public}/src/main/java/htsjdk/samtools/GATKBin.java (100%) rename public/{gatk-framework => gatk-tools-public}/src/main/java/htsjdk/samtools/GATKChunk.java (100%) rename public/{gatk-framework => gatk-tools-public}/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/CommandLineExecutable.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/CommandLineGATK.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/GenomeAnalysisEngine.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/ReadProperties.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/WalkerManager.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/Aligner.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/Alignment.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/CheckAlignment.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/BWAAligner.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/BWAConfiguration.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/BWTFiles.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/c/BWACAligner.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/c/BWAPath.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/java/AlignerTestHarness.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/java/AlignmentMatchSequence.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/java/AlignmentState.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/java/BWAAlignment.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/java/BWAJavaAligner.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/bwa/java/LowerBound.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/AMBWriter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/ANNWriter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/BWT.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/BWTReader.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/BWTSupplementaryFileGenerator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/BWTWriter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/Bases.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/Counts.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/CreateBWTFromReference.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/SequenceBlock.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/SuffixArray.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/SuffixArrayReader.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/bwt/SuffixArrayWriter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/packing/BasePackedInputStream.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/packing/BasePackedOutputStream.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/packing/CreatePACFromReference.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/packing/PackUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/packing/UnsignedIntPackedInputStream.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/alignment/reference/packing/UnsignedIntPackedOutputStream.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/arguments/DbsnpArgumentCollection.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/arguments/GATKArgumentCollection.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/arguments/StandardVariantContextInputArgumentCollection.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/arguments/ValidationExclusion.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/contexts/AlignmentContext.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/contexts/AlignmentContextUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/contexts/ReferenceContext.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/AllLocusView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/CoveredLocusView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/IntervalOverlappingRODsFromStream.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/IntervalReferenceOrderedView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/InvalidPositionException.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/LocusReferenceView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/LocusShardDataProvider.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/LocusView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/ManagingReferenceOrderedView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/RODMetaDataContainer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/ReadBasedReferenceOrderedView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/ReadReferenceView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/ReadShardDataProvider.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/ReadView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/ReferenceOrderedView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/ReferenceView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/RodLocusView.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/ShardDataProvider.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/View.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/providers/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/ActiveRegionShardBalancer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/BAMAccessPlan.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/BAMSchedule.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/BAMScheduler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/BGZFBlockLoadingDispatcher.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/BlockInputStream.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/BlockLoader.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/FileHandleCache.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/FilePointer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/GATKBAMIndex.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/GATKBAMIndexData.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/IntervalOverlapFilteringIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/IntervalSharder.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/LocusShard.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/LocusShardBalancer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/ReadShard.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/ReadShardBalancer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/SAMDataSource.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/SAMReaderID.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/Shard.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/ShardBalancer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/utilities/BAMFileStat.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/utilities/BAMTagRenamer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/utilities/FindLargeShards.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/utilities/PrintBAMRegion.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/utilities/PrintBGZFBounds.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/utilities/UnzipSingleBlock.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reads/utilities/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reference/ReferenceDataSource.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/reference/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/rmd/DataStreamSegment.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/rmd/EntireStream.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/rmd/MappedStreamSegment.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/rmd/ReferenceOrderedDataPool.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/rmd/ReferenceOrderedDataSource.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/rmd/ResourcePool.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/datasources/rmd/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/AlleleBiasedDownsamplingUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/DownsampleType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/Downsampler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/DownsamplingMethod.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/DownsamplingReadsIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/DownsamplingUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/FractionalDownsampler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/FractionalDownsamplerFactory.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/LevelingDownsampler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/PassThroughDownsampler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/PerSampleDownsamplingReadsIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/ReadsDownsampler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/ReadsDownsamplerFactory.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/ReservoirDownsampler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/ReservoirDownsamplerFactory.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/SimplePositionalDownsampler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/downsampling/SimplePositionalDownsamplerFactory.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/Accumulator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/HierarchicalMicroScheduler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/HierarchicalMicroSchedulerMBean.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/LinearMicroScheduler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/MicroScheduler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/MicroSchedulerMBean.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/OutputMergeTask.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/ReduceTree.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/ShardTraverser.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/TreeReducer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/WindowMaker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/executive/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/BadCigarFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/BadMateFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/CountingFilteringIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/DuplicateReadFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/FailsVendorQualityCheckFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/FilterManager.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/LibraryReadFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/MalformedReadFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/MappingQualityFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/MappingQualityUnavailableFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/MappingQualityZeroFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/MateSameStrandFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/MaxInsertSizeFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/MissingReadGroupFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/NDNCigarReadTransformer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/NoOriginalQualityScoresFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/NotPrimaryAlignmentFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/Platform454Filter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/PlatformFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/PlatformUnitFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/PlatformUnitFilterHelper.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/ReadFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/ReadGroupBlackListFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/ReadLengthFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/ReadNameFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/ReadStrandFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/ReassignMappingQualityFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/ReassignOneMappingQualityFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/SampleFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/SingleReadGroupFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/UnmappedReadFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/filters/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/DirectOutputTracker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/FastqFileWriter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/GATKSAMFileWriter.java} (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/OutputTracker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/ThreadGroupOutputTracker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/storage/OutputStreamStorage.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/storage/SAMFileWriterStorage.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/storage/Storage.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/storage/StorageFactory.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/storage/VariantContextWriterStorage.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/stubs/OutputStreamArgumentTypeDescriptor.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/stubs/OutputStreamStub.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/stubs/SAMFileReaderArgumentTypeDescriptor.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/stubs/SAMFileWriterArgumentTypeDescriptor.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/stubs/SAMFileWriterStub.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/stubs/Stub.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/stubs/VCFWriterArgumentTypeDescriptor.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/io/stubs/VariantContextWriterStub.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/BoundedReadIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIterator.java} (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapter.java} (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMRecordIterator.java} (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/GenomeLocusIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/IterableIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/MalformedBAMErrorReformatingIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/NullSAMIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/PeekingIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/PositionTrackingIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/PushbackIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/RNAReadTransformer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/ReadFormattingIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/ReadTransformer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/ReadTransformersMode.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/VerifyingSamIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/iterators/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/phonehome/GATKRunReport.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/phonehome/GATKRunReportException.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/RODRecordListImpl.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/RefMetaDataTracker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/ReferenceDependentFeatureCodec.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/ReferenceOrderedDatum.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/SeekableRODIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/VariantContextAdaptors.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/tracks/FeatureManager.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/tracks/IndexDictionaryUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/tracks/RMDTrack.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/tracks/RMDTrackBuilder.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/utils/FeatureToGATKFeatureIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/utils/FlashBackIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/utils/GATKFeature.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/utils/LocationAwareSeekableRODIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/utils/RMDTriplet.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/refdata/utils/RODRecordList.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/report/GATKReport.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/report/GATKReportColumn.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/report/GATKReportColumnFormat.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/report/GATKReportDataType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/report/GATKReportGatherer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/report/GATKReportTable.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/report/GATKReportVersion.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/resourcemanagement/ThreadAllocation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/samples/Affection.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/samples/Gender.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/samples/PedReader.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/samples/PedigreeValidationType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/samples/Sample.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/samples/SampleDB.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/samples/SampleDBBuilder.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/samples/Trio.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/traversals/TAROrderedReadCache.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/traversals/TraversalEngine.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/traversals/TraverseActiveRegions.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/traversals/TraverseDuplicates.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/traversals/TraverseLociNano.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/traversals/TraverseReadPairs.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/traversals/TraverseReadsNano.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/traversals/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/ActiveRegionTraversalParameters.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/ActiveRegionWalker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/Allows.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/Attribution.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/BAQMode.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/By.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/DataSource.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/Downsample.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/DuplicateWalker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/LocusWalker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/Multiplex.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/Multiplexer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/NanoSchedulable.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/PartitionBy.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/PartitionType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/RMD.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/ReadFilters.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/ReadPairWalker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/ReadWalker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/RefWalker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/Reference.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/RemoveProgramRecords.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/Requires.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/RodWalker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/TreeReducible.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/Walker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/WalkerName.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/Window.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/diffengine/BAMDiffableReader.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DiffElement.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DiffEngine.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DiffNode.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DiffObjects.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DiffValue.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/diffengine/DiffableReader.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/diffengine/Difference.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/diffengine/GATKReportDiffableReader.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine}/walkers/diffengine/VCFDiffableReader.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/tools/CatVariants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/tools/ListAnnotations.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/AlleleBalance.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/AlleleBalanceBySample.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/BaseCounts.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/ChromosomeCountConstants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/LowMQ.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/MappingQualityZeroBySample.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/NBaseCount.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/SnpEff.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/SnpEffUtil.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/VariantAnnotator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/VariantAnnotatorEngine.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/VariantOverlapAnnotator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/AnnotationInterfaceManager.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/AnnotationType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/AnnotatorCompatible.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/ExperimentalAnnotation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/GenotypeAnnotation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/InfoFieldAnnotation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/RodRequiringAnnotation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/StandardAnnotation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/annotator/interfaces/WorkInProgressAnnotation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/beagle/BeagleOutputToVCF.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/beagle/ProduceBeagleInput.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/beagle/VariantsToBeagleUnphased.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/coverage/CallableLoci.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/coverage/CompareCallableLoci.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/coverage/CoverageUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/coverage/DepthOfCoverage.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/coverage/DepthOfCoverageStats.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/coverage/DoCOutputType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/coverage/GCContentByInterval.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/CoveredByNSamplesSites.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/ErrorRatePerCycle.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/ReadGroupProperties.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/diagnostics/ReadLengthDistribution.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers}/examples/GATKDocsExample.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers}/examples/GATKPaperGenotyper.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/fasta/FastaAlternateReferenceMaker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/fasta/FastaReferenceMaker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/fasta/FastaSequence.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/fasta/FastaStats.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/filters/ClusteredSnps.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/filters/FiltrationContext.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/filters/FiltrationContextWindow.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/filters/VariantFiltration.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/haplotypecaller/HCMappingQualityFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/CheckPileup.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/CountBases.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/CountIntervals.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/CountLoci.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/CountMales.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/CountRODs.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/CountRODsByRef.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/CountReadEvents.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/CountReads.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/CountTerminusEvent.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/DocumentationTest.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/ErrorThrowing.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/FlagStat.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/Pileup.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/PrintRODs.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/QCRef.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/ReadClippingStats.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/qc/RodSystemValidation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/readutils/ClipReads.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/readutils/PrintReads.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/readutils/ReadAdaptorTrimmer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/readutils/SplitSamFile.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/validation/ValidationAmplicons.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/VariantEval.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/VariantEvalReportWriter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/CompOverlap.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/CountVariants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/IndelLengthHistogram.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/IndelSummary.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/MendelianViolationEvaluator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/MultiallelicSummary.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/PrintMissingComp.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/StandardEval.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/ThetaVariantEvaluator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/TiTvVariantEvaluator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/ValidationReport.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/VariantEvaluator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/evaluators/VariantSummary.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/AlleleCount.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/AlleleFrequency.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/CompRod.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/Contig.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/CpG.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/Degeneracy.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/DynamicStratification.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/EvalRod.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/Filter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/FunctionalClass.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/IndelSize.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/IntervalStratification.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/JexlExpression.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/Novelty.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/OneBPIndel.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/RequiredStratification.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/Sample.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/SnpEffPositionModifier.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/StandardStratification.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/TandemRepeat.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/VariantStratifier.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/VariantType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/manager/StratNode.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/manager/StratNodeIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/manager/StratificationManager.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/stratifications/manager/Stratifier.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/util/Analysis.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/util/AnalysisModuleScanner.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/util/DataPoint.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/util/EvaluationContext.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/util/Molten.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/util/SortableJexlVCMatchExp.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/varianteval/util/VariantEvalUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/VQSRCalibrationCurve.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/CombineVariants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/ConcordanceMetrics.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/FilterLiftedVariants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/GenotypeConcordance.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/LeftAlignAndTrimVariants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/LiftoverVariants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/RandomlySplitVariants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/SelectHeaders.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/SelectVariants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/ValidateVariants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/VariantValidationAssessor.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/VariantsToAllelicPrimitives.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/VariantsToBinaryPed.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/VariantsToTable.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools}/walkers/variantutils/VariantsToVCF.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/AutoFormattingTime.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/BaseUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/BitSetUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/ContigComparator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/DeprecatedToolChecks.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/GenomeLocParser.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/GenomeLocSortedSet.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/HeapSizeMonitor.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/IndelUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/LRUCache.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/MRUCachingSAMSequenceDictionary.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/MannWhitneyU.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/MathUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/Median.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/MendelianViolation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/MultiThreadedErrorTracker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/NGSPlatform.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/PathUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/QualityUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/R/RScriptExecutor.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/R/RScriptExecutorException.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/R/RScriptLibrary.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/R/RUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/SampleUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/SequenceDictionaryUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/UnvalidatingGenomeLoc.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/Utils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/activeregion/ActiveRegion.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/activeregion/ActiveRegionReadState.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/activeregion/ActivityProfile.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/activeregion/ActivityProfileState.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/activeregion/BandPassActivityProfile.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/analysis/AminoAcid.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/analysis/AminoAcidTable.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/analysis/AminoAcidUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/baq/BAQ.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/baq/BAQReadTransformer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/baq/ReadTransformingIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/classloader/JVMUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/classloader/PluginManager.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/classloader/ProtectedPackageSource.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/classloader/PublicPackageSource.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/clipping/ClippingOp.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/clipping/ClippingRepresentation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/clipping/ReadClipper.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/beagle/BeagleCodec.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/beagle/BeagleFeature.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/hapmap/RawHapMapCodec.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/hapmap/RawHapMapFeature.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/refseq/RefSeqCodec.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/refseq/RefSeqFeature.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/refseq/Transcript.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/sampileup/SAMPileupCodec.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/sampileup/SAMPileupFeature.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/samread/SAMReadCodec.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/samread/SAMReadFeature.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/table/BedTableCodec.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/table/TableCodec.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/codecs/table/TableFeature.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/collections/DefaultHashMap.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/collections/ExpandingArrayList.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/collections/LoggingNestedIntegerArray.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/collections/NestedIntegerArray.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/collections/Pair.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/collections/PrimitivePair.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/collections/RODMergingIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/Advanced.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/Argument.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentCollection.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentDefinition.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentDefinitionGroup.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentDefinitions.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentException.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentIOType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentMatch.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentMatchFileValue.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentMatchSite.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentMatchSource.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentMatchSourceType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentMatchStringValue.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentMatchValue.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentMatches.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentSource.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ArgumentTypeDescriptor.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ClassType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/CommandLineProgram.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/CommandLineUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/EnumerationArgumentDefault.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/Gather.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/Gatherer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/Hidden.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/Input.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/IntervalArgumentCollection.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/IntervalBinding.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/MissingArgumentValueException.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/Output.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ParsedArgs.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ParsedListArgs.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ParsingEngine.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ParsingEngineArgumentFiles.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ParsingEngineArgumentProvider.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/ParsingMethod.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/RodBinding.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/RodBindingCollection.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/Tags.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/commandline/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/crypt/CryptUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/crypt/GATKKey.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/duplicates/DupUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/duplicates/DuplicateComp.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/exceptions/DynamicClassResolutionException.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/exceptions/UserException.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/fasta/ArtificialFastaUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/fasta/CachingIndexedFastaSequenceFile.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/fasta/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/file/FSLockWithShared.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/fragments/FragmentCollection.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/fragments/FragmentUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/genotyper/DiploidGenotype.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/genotyper/MostLikelyAllele.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/genotyper/PerReadAlleleLikelihoodMap.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/haplotype/EventMap.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/haplotype/Haplotype.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/haplotype/HaplotypeBaseComparator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/haplotype/HaplotypeScoreComparator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/haplotype/HaplotypeSizeAndBaseComparator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/ApplicationDetails.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/DocletUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/DocumentedGATKFeature.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/DocumentedGATKFeatureHandler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/DocumentedGATKFeatureObject.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/ForumAPIUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/ForumDiscussion.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/GATKDocUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/GATKDocWorkUnit.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/GATKDoclet.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/GenericDocumentationHandler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/HelpConstants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/HelpFormatter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/HelpUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/help/ResourceBundleExtractorDoclet.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/instrumentation/Sizeof.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/interval/IntervalMergingRule.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/interval/IntervalSetRule.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/interval/IntervalUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/io/FileExtension.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/io/HardThresholdingOutputStream.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/io/IOUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/io/Resource.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/jna/clibrary/JNAUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/jna/clibrary/LibC.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/jna/drmaa/v1_0/JnaJobInfo.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/jna/drmaa/v1_0/JnaJobTemplate.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/jna/drmaa/v1_0/JnaSession.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/jna/drmaa/v1_0/JnaSessionFactory.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/jna/drmaa/v1_0/LibDrmaa.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/jna/lsf/v7_0_6/LibBat.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils}/jna/lsf/v7_0_6/LibLsf.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/locusiterator/AlignmentStateMachine.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/locusiterator/LIBSDownsamplingInfo.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/locusiterator/LIBSPerformance.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/locusiterator/LocusIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/locusiterator/LocusIteratorByState.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/locusiterator/PerSampleReadStateManager.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/locusiterator/ReadStateManager.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/locusiterator/SamplePartitioner.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/nanoScheduler/EOFMarkedValue.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/nanoScheduler/InputProducer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/nanoScheduler/MapResult.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/nanoScheduler/MapResultsQueue.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/nanoScheduler/NSMapFunction.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/nanoScheduler/NSProgressFunction.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/nanoScheduler/NSReduceFunction.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/nanoScheduler/NanoScheduler.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/nanoScheduler/Reducer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/BatchPairHMM.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/Log10PairHMM.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/N2MemoryPairHMM.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/PairHMM.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/PairHMMModel.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pairhmm/PairHMMReadyHaplotypes.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pileup/MergingPileupElementIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pileup/PileupElement.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pileup/PileupElementFilter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pileup/PileupElementTracker.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pileup/ReadBackedPileup.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pileup/ReadBackedPileupImpl.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/pileup2/Notes (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/progressmeter/ProgressMeter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/progressmeter/ProgressMeterDaemon.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/progressmeter/ProgressMeterData.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/recalibration/BQSRArgumentSet.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/recalibration/BQSRMode.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/recalibration/EventType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/runtime/CapturedStreamOutput.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/runtime/InputStreamSettings.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/runtime/OutputStreamSettings.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/runtime/ProcessController.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/runtime/ProcessOutput.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/runtime/ProcessSettings.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/runtime/RuntimeUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/runtime/StreamLocation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/runtime/StreamOutput.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/AlignmentStartComparator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/AlignmentStartWithNoTiesComparator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/AlignmentUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ArtificialBAMBuilder.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java => gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java} (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ArtificialMultiSampleReadStream.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ArtificialPatternedSAMIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ArtificialReadsTraversal.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ArtificialSAMFileReader.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ArtificialSAMIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ArtificialSAMQueryIterator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ArtificialSAMUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ArtificialSingleSampleReadStream.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/BySampleSAMFileWriter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/CigarUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/GATKSAMReadGroupRecord.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/GATKSAMRecord.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/GATKSamRecordFactory.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/MisencodedBaseQualityReadTransformer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/NWaySAMFileWriter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ReadUnclippedStartWithNoTiesComparator.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/ReadUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/SAMFileReaderBuilder.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/SimplifyingSAMFileWriter.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/sam/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/smithwaterman/Parameters.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/smithwaterman/SWPairwiseAlignment.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/smithwaterman/SWPairwiseAlignmentMain.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/smithwaterman/SWParameterSet.