diff --git a/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseIndex.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseIndex.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseIndex.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseIndex.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/Compressor.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/Compressor.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/Compressor.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsStash.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsStash.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsStash.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistribution.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistribution.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalMetric.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalMetric.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalMetric.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalMetric.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPaths.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPaths.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPaths.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPaths.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java
diff --git a/protected/java/src/org/broadinstitute/sting/package-info.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/package-info.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/SequenceComplexity.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/SequenceComplexity.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/collections/CountSet.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/collections/CountSet.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotype/LDMerger.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/LDMerger.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotype/MergeVariantsAcrossHaplotypes.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/MergeVariantsAcrossHaplotypes.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/FlexibleHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/FlexibleHMM.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/WalkerTestIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/WalkerTestIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/RankSumUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCountsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCountsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElementUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElementUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsIntegrationTests.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsIntegrationTests.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/RandomDNA.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/RandomDNA.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/genotyper/DiploidGenotypeUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/DiploidGenotypeUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotype/HaplotypeBaseComparatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeBaseComparatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotype/HaplotypeScoreComparatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeScoreComparatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/CnyPairHMMUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMMUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMModelUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java
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diff --git a/public/java/src/net/sf/samtools/GATKBAMFileSpan.java b/public/gatk-framework/src/main/java/net/sf/samtools/GATKBAMFileSpan.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWAAligner.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
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diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/Advanced.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Advanced.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchStringValue.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentMatchStringValue.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/View.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/View.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FileHandleCache.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FileHandleCache.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/DataStreamSegment.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/DataStreamSegment.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/EntireStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/EntireStream.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/MappedStreamSegment.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/MappedStreamSegment.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/DownsampleType.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsampleType.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/FractionalDownsampler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsampler.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/LevelingDownsampler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/LevelingDownsampler.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SampleFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/FastqFileWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/FastqFileWriter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/RODRecordList.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/RODRecordList.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReport.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportColumn.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportDataType.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportDataType.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/resourcemanagement/ThreadAllocation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/resourcemanagement/ThreadAllocation.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/Affection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/Affection.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionTraversalParameters.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ActiveRegionTraversalParameters.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Allows.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/BAQMode.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/By.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/DataSource.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/DataSource.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Multiplex.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Multiplex.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/NanoSchedulable.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/NanoSchedulable.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/TreeReducible.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/TreeReducible.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtil.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtil.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java
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similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitives.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitives.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java
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diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/ForumAPIUtils.java
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diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala b/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala
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rename from public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala
rename to public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala b/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala
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rename to public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala b/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala
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rename to public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala b/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala
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rename to public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala b/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala
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diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala b/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala
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rename to public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala b/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala
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rename to public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/ChunkVCF.scala b/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/ChunkVCF.scala
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rename to public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/ChunkVCF.scala
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q b/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q
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diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/VcfToPed.scala b/public/queue-framework/src/main/qscripts/org/broadinstitute/sting/queue/qscripts/lib/VcfToPed.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QCommandLine.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/QCommandPlugin.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QCommandPlugin.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/QException.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QException.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/QScript.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QScript.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QScript.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QScriptManager.scala
similarity index 100%
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QScriptManager.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/QSettings.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QSettings.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/QSettings.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/CommandLineJobManager.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/CommandLinePluginManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/CommandLinePluginManager.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/CommandLinePluginManager.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/FunctionEdge.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/InProcessJobManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/InProcessJobManager.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/InProcessJobManager.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/InProcessRunner.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/JobManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/JobManager.scala
similarity index 100%
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/JobRunInfo.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/JobRunInfo.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/JobRunner.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/JobRunner.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/MappingEdge.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/MappingEdge.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QEdge.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QEdge.scala
similarity index 100%
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QGraph.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QGraphSettings.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QNode.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QNode.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QStatusMessenger.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QStatusMessenger.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/QStatusMessenger.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/RunnerStatus.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/RunnerStatus.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobManager.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobManager.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobManager.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobManager.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobRunner.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobRunner.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/shell/ShellJobManager.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/cancer/MuTect.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/cancer/MuTect.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/cancer/MuTect.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ReadScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/ReadScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/InProcessFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/InProcessFunction.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/function/InProcessFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/InProcessFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/ListWriterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/ListWriterFunction.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/function/ListWriterFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/ListWriterFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/QFunction.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/QFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ConcatenateLogsFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ConcatenateLogsFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ConcatenateLogsFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ConcatenateLogsFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/ClassFieldCache.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ClassFieldCache.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/ClassFieldCache.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ClassFieldCache.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/CollectionUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/CollectionUtils.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/CollectionUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/CollectionUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/DoC/package.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/DoC/package.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/DoC/package.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/DoC/package.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailMessage.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailMessage.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/EmailSettings.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailSettings.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/EmailSettings.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailSettings.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/Logging.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Logging.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/Logging.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Logging.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobReport.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobReport.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QJobsReporter.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobsReporter.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/QJobsReporter.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobsReporter.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QScriptUtils.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QScriptUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ReflectionUtils.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ReflectionUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/RemoteFile.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFile.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/RemoteFile.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFile.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/RemoteFileConverter.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFileConverter.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFileConverter.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Retry.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Retry.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/RetryException.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RetryException.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RetryException.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/ScalaCompoundArgumentTypeDescriptor.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ScalaCompoundArgumentTypeDescriptor.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/ShellUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ShellUtils.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/StringFileConversions.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/StringFileConversions.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/SystemUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/SystemUtils.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/SystemUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/SystemUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/TextFormatUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/TextFormatUtils.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/TextFormatUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/TextFormatUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
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rename from public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
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rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
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rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
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rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
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rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala
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rename from public/scala/test/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala
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rename from public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala
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rename from public/scala/test/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala