diff --git a/protected/java/src/org/broadinstitute/sting/gatk/DummyProtectedClass.java b/protected/java/src/org/broadinstitute/sting/gatk/DummyProtectedClass.java
deleted file mode 100644
index c1324aea4..000000000
--- a/protected/java/src/org/broadinstitute/sting/gatk/DummyProtectedClass.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package org.broadinstitute.sting.gatk;
-
-/*
- * Copyright (c) 2009 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
-
-public class DummyProtectedClass implements ProtectedPackageSource {
-
-    // THIS CLASS IS USED JUST SO THAT WE CAN TEST WHETHER WE ARE USING THE LITE OR FULL VERSION OF THE GATK
-    // **** DO NOT REMOVE! ****
-}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/protected/java/src/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/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/protected/java/src/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/protected/java/src/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/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatistics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatistics.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatistics.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatistics.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
index 30650e9c0..e51e41e88 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
@@ -60,7 +60,7 @@ public class ErrorModel  {
 
         boolean hasCalledAlleles = false;
 
-        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
+        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
         if (refSampleVC != null) {
 
             for (Allele allele : refSampleVC.getAlleles()) {
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
index ce66ce8d0..2788f201c 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
@@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -231,7 +232,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
             ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup();
             if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){
                 // no likelihoods have been computed for this sample at this site
-                perReadAlleleLikelihoodMap.put(sample.getKey(), org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap());
+                perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap());
             }
 
             // create the GenotypeLikelihoods object
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 56965c022..ce59a90fc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -119,7 +119,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
 
             if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){
                 // no likelihoods have been computed for this sample at this site
-                perReadAlleleLikelihoodMap.put(sample.getKey(), PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap());
+                perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap());
             }
             final ReadBackedPileup pileup = context.getBasePileup();
             if (pileup != null) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index c10f7264e..80a787fe0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -55,7 +55,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
     protected SNPGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
         super(UAC, logger);
         useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
-        perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
+        perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
     }
 
     public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
similarity index 94%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index b5386ff6b..3dc0c3b71 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
-import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
@@ -41,7 +40,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -230,25 +228,6 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
      **/
     public void initialize() {
 
-        // Check for protected modes
-        if (GATKLiteUtils.isGATKLite()) {
-            // no polyploid/pooled mode in GATK Like
-            if (UAC.samplePloidy != GATKVariantContextUtils.DEFAULT_PLOIDY ||
-                    UAC.referenceSampleName != null ||
-                    UAC.referenceSampleRod.isBound())  {
-                throw new UserException.NotSupportedInGATKLite("you cannot enable usage of ploidy values other than 2");
-            }
-
-            if ( UAC.CONTAMINATION_FRACTION > 0.0 ) {
-                if ( UAC.CONTAMINATION_FRACTION == StandardCallerArgumentCollection.DEFAULT_CONTAMINATION_FRACTION ) {
-                    UAC.CONTAMINATION_FRACTION = 0.0;
-                    logger.warn("setting contamination down-sampling fraction to 0.0 because it is not enabled in GATK-lite");
-                } else {
-                    throw new UserException.NotSupportedInGATKLite("you cannot enable usage of contamination down-sampling");
-                }
-            }
-        }
-
         if ( UAC.TREAT_ALL_READS_AS_SINGLE_POOL ) {
             samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME);
         } else {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index 8b7b0b918..0c7e43525 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -223,7 +223,7 @@ public class GenotypingEngine {
         final Map<String, PerReadAlleleLikelihoodMap> returnMap = new HashMap<String, PerReadAlleleLikelihoodMap>();
         final GenomeLoc callLoc = parser.createGenomeLoc(call);
         for( final Map.Entry<String, PerReadAlleleLikelihoodMap> sample : perSampleReadMap.entrySet() ) {
-            final PerReadAlleleLikelihoodMap likelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
+            final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap();
 
             for( final Map.Entry<GATKSAMRecord,Map<Allele,Double>> mapEntry : sample.getValue().getLikelihoodReadMap().entrySet() ) {
                 // only count the read if it overlaps the event, otherwise it is not added to the output read list at all
@@ -277,7 +277,7 @@ public class GenotypingEngine {
 
         final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap = new HashMap<String, PerReadAlleleLikelihoodMap>();
         for( final Map.Entry<String, PerReadAlleleLikelihoodMap> haplotypeReadMapEntry : haplotypeReadMap.entrySet() ) { // for each sample
-            final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
+            final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
             for( final Map.Entry<Allele, List<Haplotype>> alleleMapperEntry : alleleMapper.entrySet() ) { // for each output allele
                 final List<Haplotype> mappedHaplotypes = alleleMapperEntry.getValue();
                 for( final Map.Entry<GATKSAMRecord, Map<Allele,Double>> readEntry : haplotypeReadMapEntry.getValue().getLikelihoodReadMap().entrySet() ) { // for each read
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 1be484075..8e90285d9 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -104,7 +104,7 @@ public class LikelihoodCalculationEngine {
 
     private PerReadAlleleLikelihoodMap computeReadLikelihoods( final ArrayList<Haplotype> haplotypes, final ArrayList<GATKSAMRecord> reads) {
 
-        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
+        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
         final int numHaplotypes = haplotypes.size();
         for( final GATKSAMRecord read : reads ) {
             final byte[] overallGCP = new byte[read.getReadLength()];
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
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similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
diff --git a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
deleted file mode 100644
index 4a13fb615..000000000
--- a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * Copyright (c) 2011 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-package org.broadinstitute.sting.utils.genotyper;
-
-
-import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
-import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.variant.variantcontext.Allele;
-
-import java.io.PrintStream;
-import java.util.*;
-
-public class AdvancedPerReadAlleleLikelihoodMap extends StandardPerReadAlleleLikelihoodMap implements ProtectedPackageSource {
-
-    public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) {
-        return AlleleBiasedDownsamplingUtils.createAlleleBiasedBasePileup(pileup, downsamplingFraction, log);
-    }
-
-    public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) {
-        // special case removal of all or no reads
-        if ( downsamplingFraction <= 0.0 )
-            return;
-        if ( downsamplingFraction >= 1.0 ) {
-            likelihoodReadMap.clear();
-            return;
-        }
-
-        // start by stratifying the reads by the alleles they represent at this position
-        final Map<Allele, List<GATKSAMRecord>> alleleReadMap = new HashMap<Allele, List<GATKSAMRecord>>(alleles.size());
-        for ( Allele allele : alleles )
-            alleleReadMap.put(allele, new ArrayList<GATKSAMRecord>());
-
-        for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet() ) {
-            // do not remove reduced reads!
-            if ( !entry.getKey().isReducedRead() ) {
-                final Allele bestAllele = getMostLikelyAllele(entry.getValue());
-                if ( bestAllele != Allele.NO_CALL )
-                    alleleReadMap.get(bestAllele).add(entry.getKey());
-            }
-        }
-
-        // compute the reads to remove and actually remove them
-        final List<GATKSAMRecord> readsToRemove = AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(alleleReadMap, downsamplingFraction, log);
-        for ( final GATKSAMRecord read : readsToRemove )
-            likelihoodReadMap.remove(read);
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
similarity index 69%
rename from public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
rename to protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
index ff85c33a0..5dcd5eb6c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
@@ -25,26 +25,23 @@
 package org.broadinstitute.sting.utils.genotyper;
 
 
-import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.io.PrintStream;
-import java.lang.reflect.Constructor;
 import java.util.*;
 
-public abstract class PerReadAlleleLikelihoodMap {
+public class PerReadAlleleLikelihoodMap {
 
     public static final double INFORMATIVE_LIKELIHOOD_THRESHOLD = 0.2;
 
     protected List<Allele> alleles;
     protected Map<GATKSAMRecord, Map<Allele, Double>> likelihoodReadMap;
 
-    public abstract void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log);
-    public abstract ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log);
+    public PerReadAlleleLikelihoodMap() {}
 
     public void add(GATKSAMRecord read, Allele a, Double likelihood) {
         Map<Allele,Double> likelihoodMap;
@@ -63,6 +60,39 @@ public abstract class PerReadAlleleLikelihoodMap {
 
     }
 
+    public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) {
+        return AlleleBiasedDownsamplingUtils.createAlleleBiasedBasePileup(pileup, downsamplingFraction, log);
+    }
+
+    public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) {
+        // special case removal of all or no reads
+        if ( downsamplingFraction <= 0.0 )
+            return;
+        if ( downsamplingFraction >= 1.0 ) {
+            likelihoodReadMap.clear();
+            return;
+        }
+
+        // start by stratifying the reads by the alleles they represent at this position
+        final Map<Allele, List<GATKSAMRecord>> alleleReadMap = new HashMap<Allele, List<GATKSAMRecord>>(alleles.size());
+        for ( Allele allele : alleles )
+            alleleReadMap.put(allele, new ArrayList<GATKSAMRecord>());
+
+        for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet() ) {
+            // do not remove reduced reads!
+            if ( !entry.getKey().isReducedRead() ) {
+                final Allele bestAllele = getMostLikelyAllele(entry.getValue());
+                if ( bestAllele != Allele.NO_CALL )
+                    alleleReadMap.get(bestAllele).add(entry.getKey());
+            }
+        }
+
+        // compute the reads to remove and actually remove them
+        final List<GATKSAMRecord> readsToRemove = AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(alleleReadMap, downsamplingFraction, log);
+        for ( final GATKSAMRecord read : readsToRemove )
+            likelihoodReadMap.remove(read);
+    }
+
     public int size() {
         return likelihoodReadMap.size();
     }
@@ -122,16 +152,4 @@ public abstract class PerReadAlleleLikelihoodMap {
         }
         return (maxLike - prevMaxLike > INFORMATIVE_LIKELIHOOD_THRESHOLD ? mostLikelyAllele : Allele.NO_CALL );
     }
-
-    public static PerReadAlleleLikelihoodMap getBestAvailablePerReadAlleleLikelihoodMap() {
-        final Class PerReadAlleleLikelihoodMapClass = GATKLiteUtils.getProtectedClassIfAvailable(PerReadAlleleLikelihoodMap.class);
-        try {
-            final Constructor constructor = PerReadAlleleLikelihoodMapClass.getDeclaredConstructor((Class[])null);
-            constructor.setAccessible(true);
-            return (PerReadAlleleLikelihoodMap)constructor.newInstance();
-        }
-        catch (Exception e) {
-            throw new ReviewedStingException("Unable to create RecalibrationEngine class instance " + PerReadAlleleLikelihoodMapClass.getSimpleName());
-        }
-    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 1187039bb..54907f9f2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -53,7 +53,6 @@ import org.broadinstitute.sting.gatk.samples.SampleDB;
 import org.broadinstitute.sting.gatk.samples.SampleDBBuilder;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -217,13 +216,6 @@ public class GenomeAnalysisEngine {
         baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, disableIndelQuals, preserveQLessThan, emitOriginalQuals);
     }
 
-    /**
-     * Utility method to determine whether this is the lite version of the GATK
-     */
-    public boolean isGATKLite() {
-        return GATKLiteUtils.isGATKLite();
-    }
-
     /**
      * Actually run the GATK with the specified walker.
      *
@@ -330,10 +322,7 @@ public class GenomeAnalysisEngine {
         try {
             return walkerManager.createByName(walkerName);
         } catch ( UserException e ) {
-            if ( isGATKLite() && GATKLiteUtils.isAvailableOnlyInFullGATK(walkerName) ) {
-                e = new UserException.NotSupportedInGATKLite("the " + walkerName + " walker is available only in the full version of the GATK");
-            }
-            else if ( isDeprecatedWalker(walkerName) ) {
+            if ( isDeprecatedWalker(walkerName) ) {
                 e = new UserException.DeprecatedWalker(walkerName, getDeprecatedMajorVersionNumber(walkerName));
             }
             throw e;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java
deleted file mode 100755
index dbb628135..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- * Copyright (c) 2011 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.walkers.bqsr;
-
-import org.broadinstitute.sting.commandline.Gatherer;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.recalibration.RecalUtils;
-import org.broadinstitute.sting.utils.recalibration.RecalibrationReport;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.PrintStream;
-import java.util.List;
-
-/**
- * User: carneiro
- * Date: 3/29/11
- */
-
-
-public class BQSRGatherer extends Gatherer  {
-    
-    private static final String EMPTY_INPUT_LIST = "list of inputs files is empty";
-    private static final String MISSING_OUTPUT_FILE = "missing output file name";
-
-    @Override
-    public void gather(List<File> inputs, File output) {
-        final PrintStream outputFile;
-        try {
-            outputFile = new PrintStream(output);
-        } catch(FileNotFoundException e) {
-            throw new UserException.MissingArgument("output", MISSING_OUTPUT_FILE);
-        }
-
-        RecalibrationReport generalReport = null;
-        for (File input : inputs) {
-            final RecalibrationReport inputReport = new RecalibrationReport(input);
-            if (generalReport == null)
-                generalReport = inputReport;
-            else
-                generalReport.combine(inputReport);
-        }
-        if (generalReport == null)
-            throw new ReviewedStingException(EMPTY_INPUT_LIST);
-
-        generalReport.calculateQuantizedQualities();
-
-        RecalibrationArgumentCollection RAC = generalReport.getRAC();
-        if ( RAC.RECAL_PDF_FILE != null ) {
-            RAC.RECAL_TABLE_FILE = output;
-            if ( RAC.existingRecalibrationReport != null ) {
-                final RecalibrationReport originalReport = new RecalibrationReport(RAC.existingRecalibrationReport);
-                RecalUtils.generateRecalibrationPlot(RAC, originalReport.getRecalibrationTables(), generalReport.getRecalibrationTables(), generalReport.getCovariates());
-            }
-            else {
-                RecalUtils.generateRecalibrationPlot(RAC, generalReport.getRecalibrationTables(), generalReport.getCovariates());
-            }
-        }
-
-        generalReport.output(outputFile);
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
deleted file mode 100755
index 2c774d94d..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
+++ /dev/null
@@ -1,534 +0,0 @@
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.walkers.bqsr;
-
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-import net.sf.samtools.CigarElement;
-import net.sf.samtools.SAMFileHeader;
-import org.broad.tribble.Feature;
-import org.broadinstitute.sting.commandline.Advanced;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.filters.*;
-import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.variant.utils.BaseUtils;
-import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
-import org.broadinstitute.sting.utils.clipping.ReadClipper;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.recalibration.*;
-import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-/**
- * First pass of the base quality score recalibration -- Generates recalibration table based on various user-specified covariates (such as read group, reported quality score, machine cycle, and nucleotide context).
- *
- * <p>
- * This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal operating
- * only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors and indicative
- * of poor base quality. This walker generates tables based on various user-specified covariates (such as read group,
- * reported quality score, cycle, and context). Since there is a large amount of data one can then calculate an empirical
- * probability of error given the particular covariates seen at this site, where p(error) = num mismatches / num observations.
- * The output file is a table (of the several covariate values, num observations, num mismatches, empirical quality score).
- * <p>
- * Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and will be added for the user regardless of whether or not they were specified.
- *
- * <p>
- *
- * <h2>Input</h2>
- * <p>
- * The input read data whose base quality scores need to be assessed.
- * <p>
- * A database of known polymorphic sites to skip over.
- * </p>
- *
- * <h2>Output</h2>
- * <p>
- * A GATK Report file with many tables:
- * <ol>
- *     <li>The list of arguments</li>
- *     <li>The quantized qualities table</li>
- *     <li>The recalibration table by read group</li>
- *     <li>The recalibration table by quality score</li>
- *     <li>The recalibration table for all the optional covariates</li>
- * </ol>
- *
- * The GATK Report is intended to be easy to read by humans or computers. Check out the documentation of the GATKReport to learn how to manipulate this table.
- * </p>
- *
- * <h2>Examples</h2>
- * <pre>
- * java -Xmx4g -jar GenomeAnalysisTK.jar \
- *   -T BaseRecalibrator \
- *   -I my_reads.bam \
- *   -R resources/Homo_sapiens_assembly18.fasta \
- *   -knownSites bundle/hg18/dbsnp_132.hg18.vcf \
- *   -knownSites another/optional/setOfSitesToMask.vcf \
- *   -o recal_data.grp
- * </pre>
- */
-
-@DocumentedGATKFeature(groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class})
-@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
-@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class})
-@PartitionBy(PartitionType.READ)
-public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSchedulable {
-    /**
-     * all the command line arguments for BQSR and it's covariates
-     */
-    @ArgumentCollection
-    private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
-
-    /**
-     * When you have nct > 1, BQSR uses nct times more memory to compute its recalibration tables, for efficiency
-     * purposes.  If you have many covariates, and therefore are using a lot of memory, you can use this flag
-     * to safely access only one table.  There may be some CPU cost, but as long as the table is really big
-     * there should be relatively little CPU costs.
-     */
-    @Argument(fullName = "lowMemoryMode", shortName="lowMemoryMode", doc="Reduce memory usage in multi-threaded code at the expense of threading efficiency", required = false)
-    public boolean lowMemoryMode = false;
-
-    @Advanced
-    @Argument(fullName = "bqsrBAQGapOpenPenalty", shortName="bqsrBAQGOP", doc="BQSR BAQ gap open penalty (Phred Scaled).  Default value is 40.  30 is perhaps better for whole genome call sets", required = false)
-    public double BAQGOP = BAQ.DEFAULT_GOP;
-
-    /**
-     * an object that keeps track of the information necessary for quality score quantization
-     */
-    private QuantizationInfo quantizationInfo;
-
-    /**
-     * list to hold the all the covariate objects that were requested (required + standard + experimental)
-     */
-    private Covariate[] requestedCovariates;
-
-    private RecalibrationEngine recalibrationEngine;
-
-    private int minimumQToUse;
-
-    private static final String NO_DBSNP_EXCEPTION = "This calculation is critically dependent on being able to skip over known variant sites. Please provide a VCF file containing known sites of genetic variation.";
-
-    private BAQ baq; // BAQ the reads on the fly to generate the alignment uncertainty vector
-    private IndexedFastaSequenceFile referenceReader; // fasta reference reader for use with BAQ calculation
-    private final static byte NO_BAQ_UNCERTAINTY = (byte)'@';
-
-    /**
-     * Parse the -cov arguments and create a list of covariates to be used here
-     * Based on the covariates' estimates for initial capacity allocate the data hashmap
-     */
-    public void initialize() {
-        baq = new BAQ(BAQGOP); // setup the BAQ object with the provided gap open penalty
-
-        // check for unsupported access
-        if (getToolkit().isGATKLite() && !getToolkit().getArguments().disableIndelQuals)
-            throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument");
-
-        if (RAC.FORCE_PLATFORM != null)
-            RAC.DEFAULT_PLATFORM = RAC.FORCE_PLATFORM;
-
-        if (RAC.knownSites.isEmpty() && !RAC.RUN_WITHOUT_DBSNP) // Warn the user if no dbSNP file or other variant mask was specified
-            throw new UserException.CommandLineException(NO_DBSNP_EXCEPTION);
-
-        if (RAC.LIST_ONLY) {
-            RecalUtils.listAvailableCovariates(logger);
-            System.exit(0);
-        }
-        RAC.existingRecalibrationReport = getToolkit().getArguments().BQSR_RECAL_FILE; // if we have a recalibration file, record it so it goes on the report table
-
-        Pair<ArrayList<Covariate>, ArrayList<Covariate>> covariates = RecalUtils.initializeCovariates(RAC); // initialize the required and optional covariates
-        ArrayList<Covariate> requiredCovariates = covariates.getFirst();
-        ArrayList<Covariate> optionalCovariates = covariates.getSecond();
-
-        requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()];
-        int covariateIndex = 0;
-        for (final Covariate covariate : requiredCovariates)
-            requestedCovariates[covariateIndex++] = covariate;
-        for (final Covariate covariate : optionalCovariates)
-            requestedCovariates[covariateIndex++] = covariate;
-
-        logger.info("The covariates being used here: ");
-        for (Covariate cov : requestedCovariates) { // list all the covariates being used
-            logger.info("\t" + cov.getClass().getSimpleName());
-            cov.initialize(RAC); // initialize any covariate member variables using the shared argument collection
-        }
-
-        try {
-            RAC.RECAL_TABLE = new PrintStream(RAC.RECAL_TABLE_FILE);
-        } catch (IOException e) {
-            throw new UserException.CouldNotCreateOutputFile(RAC.RECAL_TABLE_FILE, e);
-        }
-
-        initializeRecalibrationEngine();
-        minimumQToUse = getToolkit().getArguments().PRESERVE_QSCORES_LESS_THAN;
-        referenceReader = getToolkit().getReferenceDataSource().getReference();
-    }
-
-    /**
-     * Initialize the recalibration engine
-     */
-    private void initializeRecalibrationEngine() {
-        int numReadGroups = 0;
-        for ( final SAMFileHeader header : getToolkit().getSAMFileHeaders() )
-            numReadGroups += header.getReadGroups().size();
-
-        recalibrationEngine = new RecalibrationEngine(requestedCovariates, numReadGroups, RAC.RECAL_TABLE_UPDATE_LOG, lowMemoryMode);
-    }
-
-    private boolean isLowQualityBase( final GATKSAMRecord read, final int offset ) {
-        return read.getBaseQualities()[offset] < minimumQToUse;
-    }
-
-    /**
-     * For each read at this locus get the various covariate values and increment that location in the map based on
-     * whether or not the base matches the reference at this particular location
-     */
-    public Long map( final ReferenceContext ref, final GATKSAMRecord originalRead, final RefMetaDataTracker metaDataTracker ) {
-
-        final GATKSAMRecord read = ReadClipper.hardClipSoftClippedBases( ReadClipper.hardClipAdaptorSequence(originalRead) );
-        if( read.isEmpty() ) { return 0L; } // the whole read was inside the adaptor so skip it
-
-        RecalUtils.parsePlatformForRead(read, RAC);
-        if (!RecalUtils.isColorSpaceConsistent(RAC.SOLID_NOCALL_STRATEGY, read)) { // parse the solid color space and check for color no-calls
-            return 0L; // skip this read completely
-        }
-
-        final int[] isSNP = calculateIsSNP(read, ref, originalRead);
-        final int[] isInsertion = calculateIsIndel(read, EventType.BASE_INSERTION);
-        final int[] isDeletion = calculateIsIndel(read, EventType.BASE_DELETION);
-        final int nErrors = nEvents(isSNP, isInsertion, isDeletion);
-
-        // note for efficiency regions we don't compute the BAQ array unless we actually have
-        // some error to marginalize over.  For ILMN data ~85% of reads have no error
-        final byte[] baqArray = nErrors == 0 ? flatBAQArray(read) : calculateBAQArray(read);
-
-        if( baqArray != null ) { // some reads just can't be BAQ'ed
-            final ReadCovariates covariates = RecalUtils.computeCovariates(read, requestedCovariates);
-            final boolean[] skip = calculateSkipArray(read, metaDataTracker); // skip known sites of variation as well as low quality and non-regular bases
-            final double[] snpErrors = calculateFractionalErrorArray(isSNP, baqArray);
-            final double[] insertionErrors = calculateFractionalErrorArray(isInsertion, baqArray);
-            final double[] deletionErrors = calculateFractionalErrorArray(isDeletion, baqArray);
-
-            // aggregate all of the info into our info object, and update the data
-            final ReadRecalibrationInfo info = new ReadRecalibrationInfo(read, covariates, skip, snpErrors, insertionErrors, deletionErrors);
-            recalibrationEngine.updateDataForRead(info);
-            return 1L;
-        } else {
-            return 0L;
-        }
-    }
-
-    /**
-     * Compute the number of mutational events across all hasEvent vectors
-     *
-     * Simply the sum of entries in hasEvents
-     *
-     * @param hasEvents a vector a vectors of 0 (no event) and 1 (has event)
-     * @return the total number of events across all hasEvent arrays
-     */
-    private int nEvents(final int[]... hasEvents) {
-        int n = 0;
-        for ( final int[] hasEvent : hasEvents ) {
-            n += MathUtils.sum(hasEvent);
-        }
-        return n;
-    }
-
-    protected boolean[] calculateSkipArray( final GATKSAMRecord read, final RefMetaDataTracker metaDataTracker ) {
-        final byte[] bases = read.getReadBases();
-        final boolean[] skip = new boolean[bases.length];
-        final boolean[] knownSites = calculateKnownSites(read, metaDataTracker.getValues(RAC.knownSites));
-        for( int iii = 0; iii < bases.length; iii++ ) {
-            skip[iii] = !BaseUtils.isRegularBase(bases[iii]) || isLowQualityBase(read, iii) || knownSites[iii] || badSolidOffset(read, iii);
-        }
-        return skip;
-    }
-
-    protected boolean badSolidOffset( final GATKSAMRecord read, final int offset ) {
-        return ReadUtils.isSOLiDRead(read) && RAC.SOLID_RECAL_MODE != RecalUtils.SOLID_RECAL_MODE.DO_NOTHING && !RecalUtils.isColorSpaceConsistent(read, offset);
-    }
-
-    protected boolean[] calculateKnownSites( final GATKSAMRecord read, final List<Feature> features ) {
-        final int readLength = read.getReadBases().length;
-        final boolean[] knownSites = new boolean[readLength];
-        Arrays.fill(knownSites, false);
-        for( final Feature f : features ) {
-            int featureStartOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), f.getStart(), ReadUtils.ClippingTail.LEFT_TAIL, true); // BUGBUG: should I use LEFT_TAIL here?
-            if( featureStartOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) {
-                featureStartOnRead = 0;
-            }
-
-            int featureEndOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), f.getEnd(), ReadUtils.ClippingTail.LEFT_TAIL, true);
-            if( featureEndOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) {
-                featureEndOnRead = readLength;
-            }
-
-            if( featureStartOnRead > readLength ) {
-                featureStartOnRead = featureEndOnRead = readLength;
-            }
-
-            Arrays.fill(knownSites, Math.max(0, featureStartOnRead), Math.min(readLength, featureEndOnRead + 1), true);
-        }
-        return knownSites;
-    }
-
-    // BUGBUG: can be merged with calculateIsIndel
-    protected static int[] calculateIsSNP( final GATKSAMRecord read, final ReferenceContext ref, final GATKSAMRecord originalRead ) {
-        final byte[] readBases = read.getReadBases();
-        final byte[] refBases = Arrays.copyOfRange(ref.getBases(), read.getAlignmentStart() - originalRead.getAlignmentStart(), ref.getBases().length + read.getAlignmentEnd() - originalRead.getAlignmentEnd());
-        final int[] snp = new int[readBases.length];
-        int readPos = 0;
-        int refPos = 0;
-        for ( final CigarElement ce : read.getCigar().getCigarElements() ) {
-            final int elementLength = ce.getLength();
-            switch (ce.getOperator()) {
-                case M:
-                case EQ:
-                case X:
-                    for( int iii = 0; iii < elementLength; iii++ ) {
-                        snp[readPos] = ( BaseUtils.basesAreEqual(readBases[readPos], refBases[refPos]) ? 0 : 1 );
-                        readPos++;
-                        refPos++;
-                    }
-                    break;
-                case D:
-                case N:
-                    refPos += elementLength;
-                    break;
-                case I:
-                case S: // ReferenceContext doesn't have the soft clipped bases!
-                    readPos += elementLength;
-                    break;
-                case H:
-                case P:
-                    break;
-                default:
-                    throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator());
-            }
-        }
-        return snp;
-    }
-
-    protected static int[] calculateIsIndel( final GATKSAMRecord read, final EventType mode ) {
-        final byte[] readBases = read.getReadBases();
-        final int[] indel = new int[readBases.length];
-        Arrays.fill(indel, 0);
-        int readPos = 0;
-        for ( final CigarElement ce : read.getCigar().getCigarElements() ) {
-            final int elementLength = ce.getLength();
-            switch (ce.getOperator()) {
-                case M:
-                case EQ:
-                case X:
-                case S:
-                {
-                    readPos += elementLength;
-                    break;
-                }
-                case D:
-                {
-                    final int index = ( read.getReadNegativeStrandFlag() ? readPos : ( readPos > 0 ? readPos - 1 : readPos ) );
-                    indel[index] = ( mode.equals(EventType.BASE_DELETION) ? 1 : 0 );
-                    break;
-                }
-                case I:
-                {
-                    final boolean forwardStrandRead = !read.getReadNegativeStrandFlag();
-                    if( forwardStrandRead ) {
-                        indel[(readPos > 0 ? readPos - 1 : readPos)] = ( mode.equals(EventType.BASE_INSERTION) ? 1 : 0 );
-                    }
-                    for (int iii = 0; iii < elementLength; iii++) {
-                        readPos++;
-                    }
-                    if( !forwardStrandRead ) {
-                        indel[(readPos < indel.length ? readPos : readPos - 1)] = ( mode.equals(EventType.BASE_INSERTION) ? 1 : 0 );
-                    }
-                    break;
-                }
-                case N:
-                case H:
-                case P:
-                    break;
-                default:
-                    throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator());
-            }
-        }
-        return indel;
-    }
-
-    protected static double[] calculateFractionalErrorArray( final int[] errorArray, final byte[] baqArray ) {
-        if(errorArray.length != baqArray.length ) {
-            throw new ReviewedStingException("Array length mismatch detected. Malformed read?");
-        }
-
-        final int BLOCK_START_UNSET = -1;
-
-        final double[] fractionalErrors = new double[baqArray.length];
-        Arrays.fill(fractionalErrors, 0.0);
-        boolean inBlock = false;
-        int blockStartIndex = BLOCK_START_UNSET;
-        int iii;
-        for( iii = 0; iii < fractionalErrors.length; iii++ ) {
-            if( baqArray[iii] == NO_BAQ_UNCERTAINTY ) {
-                if( !inBlock ) {
-                    fractionalErrors[iii] = (double) errorArray[iii];
-                } else {
-                    calculateAndStoreErrorsInBlock(iii, blockStartIndex, errorArray, fractionalErrors);
-                    inBlock = false; // reset state variables
-                    blockStartIndex = BLOCK_START_UNSET; // reset state variables
-                }
-            } else {
-                inBlock = true;
-                if( blockStartIndex == BLOCK_START_UNSET ) { blockStartIndex = iii; }
-            }
-        }
-        if( inBlock ) {
-            calculateAndStoreErrorsInBlock(iii-1, blockStartIndex, errorArray, fractionalErrors);
-        }
-        if( fractionalErrors.length != errorArray.length ) {
-            throw new ReviewedStingException("Output array length mismatch detected. Malformed read?");
-        }
-        return fractionalErrors;
-    }
-
-    private static void calculateAndStoreErrorsInBlock( final int iii,
-                                                        final int blockStartIndex,
-                                                        final int[] errorArray,
-                                                        final double[] fractionalErrors ) {
-        int totalErrors = 0;
-        for( int jjj = Math.max(0,blockStartIndex-1); jjj <= iii; jjj++ ) {
-            totalErrors += errorArray[jjj];
-        }
-        for( int jjj = Math.max(0, blockStartIndex-1); jjj <= iii; jjj++ ) {
-            fractionalErrors[jjj] = ((double) totalErrors) / ((double)(iii - Math.max(0,blockStartIndex-1) + 1));
-        }
-    }
-
-    /**
-     * Create a BAQ style array that indicates no alignment uncertainty
-     * @param read the read for which we want a BAQ array
-     * @return a BAQ-style non-null byte[] counting NO_BAQ_UNCERTAINTY values
-     * // TODO -- could be optimized avoiding this function entirely by using this inline if the calculation code above
-     */
-    private byte[] flatBAQArray(final GATKSAMRecord read) {
-        final byte[] baq = new byte[read.getReadLength()];
-        Arrays.fill(baq, NO_BAQ_UNCERTAINTY);
-        return baq;
-    }
-
-    /**
-     * Compute an actual BAQ array for read, based on its quals and the reference sequence
-     * @param read the read to BAQ
-     * @return a non-null BAQ tag array for read
-     */
-    private byte[] calculateBAQArray( final GATKSAMRecord read ) {
-        baq.baqRead(read, referenceReader, BAQ.CalculationMode.RECALCULATE, BAQ.QualityMode.ADD_TAG);
-        return BAQ.getBAQTag(read);
-    }
-
-    /**
-     * Initialize the reduce step by returning 0L
-     *
-     * @return returns 0L
-     */
-    public Long reduceInit() {
-        return 0L;
-    }
-
-    /**
-     * The Reduce method doesn't do anything for this walker.
-     *
-     * @param mapped Result of the map. This value is immediately ignored.
-     * @param sum    The summing CountedData used to output the CSV data
-     * @return returns The sum used to output the CSV data
-     */
-    public Long reduce(Long mapped, Long sum) {
-        sum += mapped;
-        return sum;
-    }
-
-    @Override
-    public void onTraversalDone(Long result) {
-        recalibrationEngine.finalizeData();
-
-        logger.info("Calculating quantized quality scores...");
-        quantizeQualityScores();
-
-        logger.info("Writing recalibration report...");
-        generateReport();
-        logger.info("...done!");
-
-        if ( RAC.RECAL_PDF_FILE != null ) {
-            logger.info("Generating recalibration plots...");
-            generatePlots();
-        }
-
-        logger.info("Processed: " + result + " reads");
-    }
-
-    private RecalibrationTables getRecalibrationTable() {
-        return recalibrationEngine.getFinalRecalibrationTables();
-    }
-
-    private void generatePlots() {
-        File recalFile = getToolkit().getArguments().BQSR_RECAL_FILE;
-        if (recalFile != null) {
-            RecalibrationReport report = new RecalibrationReport(recalFile);
-            RecalUtils.generateRecalibrationPlot(RAC, report.getRecalibrationTables(), getRecalibrationTable(), requestedCovariates);
-        }
-        else
-            RecalUtils.generateRecalibrationPlot(RAC, getRecalibrationTable(), requestedCovariates);
-    }
-
-    /**
-     * go through the quality score table and use the # observations and the empirical quality score
-     * to build a quality score histogram for quantization. Then use the QuantizeQual algorithm to
-     * generate a quantization map (recalibrated_qual -> quantized_qual)
-     */
-    private void quantizeQualityScores() {
-        quantizationInfo = new QuantizationInfo(getRecalibrationTable(), RAC.QUANTIZING_LEVELS);
-    }
-
-    private void generateReport() {
-        RecalUtils.outputRecalibrationReport(RAC, quantizationInfo, getRecalibrationTable(), requestedCovariates, RAC.SORT_BY_ALL_COLUMNS);
-    }
-}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java
deleted file mode 100644
index b884b89db..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java
+++ /dev/null
@@ -1,163 +0,0 @@
-/*
- * Copyright (c) 2012 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.walkers.bqsr;
-
-import com.google.java.contract.Ensures;
-import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.recalibration.EventType;
-import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-
-/**
- * Created with IntelliJ IDEA.
- * User: depristo
- * Date: 12/18/12
- * Time: 3:50 PM
- *
- * TODO -- merge in ReadCovariates?
- */
-public final class ReadRecalibrationInfo {
-    private final GATKSAMRecord read;
-    private final int length;
-    private final ReadCovariates covariates;
-    private final boolean[] skips;
-    private final byte[] baseQuals, insertionQuals, deletionQuals;
-    private final double[] snpErrors, insertionErrors, deletionErrors;
-
-    public ReadRecalibrationInfo(final GATKSAMRecord read,
-                                 final ReadCovariates covariates,
-                                 final boolean[] skips,
-                                 final double[] snpErrors,
-                                 final double[] insertionErrors,
-                                 final double[] deletionErrors) {
-        if ( read == null ) throw new IllegalArgumentException("read cannot be null");
-        if ( covariates == null ) throw new IllegalArgumentException("covariates cannot be null");
-        if ( skips == null ) throw new IllegalArgumentException("skips cannot be null");
-        if ( snpErrors == null ) throw new IllegalArgumentException("snpErrors cannot be null");
-        if ( insertionErrors == null ) throw new IllegalArgumentException("insertionErrors cannot be null");
-        if ( deletionErrors == null ) throw new IllegalArgumentException("deletionErrors cannot be null");
-
-        this.read = read;
-        this.baseQuals = read.getBaseQualities();
-        this.length = baseQuals.length;
-        this.covariates = covariates;
-        this.skips = skips;
-        this.insertionQuals = read.getExistingBaseInsertionQualities();
-        this.deletionQuals = read.getExistingBaseDeletionQualities();
-        this.snpErrors = snpErrors;
-        this.insertionErrors = insertionErrors;
-        this.deletionErrors = deletionErrors;
-
-        if ( skips.length != length ) throw new IllegalArgumentException("skips.length " + snpErrors.length + " != length " + length);
-        if ( snpErrors.length != length ) throw new IllegalArgumentException("snpErrors.length " + snpErrors.length + " != length " + length);
-        if ( insertionErrors.length != length ) throw new IllegalArgumentException("insertionErrors.length " + snpErrors.length + " != length " + length);
-        if ( deletionErrors.length != length ) throw new IllegalArgumentException("deletionErrors.length " + snpErrors.length + " != length " + length);
-    }
-
-    /**
-     * Get the qual score for event type at offset
-     *
-     * @param eventType the type of event we want the qual for
-     * @param offset the offset into this read for the qual
-     * @return a valid quality score for event at offset
-     */
-    @Requires("validOffset(offset)")
-    @Ensures("validQual(result)")
-    public byte getQual(final EventType eventType, final int offset) {
-        switch ( eventType ) {
-            case BASE_SUBSTITUTION: return baseQuals[offset];
-            // note optimization here -- if we don't have ins/del quals we just return the default byte directly
-            case BASE_INSERTION: return insertionQuals == null ? GATKSAMRecord.DEFAULT_INSERTION_DELETION_QUAL : insertionQuals[offset];
-            case BASE_DELETION: return deletionQuals == null ? GATKSAMRecord.DEFAULT_INSERTION_DELETION_QUAL : deletionQuals[offset];
-            default: throw new IllegalStateException("Unknown event type " + eventType);
-        }
-    }
-
-    /**
-     * Get the error fraction for event type at offset
-     *
-     * The error fraction is a value between 0 and 1 that indicates how much certainty we have
-     * in the error occurring at offset.  A value of 1 means that the error definitely occurs at this
-     * site, a value of 0.0 means it definitely doesn't happen here.  0.5 means that half the weight
-     * of the error belongs here
-     *
-     * @param eventType the type of event we want the qual for
-     * @param offset the offset into this read for the qual
-     * @return a fractional weight for an error at this offset
-     */
-    @Requires("validOffset(offset)")
-    @Ensures("result >= 0.0 && result <= 1.0")
-    public double getErrorFraction(final EventType eventType, final int offset) {
-        switch ( eventType ) {
-            case BASE_SUBSTITUTION: return snpErrors[offset];
-            case BASE_INSERTION: return insertionErrors[offset];
-            case BASE_DELETION: return deletionErrors[offset];
-            default: throw new IllegalStateException("Unknown event type " + eventType);
-        }
-    }
-
-    /**
-     * Get the read involved in this recalibration info
-     * @return a non-null GATKSAMRecord
-     */
-    @Ensures("result != null")
-    public GATKSAMRecord getRead() {
-        return read;
-    }
-
-    /**
-     * Should offset in this read be skipped (because it's covered by a known variation site?)
-     * @param offset a valid offset into this info
-     * @return true if offset should be skipped, false otherwise
-     */
-    @Requires("validOffset(offset)")
-    public boolean skip(final int offset) {
-        return skips[offset];
-    }
-
-    /**
-     * Get the ReadCovariates object carrying the mapping from offsets -> covariate key sets
-     * @return a non-null ReadCovariates object
-     */
-    @Ensures("result != null")
-    public ReadCovariates getCovariatesValues() {
-        return covariates;
-    }
-
-    /**
-     * Ensures an offset is valid.  Used in contracts
-     * @param offset a proposed offset
-     * @return true if offset is valid w.r.t. the data in this object, false otherwise
-     */
-    private boolean validOffset(final int offset) {
-        return offset >= 0 && offset < baseQuals.length;
-    }
-
-    private boolean validQual(final byte result) {
-        return result >= 0 && result <= QualityUtils.MAX_QUAL_SCORE;
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
deleted file mode 100755
index 622413b18..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
+++ /dev/null
@@ -1,251 +0,0 @@
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.walkers.bqsr;
-
-import org.broad.tribble.Feature;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.report.GATKReportTable;
-import org.broadinstitute.sting.utils.recalibration.RecalUtils;
-
-import java.io.File;
-import java.io.PrintStream;
-import java.util.Collections;
-import java.util.List;
-
-/**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Nov 27, 2009
- *
- * A collection of the arguments that are common to both CovariateCounterWalker and TableRecalibrationWalker.
- * This set of arguments will also be passed to the constructor of every Covariate when it is instantiated.
- */
-
-public class RecalibrationArgumentCollection {
-
-    /**
-     * This algorithm treats every reference mismatch as an indication of error. However, real genetic variation is expected to mismatch the reference,
-     * so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites. This tool accepts any number of RodBindings (VCF, Bed, etc.)
-     * for use as this database. For users wishing to exclude an interval list of known variation simply use -XL my.interval.list to skip over processing those sites.
-     * Please note however that the statistics reported by the tool will not accurately reflected those sites skipped by the -XL argument.
-     */
-    @Input(fullName = "knownSites", shortName = "knownSites", doc = "A database of known polymorphic sites to skip over in the recalibration algorithm", required = false)
-    public List<RodBinding<Feature>> knownSites = Collections.emptyList();
-
-    /**
-     * After the header, data records occur one per line until the end of the file. The first several items on a line are the
-     * values of the individual covariates and will change depending on which covariates were specified at runtime. The last
-     * three items are the data- that is, number of observations for this combination of covariates, number of reference mismatches,
-     * and the raw empirical quality score calculated by phred-scaling the mismatch rate.   Use '/dev/stdout' to print to standard out.
-     */
-    @Gather(BQSRGatherer.class)
-    @Output(doc = "The output recalibration table file to create", required = true)
-    public File RECAL_TABLE_FILE = null;
-    public PrintStream RECAL_TABLE;
-
-    /**
-     * If not provided, then no plots will be generated (useful for queue scatter/gathering).
-     * However, we *highly* recommend that users generate these plots whenever possible for QC checking.
-     */
-    @Output(fullName = "plot_pdf_file", shortName = "plots", doc = "The output recalibration pdf file to create", required = false)
-    public File RECAL_PDF_FILE = null;
-
-    /**
-     * If not provided, then a temporary file is created and then deleted upon completion.
-     * For advanced users only.
-     */
-    @Advanced
-    @Argument(fullName = "intermediate_csv_file", shortName = "intermediate", doc = "The intermediate csv file to create", required = false)
-    public File RECAL_CSV_FILE = null;
-
-    /**
-     * Note that the --list argument requires a fully resolved and correct command-line to work.
-     */
-    @Argument(fullName = "list", shortName = "ls", doc = "List the available covariates and exit", required = false)
-    public boolean LIST_ONLY = false;
-
-    /**
-     * Note that the ReadGroup and QualityScore covariates are required and do not need to be specified.
-     * Also, unless --no_standard_covs is specified, the Cycle and Context covariates are standard and are included by default.
-     * Use the --list argument to see the available covariates.
-     */
-    @Argument(fullName = "covariate", shortName = "cov", doc = "One or more covariates to be used in the recalibration. Can be specified multiple times", required = false)
-    public String[] COVARIATES = null;
-
-    /*
-     * The Cycle and Context covariates are standard and are included by default unless this argument is provided.
-     * Note that the ReadGroup and QualityScore covariates are required and cannot be excluded.
-     */
-    @Argument(fullName = "no_standard_covs", shortName = "noStandard", doc = "Do not use the standard set of covariates, but rather just the ones listed using the -cov argument", required = false)
-    public boolean DO_NOT_USE_STANDARD_COVARIATES = false;
-
-    /**
-     * This calculation is critically dependent on being able to skip over known polymorphic sites. Please be sure that you know what you are doing if you use this option.
-     */
-    @Advanced
-    @Argument(fullName = "run_without_dbsnp_potentially_ruining_quality", shortName = "run_without_dbsnp_potentially_ruining_quality", required = false, doc = "If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only.")
-    public boolean RUN_WITHOUT_DBSNP = false;
-
-    /**
-     * CountCovariates and TableRecalibration accept a --solid_recal_mode <MODE> flag which governs how the recalibrator handles the
-     * reads which have had the reference inserted because of color space inconsistencies.
-     */
-    @Argument(fullName = "solid_recal_mode", shortName = "sMode", required = false, doc = "How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS")
-    public RecalUtils.SOLID_RECAL_MODE SOLID_RECAL_MODE = RecalUtils.SOLID_RECAL_MODE.SET_Q_ZERO;
-
-    /**
-     * CountCovariates and TableRecalibration accept a --solid_nocall_strategy <MODE> flag which governs how the recalibrator handles
-     * no calls in the color space tag. Unfortunately because of the reference inserted bases mentioned above, reads with no calls in
-     * their color space tag can not be recalibrated.
-     */
-    @Argument(fullName = "solid_nocall_strategy", shortName = "solid_nocall_strategy", doc = "Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ", required = false)
-    public RecalUtils.SOLID_NOCALL_STRATEGY SOLID_NOCALL_STRATEGY = RecalUtils.SOLID_NOCALL_STRATEGY.THROW_EXCEPTION;
-
-    /**
-     * The context covariate will use a context of this size to calculate it's covariate value for base mismatches
-     */
-    @Argument(fullName = "mismatches_context_size", shortName = "mcs", doc = "size of the k-mer context to be used for base mismatches", required = false)
-    public int MISMATCHES_CONTEXT_SIZE = 2;
-
-    /**
-     * The context covariate will use a context of this size to calculate it's covariate value for base insertions and deletions
-     */
-    @Argument(fullName = "indels_context_size", shortName = "ics", doc = "size of the k-mer context to be used for base insertions and deletions", required = false)
-    public int INDELS_CONTEXT_SIZE = 3;
-
-    /**
-     * The cycle covariate will generate an error if it encounters a cycle greater than this value.
-     * This argument is ignored if the Cycle covariate is not used.
-     */
-    @Argument(fullName = "maximum_cycle_value", shortName = "maxCycle", doc = "the maximum cycle value permitted for the Cycle covariate", required = false)
-    public int MAXIMUM_CYCLE_VALUE = 500;
-
-    /**
-     * A default base qualities to use as a prior (reported quality) in the mismatch covariate model. This value will replace all base qualities in the read for this default value. Negative value turns it off (default is off)
-     */
-    @Argument(fullName = "mismatches_default_quality", shortName = "mdq", doc = "default quality for the base mismatches covariate", required = false)
-    public byte MISMATCHES_DEFAULT_QUALITY = -1;
-
-    /**
-     * A default base qualities to use as a prior (reported quality) in the insertion covariate model. This parameter is used for all reads without insertion quality scores for each base. (default is on)
-     */
-    @Argument(fullName = "insertions_default_quality", shortName = "idq", doc = "default quality for the base insertions covariate", required = false)
-    public byte INSERTIONS_DEFAULT_QUALITY = 45;
-
-    /**
-     * A default base qualities to use as a prior (reported quality) in the mismatch covariate model. This value will replace all base qualities in the read for this default value. Negative value turns it off (default is off)
-     */
-    @Argument(fullName = "deletions_default_quality", shortName = "ddq", doc = "default quality for the base deletions covariate", required = false)
-    public byte DELETIONS_DEFAULT_QUALITY = 45;
-
-    /**
-     * Reads with low quality bases on either tail (beginning or end) will not be considered in the context. This parameter defines the quality below which (inclusive) a tail is considered low quality
-     */
-    @Argument(fullName = "low_quality_tail", shortName = "lqt", doc = "minimum quality for the bases in the tail of the reads to be considered", required = false)
-    public byte LOW_QUAL_TAIL = 2;
-
-    /**
-     * BQSR generates a quantization table for quick quantization later by subsequent tools. BQSR does not quantize the base qualities, this is done by the engine with the -qq or -BQSR options.
-     * This parameter tells BQSR the number of levels of quantization to use to build the quantization table.
-     */
-    @Argument(fullName = "quantizing_levels", shortName = "ql", required = false, doc = "number of distinct quality scores in the quantized output")
-    public int QUANTIZING_LEVELS = 16;
-
-    /**
-     * The tag name for the binary tag covariate (if using it)