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/smithwaterman/SmithWaterman.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/text/ListFileUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/text/TextFormattingUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/text/XReadLines.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/threading/EfficiencyMonitoringThreadFactory.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/threading/NamedThreadFactory.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/threading/ThreadEfficiencyMonitor.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/threading/ThreadLocalArray.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/threading/ThreadPoolMonitor.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/threading/package-info.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/variant/GATKVCFIndexType.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/variant/GATKVCFUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/variant/GATKVariantContextUtils.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/variant/HomoSapiensConstants.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/wiggle/WiggleHeader.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-tools-public/src/main/java/org/broadinstitute/gatk}/utils/wiggle/WiggleWriter.java (100%) rename public/{gatk-framework => gatk-tools-public}/src/main/resources/GATK_public.key (100%) rename public/{gatk-framework/src/main/resources/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/resources/org/broadinstitute/gatk/engine}/phonehome/resources/GATK_AWS_access.key (100%) rename public/{gatk-framework/src/main/resources/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/resources/org/broadinstitute/gatk/engine}/phonehome/resources/GATK_AWS_secret.key (100%) rename public/{gatk-framework/src/main/resources/org/broadinstitute/sting/gatk => gatk-tools-public/src/main/resources/org/broadinstitute/gatk/tools}/walkers/variantrecalibration/plot_Tranches.R (100%) rename public/{gatk-framework/src/main/resources/org/broadinstitute/sting => gatk-tools-public/src/main/resources/org/broadinstitute/gatk}/utils/recalibration/BQSR.R (100%) rename public/{gatk-framework => gatk-tools-public}/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java (100%) rename public/{gatk-framework => gatk-tools-public}/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/CommandLineGATKUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/EngineFeaturesIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/GenomeAnalysisEngineUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/MaxRuntimeIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/ReadMetricsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/WalkerManagerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/providers/AllLocusViewUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/providers/CoveredLocusViewUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/providers/IntervalReferenceOrderedViewUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/providers/LocusReferenceViewUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/providers/LocusViewTemplate.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/providers/ReadReferenceViewUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/providers/ReferenceOrderedViewUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/providers/ReferenceViewTemplate.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/providers/ShardDataProviderUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/ActiveRegionShardBalancerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/DownsamplerBenchmark.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/FilePointerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/GATKBAMIndexUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/GATKWalkerBenchmark.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/MockLocusShard.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/PicardBaselineBenchmark.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/ReadProcessingBenchmark.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/ReadShardBalancerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/SAMDataSourceUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/SAMReaderIDUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/SeekableBufferedStreamUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reads/TheoreticalMinimaBenchmark.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/reference/ReferenceDataSourceIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/downsampling/DownsamplingIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/downsampling/DownsamplingReadsIteratorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/downsampling/FractionalDownsamplerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/downsampling/LevelingDownsamplerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/downsampling/ReservoirDownsamplerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/downsampling/SimplePositionalDownsamplerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/executive/ReduceTreeUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/filters/AllowNCigarMalformedReadFilterUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/filters/BadCigarFilterUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/filters/BadReadGroupsIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/filters/MalformedReadFilterUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/filters/NDNCigarReadTransformerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/filters/ReadFilterTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/filters/ReadGroupBlackListFilterUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/filters/UnsafeMalformedReadFilterUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/iterators/BoundedReadIteratorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java} (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/iterators/ReadFormattingIteratorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/iterators/VerifyingSamIteratorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/phonehome/GATKRunReportUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/refdata/RefMetaDataTrackerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/refdata/tracks/FeatureManagerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/refdata/tracks/RMDTrackBuilderUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/refdata/utils/CheckableCloseableTribbleIterator.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/refdata/utils/FlashBackIteratorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/refdata/utils/TestFeatureReader.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/refdata/utils/TestRMDTrackBuilder.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/report/GATKReportUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/samples/PedReaderUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/samples/SampleDBUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/samples/SampleUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/traversals/DummyActiveRegionWalker.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/traversals/TAROrderedReadCacheUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/traversals/TraverseActiveRegionsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/traversals/TraverseDuplicatesUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine}/traversals/TraverseReadsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers}/WalkerTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/tools/CatVariantsIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/BAQIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/CNV/SymbolicAllelesIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/annotator/SnpEffUtilUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/coverage/CallableLociIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/coverage/DepthOfCoverageB36IntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/coverage/DepthOfCoverageIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/qc/CheckPileupIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/qc/CountReadsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/qc/DictionaryConsistencyIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/qc/FlagStatIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/qc/PileupWalkerIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/readutils/ClipReadsWalkersIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/readutils/PrintReadsIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/readutils/PrintReadsLargeScaleTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/readutils/PrintReadsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/FilterLiftedVariantsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/gatk => gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools}/walkers/variantutils/SelectVariantsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/AutoFormattingTimeUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/BaseTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/BaseUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/BitSetUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/ExampleToCopyUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting/StingTextReporter.java => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java} (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/GenomeLocParserBenchmark.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/GenomeLocParserUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/GenomeLocSortedSetUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/GenomeLocUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/MD5DB.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/MD5Mismatch.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/MRUCachingSAMSequencingDictionaryUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/MWUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/MathUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/MedianUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/NGSPlatformUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/PathUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/QualityUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/R/RScriptExecutorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/R/RScriptLibraryUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/R/RUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/SampleUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/SequenceDictionaryUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/SimpleTimerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/TestNGTestTransformer.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/UtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/activeregion/ActiveRegionUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/activeregion/ActivityProfileStateUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/activeregion/ActivityProfileUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/activeregion/BandPassActivityProfileUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/baq/BAQUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/classloader/JVMUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/clipping/ReadClipperTestUtils.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/clipping/ReadClipperUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/codecs/hapmap/HapMapUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/collections/DefaultHashMapUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/collections/ExpandingArrayListUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/commandline/ArgumentMatchSiteUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/commandline/ArgumentMatchSourceUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/commandline/ArgumentTypeDescriptorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/commandline/InvalidArgumentIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/commandline/LoggingIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/commandline/ParsingEngineUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/commandline/RodBindingCollectionUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/commandline/RodBindingUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/crypt/CryptUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/crypt/GATKKeyIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/crypt/GATKKeyUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/file/FSLockWithSharedUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/fragments/FragmentUtilsBenchmark.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/fragments/FragmentUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/haplotype/EventMapUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/haplotype/HaplotypeUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/interval/IntervalIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/interval/IntervalUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/io/IOUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/jna/clibrary/LibCUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/jna/drmaa/v1_0/JnaSessionQueueTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/jna/drmaa/v1_0/LibDrmaaQueueTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils}/jna/lsf/v7_0_6/LibBatQueueTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/locusiterator/AlignmentStateMachineUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/locusiterator/LIBS_position.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/locusiterator/LocusIteratorBenchmark.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/locusiterator/LocusIteratorByStateBaseTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/locusiterator/LocusIteratorByStateUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/locusiterator/PerSampleReadStateManagerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/nanoScheduler/InputProducerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/nanoScheduler/MapResultUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/nanoScheduler/NanoSchedulerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/nanoScheduler/ReducerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/pileup/PileupElementUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/pileup/ReadBackedPileupUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/progressmeter/ProgressMeterDaemonUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/progressmeter/ProgressMeterDataUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/recalibration/EventTypeUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/report/ReportMarshallerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/runtime/ProcessControllerUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/runtime/RuntimeUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/sam/AlignmentUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/sam/ArtificialBAMBuilderUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/sam/ArtificialSAMFileWriterUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/sam/ArtificialSAMQueryIteratorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/sam/ArtificialSAMUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/sam/GATKSAMRecordUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/sam/MisencodedBaseQualityUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/sam/ReadUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/smithwaterman/SmithWatermanBenchmark.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/text/ListFileUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/text/TextFormattingUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/threading/ThreadPoolMonitorUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/variant/GATKVCFUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/variant/GATKVariantContextUtilsUnitTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/variant/VCFIntegrationTest.java (100%) rename public/{gatk-framework/src/test/java/org/broadinstitute/sting => gatk-tools-public/src/test/java/org/broadinstitute/gatk}/utils/variant/VariantContextBenchmark.java (100%) rename public/{gatk-framework => gatk-tools-public}/src/test/resources/testProperties.properties (100%) rename public/{sting-utils => gatk-utils}/pom.xml (100%) rename public/{sting-utils/src/main/config/org/broadinstitute/sting => gatk-utils/src/main/config/org/broadinstitute/gatk}/utils/help/log4j.properties (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-utils/src/main/java/org/broadinstitute/gatk}/utils/GenomeLoc.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-utils/src/main/java/org/broadinstitute/gatk}/utils/HasGenomeLocation.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-utils/src/main/java/org/broadinstitute/gatk}/utils/SimpleTimer.java (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/StingException.java => gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java} (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java => gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java} (100%) rename public/{gatk-framework/src/main/java/org/broadinstitute/sting => gatk-utils/src/main/java/org/broadinstitute/gatk}/utils/package-info.java (100%) rename public/{sting-utils/src/main/resources/org/broadinstitute/sting => gatk-utils/src/main/resources/org/broadinstitute/gatk}/utils/pairhmm/libVectorLoglessPairHMM.so (100%) diff --git a/public/gatk-package/pom.xml b/protected/gatk-package-distribution/pom.xml similarity index 100% rename from public/gatk-package/pom.xml rename to protected/gatk-package-distribution/pom.xml diff --git a/public/gatk-package/src/main/assembly/binary-dist.xml b/protected/gatk-package-distribution/src/main/assembly/binary-dist.xml similarity index 100% rename from public/gatk-package/src/main/assembly/binary-dist.xml rename to protected/gatk-package-distribution/src/main/assembly/binary-dist.xml diff --git a/protected/gatk-queue-extensions-distribution/pom.xml b/protected/gatk-queue-extensions-distribution/pom.xml new file mode 100644 index 000000000..1e6ec727d --- /dev/null +++ b/protected/gatk-queue-extensions-distribution/pom.xml @@ -0,0 +1,217 @@ + + + 4.0.0 + + + org.broadinstitute.gatk + gatk-aggregator + 3.2-SNAPSHOT + ../.. + + + gatk-queue-extensions-distribution + jar + GATK Queue Extensions Distribution + + + ${project.basedir}/../.. + ${project.build.directory}/generated-sources/gatk-extensions + ${gatk.basedir}/public/gatk-queue-extensions-public + ${gatk.queue.extensions.public}/src/main/scala + false + gatk-queue-package-distribution + + + + + ${project.groupId} + gatk-tools-protected + ${project.version} + + + ${project.groupId} + gatk-queue + ${project.version} + + + org.scala-lang + scala-compiler + + + log4j + log4j + + + + ${project.groupId} + gatk-queue-extensions-generator + ${project.version} + runtime + + + + + ${project.groupId} + gatk-tools-public + ${project.version} + test-jar + test + + + ${project.groupId} + gatk-queue + ${project.version} + test-jar + test + + + + + + + + org.codehaus.mojo + exec-maven-plugin + + + generate-gatk-extensions + + exec + + generate-sources + + ${gatk.generate-gatk-extensions.skipped} + java + + -classpath + + org.broadinstitute.gatk.queue.extensions.gatk.GATKExtensionsGenerator + -l + WARN + -outDir + ${gatk.extensions.sources} + + + + + + + org.codehaus.mojo + build-helper-maven-plugin + + + add-gatk-extensions + + add-source + + generate-sources + + + ${gatk.queue.extensions.sources} + ${gatk.extensions.sources} + + + + + + + org.scala-tools + maven-scala-plugin + + + com.pyx4j + maven-junction-plugin + + + link-public-qscript + process-test-resources + + + unlink-public-qscript + clean + + + link-extensions-sources + generate-sources + + + + + org.apache.maven.plugins + maven-invoker-plugin + + + package-unittests + + + package-integrationtests + + + package-largescaletests + + + package-knowledgebasetests + + + package-queuetests + + + + + + + + + private-testdata + + + ${basedir}/../../private/pom.xml + + + + + + + com.pyx4j + maven-junction-plugin + + + link-private-testdata + process-test-resources + + + unlink-private-testdata + clean + + + link-private-qscript + process-test-resources + + + unlink-private-qscript + clean + + + + + + + + + diff --git a/public/queue-package/pom.xml b/protected/gatk-queue-package-distribution/pom.xml similarity index 100% rename from public/queue-package/pom.xml rename to protected/gatk-queue-package-distribution/pom.xml diff --git a/public/queue-package/src/main/assembly/binary-dist.xml b/protected/gatk-queue-package-distribution/src/main/assembly/binary-dist.xml similarity index 100% rename from public/queue-package/src/main/assembly/binary-dist.xml rename to protected/gatk-queue-package-distribution/src/main/assembly/binary-dist.xml diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-tools-protected/pom.xml similarity index 100% rename from protected/gatk-protected/pom.xml rename to protected/gatk-tools-protected/pom.xml diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardCallerArgumentCollection.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardCallerArgumentCollection.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/package-info.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/package-info.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummaries.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummaries.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasTest.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandOddsRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandOddsRatio.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGatherer.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGatherer.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationArgumentCollection.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationArgumentCollection.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistribution.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistribution.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/AbstractStratification.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/AbstractStratification.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/CallableStatus.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/CallableStatus.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalMetric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalMetric.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalMetric.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalMetric.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetric.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetric.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStratification.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStratification.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/Metric.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/Metric.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/PluginUtils.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/PluginUtils.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetric.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetric.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleStratification.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleStratification.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/ThresHolder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/ThresHolder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/Metrics.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/Metrics.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/BaseMismatchModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/BaseMismatchModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypePriors.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypePriors.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypingEngine.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypingOutputMode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingOutputMode.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypingOutputMode.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingOutputMode.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/OutputMode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/OutputMode.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/OutputMode.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/OutputMode.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PoolGenotypePriors.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PoolGenotypePriors.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ProbabilityVector.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ProbabilityVector.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/VariantCallContext.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/VariantCallContext.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalc.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalc.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceTest.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceTest.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResult.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResult.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcTestBuilder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcTestBuilder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalc.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalc.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACcounts.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACcounts.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACset.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACset.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalc.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalc.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactCallLogger.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactCallLogger.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTrimmer.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTrimmer.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResult.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResult.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSet.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSet.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlock.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlock.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlockFinder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlockFinder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeRoute.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeRoute.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounter.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounter.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Kmer.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Kmer.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequence.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequence.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequenceGraphMap.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequenceGraphMap.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngine.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngine.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadAnchoring.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadAnchoring.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadCost.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadCost.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrector.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrector.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentComparator.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentComparator.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentCost.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentCost.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RefVsAnyResult.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RefVsAnyResult.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceMode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceMode.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceMode.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceMode.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestHaplotype.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestHaplotype.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/AllelePair.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/AllelePair.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/BaseArray.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/BaseArray.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CardinalityCounter.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CardinalityCounter.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CloneableIteratorLinkedList.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CloneableIteratorLinkedList.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/DisjointSet.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/DisjointSet.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/Haplotype.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/Haplotype.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/OverhangFixingManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/OverhangFixingManager.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFs.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/SequenceComplexity.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/SequenceComplexity.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/collections/CountSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/collections/CountSet.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gga/GenotypingGivenAllelesUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gga/GenotypingGivenAllelesUtils.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/LDMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/LDMerger.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/LDMerger.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/LDMerger.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/MergeVariantsAcrossHaplotypes.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/MergeVariantsAcrossHaplotypes.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/MergeVariantsAcrossHaplotypes.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/MergeVariantsAcrossHaplotypes.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/FlexibleHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/FlexibleHMM.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRReadTransformer.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRReadTransformer.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BaseRecalibration.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BaseRecalibration.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizer.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizer.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QuantizationInfo.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QuantizationInfo.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariates.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariates.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatum.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatum.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatum.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumNode.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumNode.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalUtils.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalUtils.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalUtils.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReport.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReport.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTables.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTables.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ContextCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ContextCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/Covariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/Covariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/CycleCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/CycleCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ExperimentalCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ExperimentalCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/QualityScoreCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/QualityScoreCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ReadGroupCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ReadGroupCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatLengthCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatLengthCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RequiredCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RequiredCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/StandardCovariate.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/StandardCovariate.java diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java similarity index 100% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngineUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngineUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNodeUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNodeUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjectsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjectsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReaderUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReaderUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DifferenceUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DifferenceUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/WalkerTestIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/WalkerTestIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummariesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummariesUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepthUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepthUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandOddsRatioUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandOddsRatioUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResultUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResultUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/ReadBinUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/ReadBinUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/OverhangFixingManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/OverhangFixingManagerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmpliconsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmpliconsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManagerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariantsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariantsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/RandomDNA.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/RandomDNA.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/DiploidGenotypeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/DiploidGenotypeUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparatorUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeBaseComparatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparatorUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculatorUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculatorUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeScoreComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparatorUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeScoreComparatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparatorUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/LDMergerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/LDMergerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/ActiveRegionTestDataSet.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/ActiveRegionTestDataSet.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMMUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMMUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMMUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMModelUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ContextCovariateUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ContextCovariateUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/CycleCovariateUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/CycleCovariateUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizerUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizerUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariatesUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariatesUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadGroupCovariateUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadGroupCovariateUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalUtilsUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalUtilsUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReportUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReportUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTablesUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTablesUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTestUtils.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTestUtils.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RepeatCovariatesUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RepeatCovariatesUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java similarity index 100% rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java diff --git a/public/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp b/public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.cpp similarity index 100% rename from public/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp rename to public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.cpp diff --git a/public/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h b/public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.h similarity index 100% rename from public/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h rename to public/c/bwa/org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.h diff --git a/public/gatk-engine/pom.xml b/public/gatk-engine/pom.xml new file mode 100644 index 000000000..fb4d2b290 --- /dev/null +++ b/public/gatk-engine/pom.xml @@ -0,0 +1,124 @@ + + + 4.0.0 + + + org.broadinstitute.gatk + gatk-aggregator + 3.2-SNAPSHOT + ../.. + + + gatk-engine + jar + GATK Engine + + + ${project.basedir}/../.. + + + + + ${project.groupId} + gatk-utils + ${project.version} + + + + com.google.caliper + caliper + test + + + + + + + org.apache.maven.plugins + maven-assembly-plugin + + + example-resources + ${gatk.generate-resources.phase} + + + + + org.apache.maven.plugins + maven-resources-plugin + + + copy-resource-bundle-log4j + prepare-package + + + + + + org.apache.maven.plugins + maven-invoker-plugin + + + package-unittests + + + package-integrationtests + + + package-largescaletests + + + package-knowledgebasetests + + + package-queuetests + + + + + + + + + + private-testdata + + + ${basedir}/../../private/pom.xml + + + + + + + com.pyx4j + maven-junction-plugin + + + link-private-testdata + process-test-resources + + + unlink-private-testdata + clean + + + + + + + + + diff --git a/public/gatk-framework/src/main/assembly/example-resources.xml b/public/gatk-engine/src/main/assembly/example-resources.xml similarity index 100% rename from public/gatk-framework/src/main/assembly/example-resources.xml rename to public/gatk-engine/src/main/assembly/example-resources.xml diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadMetrics.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadMetrics.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadMetrics.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadMetrics.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/package-info.java rename to public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/package-info.java diff --git a/public/gatk-framework/src/test/resources/exampleBAM.bam b/public/gatk-engine/src/test/resources/exampleBAM.bam similarity index 100% rename from public/gatk-framework/src/test/resources/exampleBAM.bam rename to public/gatk-engine/src/test/resources/exampleBAM.bam diff --git a/public/gatk-framework/src/test/resources/exampleBAM.bam.bai b/public/gatk-engine/src/test/resources/exampleBAM.bam.bai similarity index 100% rename from public/gatk-framework/src/test/resources/exampleBAM.bam.bai rename to public/gatk-engine/src/test/resources/exampleBAM.bam.bai diff --git a/public/gatk-framework/src/test/resources/exampleBAM.simple.bai b/public/gatk-engine/src/test/resources/exampleBAM.simple.bai similarity index 100% rename from public/gatk-framework/src/test/resources/exampleBAM.simple.bai rename to public/gatk-engine/src/test/resources/exampleBAM.simple.bai diff --git a/public/gatk-framework/src/test/resources/exampleBAM.simple.bam b/public/gatk-engine/src/test/resources/exampleBAM.simple.bam similarity index 100% rename from public/gatk-framework/src/test/resources/exampleBAM.simple.bam rename to public/gatk-engine/src/test/resources/exampleBAM.simple.bam diff --git a/public/gatk-framework/src/test/resources/exampleDBSNP.vcf b/public/gatk-engine/src/test/resources/exampleDBSNP.vcf similarity index 100% rename from public/gatk-framework/src/test/resources/exampleDBSNP.vcf rename to public/gatk-engine/src/test/resources/exampleDBSNP.vcf diff --git a/public/gatk-framework/src/test/resources/exampleDBSNP.vcf.idx b/public/gatk-engine/src/test/resources/exampleDBSNP.vcf.idx similarity index 100% rename from public/gatk-framework/src/test/resources/exampleDBSNP.vcf.idx rename to public/gatk-engine/src/test/resources/exampleDBSNP.vcf.idx diff --git a/public/gatk-framework/src/test/resources/exampleFASTA-3contigs.fasta b/public/gatk-engine/src/test/resources/exampleFASTA-3contigs.fasta similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA-3contigs.fasta rename to public/gatk-engine/src/test/resources/exampleFASTA-3contigs.fasta diff --git a/public/gatk-framework/src/test/resources/exampleFASTA-combined.fasta b/public/gatk-engine/src/test/resources/exampleFASTA-combined.fasta similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA-combined.fasta rename to public/gatk-engine/src/test/resources/exampleFASTA-combined.fasta diff --git a/public/gatk-framework/src/test/resources/exampleFASTA-windows.fasta b/public/gatk-engine/src/test/resources/exampleFASTA-windows.fasta similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA-windows.fasta rename to public/gatk-engine/src/test/resources/exampleFASTA-windows.fasta diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.dict b/public/gatk-engine/src/test/resources/exampleFASTA.dict similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.dict rename to public/gatk-engine/src/test/resources/exampleFASTA.dict diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.fasta b/public/gatk-engine/src/test/resources/exampleFASTA.fasta similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.fasta rename to public/gatk-engine/src/test/resources/exampleFASTA.fasta diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.fasta.amb b/public/gatk-engine/src/test/resources/exampleFASTA.fasta.amb similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.fasta.amb rename to public/gatk-engine/src/test/resources/exampleFASTA.fasta.amb diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.fasta.ann b/public/gatk-engine/src/test/resources/exampleFASTA.fasta.ann similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.fasta.ann rename to public/gatk-engine/src/test/resources/exampleFASTA.fasta.ann diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.fasta.bwt b/public/gatk-engine/src/test/resources/exampleFASTA.fasta.bwt similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.fasta.bwt rename to public/gatk-engine/src/test/resources/exampleFASTA.fasta.bwt diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.fasta.fai b/public/gatk-engine/src/test/resources/exampleFASTA.fasta.fai similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.fasta.fai rename to public/gatk-engine/src/test/resources/exampleFASTA.fasta.fai diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.fasta.pac b/public/gatk-engine/src/test/resources/exampleFASTA.fasta.pac similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.fasta.pac rename to public/gatk-engine/src/test/resources/exampleFASTA.fasta.pac diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.fasta.rbwt b/public/gatk-engine/src/test/resources/exampleFASTA.fasta.rbwt similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.fasta.rbwt rename to public/gatk-engine/src/test/resources/exampleFASTA.fasta.rbwt diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.fasta.rpac b/public/gatk-engine/src/test/resources/exampleFASTA.fasta.rpac similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.fasta.rpac rename to public/gatk-engine/src/test/resources/exampleFASTA.fasta.rpac diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.fasta.rsa b/public/gatk-engine/src/test/resources/exampleFASTA.fasta.rsa similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.fasta.rsa rename to public/gatk-engine/src/test/resources/exampleFASTA.fasta.rsa diff --git a/public/gatk-framework/src/test/resources/exampleFASTA.fasta.sa b/public/gatk-engine/src/test/resources/exampleFASTA.fasta.sa similarity index 100% rename from public/gatk-framework/src/test/resources/exampleFASTA.fasta.sa rename to public/gatk-engine/src/test/resources/exampleFASTA.fasta.sa diff --git a/public/gatk-framework/src/test/resources/exampleGATKReport.eval b/public/gatk-engine/src/test/resources/exampleGATKReport.eval similarity index 100% rename from public/gatk-framework/src/test/resources/exampleGATKReport.eval rename to public/gatk-engine/src/test/resources/exampleGATKReport.eval diff --git a/public/gatk-framework/src/test/resources/exampleGATKReportv1.tbl b/public/gatk-engine/src/test/resources/exampleGATKReportv1.tbl similarity index 100% rename from public/gatk-framework/src/test/resources/exampleGATKReportv1.tbl rename to public/gatk-engine/src/test/resources/exampleGATKReportv1.tbl diff --git a/public/gatk-framework/src/test/resources/exampleGATKReportv2.tbl b/public/gatk-engine/src/test/resources/exampleGATKReportv2.tbl similarity index 100% rename from public/gatk-framework/src/test/resources/exampleGATKReportv2.tbl rename to public/gatk-engine/src/test/resources/exampleGATKReportv2.tbl diff --git a/public/gatk-framework/src/test/resources/exampleGRP.grp b/public/gatk-engine/src/test/resources/exampleGRP.grp similarity index 100% rename from public/gatk-framework/src/test/resources/exampleGRP.grp rename to public/gatk-engine/src/test/resources/exampleGRP.grp diff --git a/public/gatk-framework/src/test/resources/exampleINTERVAL.intervals b/public/gatk-engine/src/test/resources/exampleINTERVAL.intervals similarity index 100% rename from public/gatk-framework/src/test/resources/exampleINTERVAL.intervals rename to public/gatk-engine/src/test/resources/exampleINTERVAL.intervals diff --git a/public/gatk-framework/src/test/resources/exampleNORG.bam b/public/gatk-engine/src/test/resources/exampleNORG.bam similarity index 100% rename from public/gatk-framework/src/test/resources/exampleNORG.bam