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