-     */
-    @Argument(fullName = "binary_tag_name", shortName = "bintag", required = false, doc = "the binary tag covariate name if using it")
-    public String BINARY_TAG_NAME = null;
-
-    /*
-     * whether GATK report tables should have rows in sorted order, starting from leftmost column
-     */
-    @Argument(fullName = "sort_by_all_columns", shortName = "sortAllCols", doc = "Sort the rows in the tables of reports", required = false)
-    public Boolean SORT_BY_ALL_COLUMNS  = false;
-
-    /////////////////////////////
-    // Debugging-only Arguments
-    /////////////////////////////
-
-    @Hidden
-    @Argument(fullName = "default_platform", shortName = "dP", required = false, doc = "If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.")
-    public String DEFAULT_PLATFORM = null;
-
-    @Hidden
-    @Argument(fullName = "force_platform", shortName = "fP", required = false, doc = "If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.")
-    public String FORCE_PLATFORM = null;
-
-    @Hidden
-    @Output(fullName = "recal_table_update_log", shortName = "recal_table_update_log", required = false, doc = "If provided, log all updates to the recalibration tables to the given file. For debugging/testing purposes only")
-    public PrintStream RECAL_TABLE_UPDATE_LOG = null;
-
-    public File existingRecalibrationReport = null;
-
-    public GATKReportTable generateReportTable(final String covariateNames) {
-        GATKReportTable argumentsTable;
-        if(SORT_BY_ALL_COLUMNS) {
-            argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2, GATKReportTable.TableSortingWay.SORT_BY_COLUMN);
-        } else {
-            argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2);
-        }
-        argumentsTable.addColumn("Argument");
-        argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME);
-        argumentsTable.addRowID("covariate", true);
-        argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, covariateNames);
-        argumentsTable.addRowID("no_standard_covs", true);
-        argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES);
-        argumentsTable.addRowID("run_without_dbsnp", true);
-        argumentsTable.set("run_without_dbsnp", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP);
-        argumentsTable.addRowID("solid_recal_mode", true);
-        argumentsTable.set("solid_recal_mode", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE);
-        argumentsTable.addRowID("solid_nocall_strategy", true);
-        argumentsTable.set("solid_nocall_strategy", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY);
-        argumentsTable.addRowID("mismatches_context_size", true);
-        argumentsTable.set("mismatches_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE);
-        argumentsTable.addRowID("indels_context_size", true);
-        argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE);
-        argumentsTable.addRowID("mismatches_default_quality", true);
-        argumentsTable.set("mismatches_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY);
-        argumentsTable.addRowID("insertions_default_quality", true);
-        argumentsTable.set("insertions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INSERTIONS_DEFAULT_QUALITY);
-        argumentsTable.addRowID("low_quality_tail", true);
-        argumentsTable.set("low_quality_tail", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, LOW_QUAL_TAIL);
-        argumentsTable.addRowID("default_platform", true);
-        argumentsTable.set("default_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DEFAULT_PLATFORM);
-        argumentsTable.addRowID("force_platform", true);
-        argumentsTable.set("force_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, FORCE_PLATFORM);
-        argumentsTable.addRowID("quantizing_levels", true);
-        argumentsTable.set("quantizing_levels", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, QUANTIZING_LEVELS);
-        argumentsTable.addRowID("recalibration_report", true);
-        argumentsTable.set("recalibration_report", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, existingRecalibrationReport == null ? "null" : existingRecalibrationReport.getAbsolutePath());
-        argumentsTable.addRowID("plot_pdf_file", true);
-        argumentsTable.set("plot_pdf_file", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RECAL_PDF_FILE == null ? "null" : RECAL_PDF_FILE.getAbsolutePath());
-        argumentsTable.addRowID("binary_tag_name", true);
-        argumentsTable.set("binary_tag_name", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, BINARY_TAG_NAME == null ? "null" : BINARY_TAG_NAME);
-        return argumentsTable;
-    }
-
-}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
deleted file mode 100644
index ca9fb4bca..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
+++ /dev/null
@@ -1,216 +0,0 @@
-/*
- * Copyright (c) 2012 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.walkers.bqsr;
-
-import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
-import org.broadinstitute.sting.utils.recalibration.*;
-import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-
-import java.io.PrintStream;
-import java.util.LinkedList;
-import java.util.List;
-
-public class RecalibrationEngine {
-    final protected Covariate[] covariates;
-    final private int numReadGroups;
-    final private PrintStream maybeLogStream;
-    final private boolean lowMemoryMode;
-
-    /**
-     * Has finalizeData() been called?
-     */
-    private boolean finalized = false;
-
-    /**
-     * The final (merged, etc) recalibration tables, suitable for downstream analysis.
-     */
-    private RecalibrationTables finalRecalibrationTables = null;
-
-    private final List<RecalibrationTables> recalibrationTablesList = new LinkedList<RecalibrationTables>();
-
-    private final ThreadLocal<RecalibrationTables> threadLocalTables = new ThreadLocal<RecalibrationTables>() {
-        private synchronized RecalibrationTables makeAndCaptureTable() {
-            final RecalibrationTables newTable = new RecalibrationTables(covariates, numReadGroups, maybeLogStream);
-            recalibrationTablesList.add(newTable);
-            return newTable;
-        }
-
-        @Override
-        protected synchronized RecalibrationTables initialValue() {
-            if ( lowMemoryMode ) {
-                return recalibrationTablesList.isEmpty() ? makeAndCaptureTable() : recalibrationTablesList.get(0);
-            } else {
-                return makeAndCaptureTable();
-            }
-        }
-    };
-
-    /**
-     * Get a recalibration table suitable for updating the underlying RecalDatums
-     *
-     * May return a thread-local version, or a single version, depending on the initialization
-     * arguments of this instance.
-     *
-     * @return updated tables
-     */
-    protected RecalibrationTables getUpdatableRecalibrationTables() {
-        return threadLocalTables.get();
-    }
-
-    /**
-     * Initialize the recalibration engine
-     *
-     * Called once before any calls to updateDataForRead are made.  The engine should prepare itself
-     * to handle any number of updateDataForRead calls containing ReadRecalibrationInfo containing
-     * keys for each of the covariates provided.
-     *
-     * The engine should collect match and mismatch data into the recalibrationTables data.
-     *
-     * @param covariates an array of the covariates we'll be using in this engine, order matters
-     * @param numReadGroups the number of read groups we should use for the recalibration tables
-     * @param maybeLogStream an optional print stream for logging calls to the nestedhashmap in the recalibration tables
-     */
-    public RecalibrationEngine(final Covariate[] covariates, final int numReadGroups, final PrintStream maybeLogStream, final boolean enableLowMemoryMode) {
-        if ( covariates == null ) throw new IllegalArgumentException("Covariates cannot be null");
-        if ( numReadGroups < 1 ) throw new IllegalArgumentException("numReadGroups must be >= 1 but got " + numReadGroups);
-
-        this.covariates = covariates.clone();
-        this.numReadGroups = numReadGroups;
-        this.maybeLogStream = maybeLogStream;
-        this.lowMemoryMode = enableLowMemoryMode;
-    }
-
-    /**
-     * Update the recalibration statistics using the information in recalInfo
-     * @param recalInfo data structure holding information about the recalibration values for a single read
-     */
-    @Requires("recalInfo != null")
-    public void updateDataForRead( final ReadRecalibrationInfo recalInfo ) {
-        final GATKSAMRecord read = recalInfo.getRead();
-        final ReadCovariates readCovariates = recalInfo.getCovariatesValues();
-        final RecalibrationTables tables = getUpdatableRecalibrationTables();
-        final NestedIntegerArray<RecalDatum> qualityScoreTable = tables.getQualityScoreTable();
-
-        for( int offset = 0; offset < read.getReadBases().length; offset++ ) {
-            if( ! recalInfo.skip(offset) ) {
-
-                for (final EventType eventType : EventType.values()) {
-                    final int[] keys = readCovariates.getKeySet(offset, eventType);
-                    final int eventIndex = eventType.ordinal();
-                    final byte qual = recalInfo.getQual(eventType, offset);
-                    final double isError = recalInfo.getErrorFraction(eventType, offset);
-
-                    RecalUtils.incrementDatumOrPutIfNecessary(qualityScoreTable, qual, isError, keys[0], keys[1], eventIndex);
-
-                    for (int i = 2; i < covariates.length; i++) {
-                        if (keys[i] < 0)
-                            continue;
-
-                        RecalUtils.incrementDatumOrPutIfNecessary(tables.getTable(i), qual, isError, keys[0], keys[1], keys[i], eventIndex);
-                    }
-                }
-            }
-        }
-    }
-
-
-    /**
-     * Finalize, if appropriate, all derived data in recalibrationTables.
-     *
-     * Called once after all calls to updateDataForRead have been issued.
-     *
-     * Assumes that all of the principal tables (by quality score) have been completely updated,
-     * and walks over this data to create summary data tables like by read group table.
-     */
-    public void finalizeData() {
-        if ( finalized ) throw new IllegalStateException("FinalizeData() has already been called");
-
-        // merge all of the thread-local tables
-        finalRecalibrationTables = mergeThreadLocalRecalibrationTables();
-
-        final NestedIntegerArray<RecalDatum> byReadGroupTable = finalRecalibrationTables.getReadGroupTable();
-        final NestedIntegerArray<RecalDatum> byQualTable = finalRecalibrationTables.getQualityScoreTable();
-
-        // iterate over all values in the qual table
-        for ( NestedIntegerArray.Leaf<RecalDatum> leaf : byQualTable.getAllLeaves() ) {
-            final int rgKey = leaf.keys[0];
-            final int eventIndex = leaf.keys[2];
-            final RecalDatum rgDatum = byReadGroupTable.get(rgKey, eventIndex);
-            final RecalDatum qualDatum = leaf.value;
-
-            if ( rgDatum == null ) {
-                // create a copy of qualDatum, and initialize byReadGroup table with it
-                byReadGroupTable.put(new RecalDatum(qualDatum), rgKey, eventIndex);
-            } else {
-                // combine the qual datum with the existing datum in the byReadGroup table
-                rgDatum.combine(qualDatum);
-            }
-        }
-
-        finalized = true;
-    }
-
-    /**
-     * Merge all of the thread local recalibration tables into a single one.
-     *
-     * Reuses one of the recalibration tables to hold the merged table, so this function can only be
-     * called once in the engine.
-     *
-     * @return the merged recalibration table
-     */
-    @Requires("! finalized")
-    private RecalibrationTables mergeThreadLocalRecalibrationTables() {
-        if ( recalibrationTablesList.isEmpty() ) throw new IllegalStateException("recalibration tables list is empty");
-
-        RecalibrationTables merged = null;
-        for ( final RecalibrationTables table : recalibrationTablesList ) {
-            if ( merged == null )
-                // fast path -- if there's only only one table, so just make it the merged one
-                merged = table;
-            else {
-                merged.combine(table);
-            }
-        }
-
-        return merged;
-    }
-
-    /**
-     * Get the final recalibration tables, after finalizeData() has been called
-     *
-     * This returns the finalized recalibration table collected by this engine.
-     *
-     * It is an error to call this function before finalizeData has been called
-     *
-     * @return the finalized recalibration table collected by this engine
-     */
-    public RecalibrationTables getFinalRecalibrationTables() {
-        if ( ! finalized ) throw new IllegalStateException("Cannot get final recalibration tables until finalizeData() has been called");
-        return finalRecalibrationTables;
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java
index b4ef66aaf..c8304db21 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java
@@ -1,9 +1,13 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java
index a3efea9f1..fb08d1c03 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Argument;
@@ -34,6 +34,9 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java
index d7ae3050e..3ffdf3e9d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java
@@ -23,7 +23,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Input;
@@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.io.PrintStream;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
index 93eaee209..3dd49dea8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.readutils;
 