rename to public/gatk-engine/src/test/resources/exampleNORG.bam diff --git a/public/gatk-framework/src/test/resources/exampleNORG.bam.bai b/public/gatk-engine/src/test/resources/exampleNORG.bam.bai similarity index 100% rename from public/gatk-framework/src/test/resources/exampleNORG.bam.bai rename to public/gatk-engine/src/test/resources/exampleNORG.bam.bai diff --git a/public/gatk-framework/src/test/resources/forAlleleFractionSimulation.vcf b/public/gatk-engine/src/test/resources/forAlleleFractionSimulation.vcf similarity index 100% rename from public/gatk-framework/src/test/resources/forAlleleFractionSimulation.vcf rename to public/gatk-engine/src/test/resources/forAlleleFractionSimulation.vcf diff --git a/public/gatk-framework/src/test/resources/forAlleleFractionSimulation.vcf.idx b/public/gatk-engine/src/test/resources/forAlleleFractionSimulation.vcf.idx similarity index 100% rename from public/gatk-framework/src/test/resources/forAlleleFractionSimulation.vcf.idx rename to public/gatk-engine/src/test/resources/forAlleleFractionSimulation.vcf.idx diff --git a/public/gatk-framework/src/test/resources/forSimulation.vcf b/public/gatk-engine/src/test/resources/forSimulation.vcf similarity index 100% rename from public/gatk-framework/src/test/resources/forSimulation.vcf rename to public/gatk-engine/src/test/resources/forSimulation.vcf diff --git a/public/gatk-framework/src/test/resources/forSimulation.vcf.idx b/public/gatk-engine/src/test/resources/forSimulation.vcf.idx similarity index 100% rename from public/gatk-framework/src/test/resources/forSimulation.vcf.idx rename to public/gatk-engine/src/test/resources/forSimulation.vcf.idx diff --git a/public/gatk-framework/src/test/resources/testfile.sam b/public/gatk-engine/src/test/resources/testfile.sam similarity index 100% rename from public/gatk-framework/src/test/resources/testfile.sam rename to public/gatk-engine/src/test/resources/testfile.sam diff --git a/public/gatk-queue-extgen/pom.xml b/public/gatk-queue-extensions-generator/pom.xml similarity index 100% rename from public/gatk-queue-extgen/pom.xml rename to public/gatk-queue-extensions-generator/pom.xml diff --git a/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java similarity index 100% rename from public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java rename to public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java diff --git a/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java similarity index 100% rename from public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java rename to public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java diff --git a/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/GATKExtensionsGenerator.java similarity index 100% rename from public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java rename to public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/GATKExtensionsGenerator.java diff --git a/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ReadFilterField.java similarity index 100% rename from public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java rename to public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ReadFilterField.java diff --git a/public/gatk-queue-extensions-public/pom.xml b/public/gatk-queue-extensions-public/pom.xml new file mode 100644 index 000000000..b03a8a281 --- /dev/null +++ b/public/gatk-queue-extensions-public/pom.xml @@ -0,0 +1,220 @@ + + + 4.0.0 + + + org.broadinstitute.gatk + gatk-aggregator + 3.2-SNAPSHOT + ../.. + + + gatk-queue-extensions-public + jar + GATK Queue Extensions Public + + + ${project.basedir}/../.. + ${project.build.directory}/generated-sources/gatk-extensions + false + gatk-queue-package-distribution + + + + + ${project.groupId} + gatk-tools-public + ${project.version} + + + ${project.groupId} + gatk-queue + ${project.version} + + + org.scala-lang + scala-compiler + + + log4j + log4j + + + + ${project.groupId} + gatk-queue-extensions-generator + ${project.version} + runtime + + + + + ${project.groupId} + gatk-tools-public + ${project.version} + test-jar + test + + + ${project.groupId} + gatk-queue + ${project.version} + test-jar + test + + + + + + + + org.codehaus.mojo + exec-maven-plugin + + + generate-gatk-extensions + + exec + + generate-sources + + ${gatk.generate-gatk-extensions.skipped} + java + + -classpath + + org.broadinstitute.gatk.queue.extensions.gatk.GATKExtensionsGenerator + -l + WARN + -outDir + ${gatk.extensions.sources} + + + + + + + org.codehaus.mojo + build-helper-maven-plugin + + + add-gatk-extensions + + add-source + + generate-sources + + + ${gatk.extensions.sources} + + + + + + + org.apache.maven.plugins + maven-assembly-plugin + + + example-resources + ${gatk.generate-resources.phase} + + + + + org.scala-tools + maven-scala-plugin + + + com.pyx4j + maven-junction-plugin + + + link-public-qscript + process-test-resources + + + unlink-public-qscript + clean + + + + + org.apache.maven.plugins + maven-invoker-plugin + + + package-unittests + + + package-integrationtests + + + package-largescaletests + + + package-knowledgebasetests + + + package-queuetests + + + + + + + + + private-testdata + + + ${basedir}/../../private/pom.xml + + + + + + + com.pyx4j + maven-junction-plugin + + + link-private-testdata + process-test-resources + + + unlink-private-testdata + clean + + + link-private-qscript + process-test-resources + + + unlink-private-qscript + clean + + + + + + + + + diff --git a/public/queue-framework/src/main/assembly/example-resources.xml b/public/gatk-queue-extensions-public/src/main/assembly/example-resources.xml similarity index 100% rename from public/queue-framework/src/main/assembly/example-resources.xml rename to public/gatk-queue-extensions-public/src/main/assembly/example-resources.xml diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/CNV/xhmmCNVpipeline.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/CNV/xhmmCNVpipeline.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/GATKResourcesBundle.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/GATKResourcesBundle.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCustomWalker.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCustomWalker.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExamplePrintReads.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExamplePrintReads.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/ChunkVCF.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/ChunkVCF.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala diff --git a/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/VcfToPed.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala similarity index 100% rename from public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/VcfToPed.scala rename to public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/cancer/MuTect.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/cancer/MuTect.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/BamGatherFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/BamGatherFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/CatVariantsGatherer.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/CatVariantsGatherer.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ContigScatterFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ContigScatterFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DistributedScatterFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DistributedScatterFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/DoC/package.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/DoC/package.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKScatterFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKScatterFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/IntervalScatterFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/IntervalScatterFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/LocusScatterFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/LocusScatterFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/ReadScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ReadScatterFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/ReadScatterFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ReadScatterFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/TaggedFile.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/TaggedFile.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/VcfGatherFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/VcfGatherFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/AddOrReplaceReadGroups.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/AddOrReplaceReadGroups.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectGcBiasMetrics.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectGcBiasMetrics.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectMultipleMetrics.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectMultipleMetrics.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/FastqToSam.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/FastqToSam.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MergeSamFiles.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MergeSamFiles.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ReorderSam.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ReorderSam.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/RevertSam.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/RevertSam.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SamToFastq.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SamToFastq.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SortSam.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SortSam.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ValidateSamFile.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ValidateSamFile.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsCommandLineFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsCommandLineFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsIndexFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsIndexFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsMergeFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsMergeFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/snpeff/SnpEff.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala rename to public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/snpeff/SnpEff.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervalsUnitTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala rename to public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervalsUnitTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountLociQueueTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociQueueTest.scala rename to public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountLociQueueTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountReadsQueueTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsQueueTest.scala rename to public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountReadsQueueTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala rename to public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleReadFilterQueueTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterQueueTest.scala rename to public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleReadFilterQueueTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala rename to public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala rename to public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldQueueTest.scala rename to public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala diff --git a/public/queue-framework/pom.xml b/public/gatk-queue/pom.xml similarity index 100% rename from public/queue-framework/pom.xml rename to public/gatk-queue/pom.xml diff --git a/public/queue-framework/src/main/java/org/broadinstitute/sting/queue/QueueVersion.java b/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/QueueVersion.java similarity index 100% rename from public/queue-framework/src/main/java/org/broadinstitute/sting/queue/QueueVersion.java rename to public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/QueueVersion.java diff --git a/public/queue-framework/src/main/java/org/broadinstitute/sting/queue/package-info.java b/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/package-info.java similarity index 100% rename from public/queue-framework/src/main/java/org/broadinstitute/sting/queue/package-info.java rename to public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/package-info.java diff --git a/public/queue-framework/src/main/resources/org/broadinstitute/sting/queue/util/queueJobReport.R b/public/gatk-queue/src/main/resources/org/broadinstitute/gatk/queue/util/queueJobReport.R similarity index 100% rename from public/queue-framework/src/main/resources/org/broadinstitute/sting/queue/util/queueJobReport.R rename to public/gatk-queue/src/main/resources/org/broadinstitute/gatk/queue/util/queueJobReport.R diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QCommandLine.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QCommandLine.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QCommandPlugin.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandPlugin.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QCommandPlugin.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandPlugin.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QException.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QException.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QException.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QException.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QScript.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QScript.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QScriptManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScriptManager.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QScriptManager.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScriptManager.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QSettings.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QSettings.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/CommandLineJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobManager.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/CommandLineJobManager.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobManager.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobRunner.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobRunner.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/CommandLinePluginManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLinePluginManager.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/CommandLinePluginManager.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLinePluginManager.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/FunctionEdge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/FunctionEdge.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/FunctionEdge.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/FunctionEdge.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/InProcessJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessJobManager.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/InProcessJobManager.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessJobManager.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/InProcessRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessRunner.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/InProcessRunner.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessRunner.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/JobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobManager.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/JobManager.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobManager.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/JobRunInfo.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunInfo.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/JobRunInfo.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunInfo.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/JobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunner.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/JobRunner.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunner.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/MappingEdge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/MappingEdge.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/MappingEdge.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/MappingEdge.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QEdge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QEdge.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QEdge.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QEdge.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QGraph.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QGraph.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QGraphSettings.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QGraphSettings.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QNode.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QNode.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QNode.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QNode.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QStatusMessenger.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QStatusMessenger.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QStatusMessenger.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QStatusMessenger.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/RunnerStatus.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/RunnerStatus.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/RunnerStatus.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/RunnerStatus.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobManager.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobManager.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobManager.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobRunner.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobRunner.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobManager.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobManager.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobManager.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobManager.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobManager.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobManager.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobRunner.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobRunner.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobManager.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobManager.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobManager.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobRunner.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/shell/ShellJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobManager.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/shell/ShellJobManager.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobManager.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobRunner.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobRunner.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/CommandLineFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/CommandLineFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/CommandLineFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/CommandLineFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/InProcessFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/InProcessFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/InProcessFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/InProcessFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/JavaCommandLineFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/JavaCommandLineFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/ListWriterFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/ListWriterFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/ListWriterFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/ListWriterFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/QFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/QFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/QFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/QFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/RetryMemoryLimit.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/RetryMemoryLimit.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/CloneFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/CloneFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ConcatenateLogsFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ConcatenateLogsFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ConcatenateLogsFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ConcatenateLogsFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GatherFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GatherFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GathererFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GathererFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterGatherableFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterGatherableFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/SimpleTextGatherFunction.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/SimpleTextGatherFunction.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractIntervals.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractIntervals.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractSamples.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractSamples.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/SortByRef.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/SortByRef.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSamples.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSamples.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSites.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSites.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ClassFieldCache.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ClassFieldCache.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ClassFieldCache.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ClassFieldCache.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/CollectionUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/CollectionUtils.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/CollectionUtils.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/CollectionUtils.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailMessage.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailMessage.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailMessage.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailMessage.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailSettings.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailSettings.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailSettings.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailSettings.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Logging.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Logging.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Logging.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Logging.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/PrimitiveOptionConversions.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/PrimitiveOptionConversions.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobReport.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobReport.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobsReporter.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobsReporter.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QScriptUtils.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ReflectionUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ReflectionUtils.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ReflectionUtils.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ReflectionUtils.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFile.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFile.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFile.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFile.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFileConverter.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFileConverter.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFileConverter.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFileConverter.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Retry.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Retry.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Retry.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Retry.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RetryException.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RetryException.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RetryException.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RetryException.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ScalaCompoundArgumentTypeDescriptor.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ScalaCompoundArgumentTypeDescriptor.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ScalaCompoundArgumentTypeDescriptor.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ScalaCompoundArgumentTypeDescriptor.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ShellUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ShellUtils.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ShellUtils.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ShellUtils.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/StringFileConversions.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/StringFileConversions.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/StringFileConversions.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/StringFileConversions.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/SystemUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/SystemUtils.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/SystemUtils.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/SystemUtils.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/TextFormatUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/TextFormatUtils.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/TextFormatUtils.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/TextFormatUtils.scala diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala similarity index 100% rename from public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala rename to public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/function/CommandLineFunctionUnitTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala rename to public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/function/CommandLineFunctionUnitTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTest.scala rename to public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTestEvalSpec.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestEvalSpec.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTestEvalSpec.scala rename to public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestEvalSpec.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTestSpec.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestSpec.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTestSpec.scala rename to public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestSpec.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/ShellUtilsUnitTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala rename to public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/ShellUtilsUnitTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/StringFileConversionsUnitTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala rename to public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/StringFileConversionsUnitTest.scala diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/SystemUtilsUnitTest.scala similarity index 100% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala rename to public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/SystemUtilsUnitTest.scala diff --git a/public/sting-root/pom.xml b/public/gatk-root/pom.xml similarity index 100% rename from public/sting-root/pom.xml rename to public/gatk-root/pom.xml diff --git a/public/gatk-framework/pom.xml b/public/gatk-tools-public/pom.xml similarity index 100% rename from public/gatk-framework/pom.xml rename to public/gatk-tools-public/pom.xml diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java b/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java similarity index 100% rename from public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java rename to public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java b/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBin.java similarity index 100% rename from public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java rename to public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBin.java diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java b/public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKChunk.java similarity index 100% rename from public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java rename to public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKChunk.java diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java b/public/gatk-tools-public/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java rename to public/gatk-tools-public/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/CommandLineExecutable.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/CommandLineGATK.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadProperties.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadProperties.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/WalkerManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/WalkerManager.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Aligner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Aligner.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Alignment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Alignment.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/CheckAlignment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/CheckAlignment.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/CheckAlignment.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/CheckAlignment.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWAAligner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWAAligner.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWTFiles.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWTFiles.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWACAligner.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWACAligner.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/c/BWAPath.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWAPath.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/c/BWAPath.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/c/BWAPath.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignmentState.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignmentState.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWT.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWT.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/Bases.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/Bases.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/Counts.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/Counts.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/ValidationExclusion.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/ValidationExclusion.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContext.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContext.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContextUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/AlignmentContextUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/ReferenceContext.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/contexts/ReferenceContext.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/View.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/View.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FileHandleCache.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FileHandleCache.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderID.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderID.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/Shard.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/Shard.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/DataStreamSegment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/DataStreamSegment.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/EntireStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/EntireStream.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/MappedStreamSegment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/MappedStreamSegment.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsampleType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsampleType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsampleType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsampleType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/Downsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/Downsampler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/Downsampler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/Downsampler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingMethod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingMethod.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingMethod.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingMethod.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsampler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsampler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsampler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerFactory.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerFactory.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerFactory.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/LevelingDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsampler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/LevelingDownsampler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsampler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PassThroughDownsampler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PassThroughDownsampler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsampler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsampler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsampler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsamplerFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsamplerFactory.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsamplerFactory.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReadsDownsamplerFactory.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsampler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsampler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerFactory.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerFactory.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerFactory.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsampler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsampler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsampler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsampler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerFactory.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerFactory.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerFactory.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/Accumulator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/Accumulator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/HierarchicalMicroSchedulerMBean.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/HierarchicalMicroSchedulerMBean.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/MicroScheduler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/MicroSchedulerMBean.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/MicroSchedulerMBean.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/ReduceTree.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/ReduceTree.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/ShardTraverser.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/TreeReducer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/WindowMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/WindowMaker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadMateFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadMateFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/FilterManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/FilterManager.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/LibraryReadFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/LibraryReadFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/Platform454Filter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/Platform454Filter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadLengthFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadLengthFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SampleFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SampleFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/FastqFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/FastqFileWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/GATKSAMFileWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/GATKSAMFileWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/OutputTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/OutputTracker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/ThreadGroupOutputTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/ThreadGroupOutputTracker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/Storage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/Storage.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/Storage.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/StorageFactory.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamArgumentTypeDescriptor.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/OutputStreamStub.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileReaderArgumentTypeDescriptor.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileReaderArgumentTypeDescriptor.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/Stub.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/Stub.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/Stub.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMRecordIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GATKSAMRecordIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/IterableIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/IterableIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PeekingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PeekingIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PushbackIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/PushbackIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/RNAReadTransformer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/RNAReadTransformer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadTransformer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadTransformer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadTransformersMode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadTransformersMode.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/phonehome/GATKRunReportException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/phonehome/GATKRunReportException.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RODRecordListImpl.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RODRecordListImpl.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTracker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTracker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceDependentFeatureCodec.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceDependentFeatureCodec.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceOrderedDatum.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/ReferenceOrderedDatum.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/SeekableRODIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/SeekableRODIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/VariantContextAdaptors.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/VariantContextAdaptors.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManager.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManager.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/IndexDictionaryUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/IndexDictionaryUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrack.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrack.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilder.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilder.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/GATKFeature.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/GATKFeature.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/LocationAwareSeekableRODIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/LocationAwareSeekableRODIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RMDTriplet.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RMDTriplet.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/RODRecordList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RODRecordList.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/RODRecordList.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/refdata/utils/RODRecordList.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReport.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReport.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReport.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReport.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportColumn.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumn.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportColumn.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumn.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportColumnFormat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumnFormat.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportColumnFormat.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportColumnFormat.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportDataType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportDataType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportDataType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportDataType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportGatherer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportGatherer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportTable.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportTable.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportTable.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportVersion.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportVersion.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportVersion.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/report/GATKReportVersion.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/resourcemanagement/ThreadAllocation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/resourcemanagement/ThreadAllocation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/Affection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/Affection.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/Gender.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/Gender.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/PedReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/PedReader.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/PedigreeValidationType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/PedigreeValidationType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/Sample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/Sample.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDB.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDB.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/Trio.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/Trio.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TAROrderedReadCache.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TAROrderedReadCache.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseLociNano.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseLociNano.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ActiveRegionTraversalParameters.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ActiveRegionTraversalParameters.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Allows.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Allows.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Attribution.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Attribution.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/BAQMode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/BAQMode.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/By.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/By.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/DataSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/DataSource.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Downsample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Downsample.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/LocusWalker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Multiplex.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Multiplex.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Multiplex.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Multiplex.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Multiplexer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Multiplexer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Multiplexer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Multiplexer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/NanoSchedulable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/NanoSchedulable.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/PartitionBy.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/PartitionBy.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/PartitionType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/PartitionType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RMD.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RMD.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadFilters.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadFilters.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadWalker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RefWalker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RefWalker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Reference.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Reference.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RemoveProgramRecords.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RemoveProgramRecords.