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;
@@ -37,6 +37,9 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.clipping.ClippingOp;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java
index 37176cbf9..956c0d7d4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.readutils;
 
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMReadGroupRecord;
@@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.gatk.iterators.ReadTransformersMode;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java
index 7d70c470d..07d1f7c23 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.readutils;
 
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileWriter;
@@ -34,6 +34,10 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/GATKLiteUtils.java b/public/java/src/org/broadinstitute/sting/utils/classloader/GATKLiteUtils.java
deleted file mode 100755
index 2ab7d0618..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/classloader/GATKLiteUtils.java
+++ /dev/null
@@ -1,100 +0,0 @@
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.classloader;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
-import java.util.*;
-
-/**
- * Created by IntelliJ IDEA.
- * User: ebanks
- *
- * A set of static utility methods for working with the full vs. Lite GATK build
- */
-public class GATKLiteUtils {
-    /**
-     * Constructor access disallowed...static utility methods only!
-     */
-    private GATKLiteUtils() { }
-
-
-    private static Set<String> fullVersionGATKWalkers = new HashSet<String>();
-    static {
-        fullVersionGATKWalkers.add("HaplotypeCaller");
-        fullVersionGATKWalkers.add("ReduceReads");
-    }
-    /**
-     * Utility method to check whether a given walker is only available in the full GATK release
-     *
-     * @param walkerName   the walker class name (not the package) to check
-     */
-    public static boolean isAvailableOnlyInFullGATK(final String walkerName) {
-        return fullVersionGATKWalkers.contains(walkerName);
-    }
-
-    /**
-     * Utility method to determine whether this is the lite version of the GATK
-     */
-    public static boolean isGATKLite() {
-        if ( isLiteVersion == null ) {
-            try {
-                Class.forName(DummyProtectedClassName);
-                isLiteVersion = false;
-            } catch ( ClassNotFoundException e) {
-                isLiteVersion = true;
-            }
-        }
-        return isLiteVersion;
-    }
-    private static final String DummyProtectedClassName = "org.broadinstitute.sting.gatk.DummyProtectedClass";
-    private static Boolean isLiteVersion = null;
-
-
-    /**
-     * Utility method to pull out a protected subclass if possible, otherwise it falls back to a public subclass.
-     * Important note: the protected classes MUST implement ProtectedPackageSource!
-     *
-     * @param interfaceClass    the interface class which the target classes implement
-     */
-    public static Class getProtectedClassIfAvailable(final Class interfaceClass) {
-        List<Class<? extends Object>> classes = new PluginManager<Object>(interfaceClass).getPlugins();
-        if ( classes.isEmpty() )
-            throw new ReviewedStingException("No classes implementing the interface class " + interfaceClass.getSimpleName() + " were found");
-
-        Class result = null;
-        for ( Class<? extends Object> c : classes ) {
-            if ( ProtectedPackageSource.class.isAssignableFrom(c) ) {
-                result = c;
-                break;
-            }
-        }
-        if ( result == null )
-            result = classes.get(0);
-
-        return result;
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 01c4b7a16..c799479ed 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -92,12 +92,6 @@ public class UserException extends ReviewedStingException {
         }
     }
 