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Requires.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Requires.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RodWalker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RodWalker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/TreeReducible.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/TreeReducible.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Walker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Walker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/WalkerName.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/WalkerName.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Window.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Window.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/BAMDiffableReader.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/BAMDiffableReader.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffElement.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffElement.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngine.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngine.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNode.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNode.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjects.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffObjects.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffValue.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffValue.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReader.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReader.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/Difference.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/Difference.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/GATKReportDiffableReader.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/GATKReportDiffableReader.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/VCFDiffableReader.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/VCFDiffableReader.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/ListAnnotations.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/ListAnnotations.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCountConstants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCountConstants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtil.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtil.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageStats.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageStats.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DoCOutputType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DoCOutputType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmplicons.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationAmplicons.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/SnpEffPositionModifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/SnpEffPositionModifier.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitives.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitives.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/AutoFormattingTime.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/AutoFormattingTime.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/BaseUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/BaseUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/BitSetUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/BitSetUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/ContigComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/ContigComparator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/DeprecatedToolChecks.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/DeprecatedToolChecks.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocParser.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocSortedSet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocSortedSet.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/HeapSizeMonitor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/HeapSizeMonitor.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/IndelUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/IndelUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/LRUCache.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/LRUCache.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MRUCachingSAMSequenceDictionary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MRUCachingSAMSequenceDictionary.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MannWhitneyU.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MannWhitneyU.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MathUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MathUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/Median.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/Median.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/Median.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/Median.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MendelianViolation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MendelianViolation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MendelianViolation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MendelianViolation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MultiThreadedErrorTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MultiThreadedErrorTracker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/NGSPlatform.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/NGSPlatform.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/PathUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/PathUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/QualityUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/QualityUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/R/RScriptExecutor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/R/RScriptExecutor.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/R/RScriptExecutorException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/R/RScriptExecutorException.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/R/RScriptLibrary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/R/RScriptLibrary.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/R/RUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/R/RUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SampleUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/SampleUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SampleUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/SampleUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/UnvalidatingGenomeLoc.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/UnvalidatingGenomeLoc.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/Utils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/Utils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/Utils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/Utils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActiveRegionReadState.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActiveRegionReadState.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileState.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileState.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/analysis/AminoAcid.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/analysis/AminoAcid.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/analysis/AminoAcidTable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/analysis/AminoAcidTable.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/analysis/AminoAcidUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/analysis/AminoAcidUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQ.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQ.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQReadTransformer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQReadTransformer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQReadTransformer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/BAQReadTransformer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/ReadTransformingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/ReadTransformingIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/ReadTransformingIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/baq/ReadTransformingIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/JVMUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/PluginManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/PluginManager.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/ProtectedPackageSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/ProtectedPackageSource.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/PublicPackageSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/PublicPackageSource.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ClippingOp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ClippingOp.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ClippingRepresentation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ClippingRepresentation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ReadClipper.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ReadClipper.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableCodec.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableCodec.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableFeature.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/DefaultHashMap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/DefaultHashMap.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/ExpandingArrayList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/ExpandingArrayList.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/Pair.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/Pair.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/PrimitivePair.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/PrimitivePair.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/RODMergingIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/collections/RODMergingIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Advanced.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Advanced.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Argument.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Argument.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentCollection.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentDefinition.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentDefinition.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentDefinitions.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentDefinitions.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentException.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentIOType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentIOType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatch.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatch.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchFileValue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchFileValue.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchSite.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchSite.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchSource.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchSourceType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchSourceType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchStringValue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchStringValue.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchValue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchValue.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatches.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatches.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentSource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentSource.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ClassType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ClassType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Gather.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Gather.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Gatherer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Gatherer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Hidden.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Hidden.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Input.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Input.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalBinding.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalBinding.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/MissingArgumentValueException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/MissingArgumentValueException.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Output.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Output.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsedArgs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsedArgs.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsedListArgs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsedListArgs.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsingEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsingEngine.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsingEngineArgumentFiles.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsingEngineArgumentFiles.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsingEngineArgumentProvider.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsingEngineArgumentProvider.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsingMethod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsingMethod.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBinding.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBinding.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBindingCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBindingCollection.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Tags.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Tags.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/crypt/CryptUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/CryptUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/crypt/CryptUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/CryptUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/crypt/GATKKey.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/GATKKey.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/crypt/GATKKey.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/crypt/GATKKey.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/duplicates/DupUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/duplicates/DuplicateComp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/duplicates/DuplicateComp.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/DynamicClassResolutionException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/DynamicClassResolutionException.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/UserException.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fasta/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fasta/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/file/FSLockWithShared.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/file/FSLockWithShared.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fragments/FragmentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fragments/FragmentCollection.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fragments/FragmentUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fragments/FragmentUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAllele.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAllele.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/EventMap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/EventMap.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/Haplotype.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/Haplotype.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeBaseComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeBaseComparator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeScoreComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeScoreComparator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/ApplicationDetails.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/ApplicationDetails.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/DocletUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/DocletUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/DocumentedGATKFeature.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/DocumentedGATKFeature.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureObject.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureObject.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/ForumAPIUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/ForumAPIUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/ForumDiscussion.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/ForumDiscussion.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDocUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDocUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDoclet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDoclet.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/HelpConstants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/HelpConstants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/HelpFormatter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/HelpFormatter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/HelpUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/HelpUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/HelpUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/instrumentation/Sizeof.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/instrumentation/Sizeof.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/interval/IntervalMergingRule.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/interval/IntervalMergingRule.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/interval/IntervalSetRule.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/interval/IntervalSetRule.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/interval/IntervalUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/io/FileExtension.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/io/FileExtension.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/io/HardThresholdingOutputStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/io/HardThresholdingOutputStream.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/io/IOUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/io/IOUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/io/Resource.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/io/Resource.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/clibrary/JNAUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/clibrary/JNAUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/clibrary/LibC.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/clibrary/LibC.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaJobInfo.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaJobInfo.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaJobTemplate.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaJobTemplate.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSession.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSession.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionFactory.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaa.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaa.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachine.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LIBSDownsamplingInfo.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LIBSDownsamplingInfo.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManager.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/SamplePartitioner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/SamplePartitioner.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/EOFMarkedValue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/EOFMarkedValue.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/InputProducer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/InputProducer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/MapResult.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/MapResult.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/MapResultsQueue.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/MapResultsQueue.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/NSMapFunction.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/NSMapFunction.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/NSProgressFunction.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/NSProgressFunction.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/NSReduceFunction.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/NSReduceFunction.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/NanoScheduler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/NanoScheduler.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/Reducer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/nanoScheduler/Reducer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/BatchPairHMM.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/BatchPairHMM.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/PairHMM.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/PairHMM.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/PairHMMModel.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/PairHMMModel.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/PairHMMReadyHaplotypes.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/PairHMMReadyHaplotypes.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/PileupElement.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/PileupElementFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/PileupElementFilter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/PileupElementTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/PileupElementTracker.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup2/Notes b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup2/Notes similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup2/Notes rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/pileup2/Notes diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/progressmeter/ProgressMeter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/progressmeter/ProgressMeter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDaemon.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDaemon.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/progressmeter/ProgressMeterData.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/progressmeter/ProgressMeterData.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRArgumentSet.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRArgumentSet.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/recalibration/BQSRMode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRMode.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/recalibration/BQSRMode.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRMode.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/recalibration/EventType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/recalibration/EventType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/CapturedStreamOutput.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/CapturedStreamOutput.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/InputStreamSettings.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/InputStreamSettings.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/OutputStreamSettings.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/OutputStreamSettings.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/ProcessController.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/ProcessController.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/ProcessOutput.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/ProcessOutput.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/ProcessSettings.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/ProcessSettings.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/RuntimeUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/RuntimeUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/StreamLocation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/StreamLocation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/StreamOutput.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/runtime/StreamOutput.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartComparator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartWithNoTiesComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartWithNoTiesComparator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialMultiSampleReadStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialMultiSampleReadStream.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialReadsTraversal.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialReadsTraversal.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStream.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStream.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/BySampleSAMFileWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/BySampleSAMFileWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/CigarUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/CigarUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSamRecordFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSamRecordFactory.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSamRecordFactory.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityReadTransformer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityReadTransformer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/NWaySAMFileWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/NWaySAMFileWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUnclippedStartWithNoTiesComparator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUnclippedStartWithNoTiesComparator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/Parameters.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/Parameters.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignment.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignment.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignmentMain.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignmentMain.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SWParameterSet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SWParameterSet.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SmithWaterman.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SmithWaterman.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/text/ListFileUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/text/ListFileUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/text/TextFormattingUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/text/TextFormattingUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/text/XReadLines.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/text/XReadLines.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/EfficiencyMonitoringThreadFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/EfficiencyMonitoringThreadFactory.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/NamedThreadFactory.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/NamedThreadFactory.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/ThreadEfficiencyMonitor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/ThreadEfficiencyMonitor.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/ThreadLocalArray.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/ThreadLocalArray.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/ThreadPoolMonitor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/ThreadPoolMonitor.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/threading/package-info.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFIndexType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFIndexType.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/HomoSapiensConstants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/HomoSapiensConstants.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/wiggle/WiggleHeader.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/wiggle/WiggleHeader.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java diff --git a/public/gatk-framework/src/main/resources/GATK_public.key b/public/gatk-tools-public/src/main/resources/GATK_public.key similarity index 100% rename from public/gatk-framework/src/main/resources/GATK_public.key rename to public/gatk-tools-public/src/main/resources/GATK_public.key diff --git a/public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key b/public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_access.key similarity index 100% rename from public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key rename to public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_access.key diff --git a/public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key b/public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_secret.key similarity index 100% rename from public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key rename to public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/engine/phonehome/resources/GATK_AWS_secret.key diff --git a/public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R b/public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/tools/walkers/variantrecalibration/plot_Tranches.R similarity index 100% rename from public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R rename to public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/tools/walkers/variantrecalibration/plot_Tranches.R diff --git a/public/gatk-framework/src/main/resources/org/broadinstitute/sting/utils/recalibration/BQSR.R b/public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/utils/recalibration/BQSR.R similarity index 100% rename from public/gatk-framework/src/main/resources/org/broadinstitute/sting/utils/recalibration/BQSR.R rename to public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/utils/recalibration/BQSR.R diff --git a/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java b/public/gatk-tools-public/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java rename to public/gatk-tools-public/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java diff --git a/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java b/public/gatk-tools-public/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java rename to public/gatk-tools-public/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/CommandLineGATKUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/CommandLineGATKUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/MaxRuntimeIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/MaxRuntimeIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/ReadMetricsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/ReadMetricsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedViewUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/MockLocusShard.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/MockLocusShard.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadProcessingBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadProcessingBenchmark.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderIDUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderIDUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SeekableBufferedStreamUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SeekableBufferedStreamUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSourceIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSourceIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIteratorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/LevelingDownsamplerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/LevelingDownsamplerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/executive/ReduceTreeUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/executive/ReduceTreeUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/AllowNCigarMalformedReadFilterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/AllowNCigarMalformedReadFilterUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/BadReadGroupsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/BadReadGroupsIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilterUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadFilterTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadFilterTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/UnsafeMalformedReadFilterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/UnsafeMalformedReadFilterUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIteratorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIteratorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/phonehome/GATKRunReportUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/phonehome/GATKRunReportUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTrackerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/RefMetaDataTrackerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManagerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/FeatureManagerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/CheckableCloseableTribbleIterator.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/CheckableCloseableTribbleIterator.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/CheckableCloseableTribbleIterator.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/CheckableCloseableTribbleIterator.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIteratorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIteratorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/FlashBackIteratorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestFeatureReader.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestFeatureReader.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestRMDTrackBuilder.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestRMDTrackBuilder.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestRMDTrackBuilder.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/utils/TestRMDTrackBuilder.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/report/GATKReportUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/report/GATKReportUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/samples/SampleUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/samples/SampleUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/DummyActiveRegionWalker.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/DummyActiveRegionWalker.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TAROrderedReadCacheUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TAROrderedReadCacheUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/WalkerTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/WalkerTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/tools/CatVariantsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/tools/CatVariantsIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtilUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtilUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/qc/CheckPileupIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/qc/CheckPileupIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/qc/CountReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/qc/CountReadsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/qc/FlagStatIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/qc/FlagStatIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsLargeScaleTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsLargeScaleTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariantsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariantsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariantsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariantsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/AutoFormattingTimeUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/AutoFormattingTimeUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/BitSetUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/BitSetUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/ExampleToCopyUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/ExampleToCopyUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/StingTextReporter.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/StingTextReporter.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserBenchmark.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/MD5DB.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/MD5DB.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/MD5Mismatch.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/MD5Mismatch.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MRUCachingSAMSequencingDictionaryUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MRUCachingSAMSequencingDictionaryUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MWUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MWUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MathUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MathUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MedianUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MedianUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/NGSPlatformUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/NGSPlatformUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/PathUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/PathUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/QualityUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/QualityUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/R/RScriptExecutorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/R/RScriptExecutorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/R/RScriptLibraryUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/R/RScriptLibraryUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/R/RUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/R/RUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SampleUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SampleUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SampleUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SampleUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SequenceDictionaryUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SequenceDictionaryUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SimpleTimerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SimpleTimerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/TestNGTestTransformer.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/TestNGTestTransformer.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/UtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/UtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActiveRegionUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActiveRegionUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileStateUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileStateUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/baq/BAQUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/baq/BAQUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/classloader/JVMUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/classloader/JVMUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/collections/DefaultHashMapUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/collections/DefaultHashMapUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/collections/ExpandingArrayListUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/collections/ExpandingArrayListUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentMatchSiteUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentMatchSiteUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentMatchSourceUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentMatchSourceUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/InvalidArgumentIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/InvalidArgumentIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/InvalidArgumentIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/InvalidArgumentIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/LoggingIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/LoggingIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/LoggingIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/LoggingIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingCollectionUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingCollectionUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/crypt/CryptUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/CryptUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/crypt/CryptUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/CryptUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/crypt/GATKKeyUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/crypt/GATKKeyUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/crypt/GATKKeyUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/file/FSLockWithSharedUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/file/FSLockWithSharedUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsBenchmark.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/EventMapUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/EventMapUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/io/IOUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/io/IOUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/clibrary/LibCUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/clibrary/LibCUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionQueueTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionQueueTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaQueueTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaQueueTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatQueueTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatQueueTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachineUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachineUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LIBS_position.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LIBS_position.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorBenchmark.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateBaseTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateBaseTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManagerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManagerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/InputProducerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/InputProducerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/MapResultUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/MapResultUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/ReducerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/ReducerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/PileupElementUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/PileupElementUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDaemonUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDaemonUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDataUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDataUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/recalibration/EventTypeUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/recalibration/EventTypeUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/report/ReportMarshallerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/report/ReportMarshallerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/runtime/ProcessControllerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/runtime/ProcessControllerUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/runtime/RuntimeUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/runtime/RuntimeUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilderUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilderUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/MisencodedBaseQualityUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/smithwaterman/SmithWatermanBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/smithwaterman/SmithWatermanBenchmark.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/text/ListFileUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/text/ListFileUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/text/TextFormattingUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/text/TextFormattingUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/threading/ThreadPoolMonitorUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/threading/ThreadPoolMonitorUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VCFIntegrationTest.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VCFIntegrationTest.java diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java similarity index 100% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java rename to public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java diff --git a/public/gatk-framework/src/test/resources/testProperties.properties b/public/gatk-tools-public/src/test/resources/testProperties.properties similarity index 100% rename from public/gatk-framework/src/test/resources/testProperties.properties rename to public/gatk-tools-public/src/test/resources/testProperties.properties diff --git a/public/sting-utils/pom.xml b/public/gatk-utils/pom.xml similarity index 100% rename from public/sting-utils/pom.xml rename to public/gatk-utils/pom.xml diff --git a/public/sting-utils/src/main/config/org/broadinstitute/sting/utils/help/log4j.properties b/public/gatk-utils/src/main/config/org/broadinstitute/gatk/utils/help/log4j.properties similarity index 100% rename from public/sting-utils/src/main/config/org/broadinstitute/sting/utils/help/log4j.properties rename to public/gatk-utils/src/main/config/org/broadinstitute/gatk/utils/help/log4j.properties diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLoc.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLoc.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/HasGenomeLocation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/HasGenomeLocation.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SimpleTimer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SimpleTimer.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/StingException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/StingException.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java similarity index 100% rename from public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/package-info.java rename to public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java diff --git a/public/sting-utils/src/main/resources/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so b/public/gatk-utils/src/main/resources/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so similarity index 100% rename from public/sting-utils/src/main/resources/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so rename to public/gatk-utils/src/main/resources/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so