-    public static class NotSupportedInGATKLite extends UserException {
-        public NotSupportedInGATKLite(String message) {
-            super(String.format("GATK Lite does not support all of the features of the full version: %s", message));
-        }
-    }
-
     // todo -- fix up exception cause passing
     public static class MissingArgument extends CommandLineException {
         public MissingArgument(String arg, String message) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java
deleted file mode 100644
index 1a27c6ecb..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright (c) 2011 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-package org.broadinstitute.sting.utils.genotyper;
-
-
-import org.broadinstitute.sting.utils.classloader.PublicPackageSource;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.variant.variantcontext.Allele;
-
-import java.io.PrintStream;
-import java.util.*;
-
-public class StandardPerReadAlleleLikelihoodMap extends PerReadAlleleLikelihoodMap implements PublicPackageSource {
-
-    public StandardPerReadAlleleLikelihoodMap() {
-        likelihoodReadMap = new LinkedHashMap<GATKSAMRecord,Map<Allele,Double>>();
-        alleles = new ArrayList<Allele>();
-    }
-
-    // not implemented in the standard version
-    public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) {}
-    public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { return pileup; }
-}
diff --git a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
index d8905ad35..e96aae07a 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
@@ -28,7 +28,7 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.ArgumentException;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.walkers.PrintReads;
+import org.broadinstitute.sting.gatk.walkers.readutils.PrintReads;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.testng.annotations.Test;
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLiteIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLiteIntegrationTest.java
deleted file mode 100755
index 783a8d7fc..000000000
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLiteIntegrationTest.java
+++ /dev/null
@@ -1,35 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.genotyper;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
-import org.testng.SkipException;
-import org.testng.annotations.Test;
-
-import java.util.Arrays;
-
-// ********************************************************************************** //
-// Note that this class also serves as an integration test for the VariantAnnotator!  //
-// ********************************************************************************** //
-
-public class UnifiedGenotyperLiteIntegrationTest extends WalkerTest {
-
-    private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // testing contamination down-sampling gets ignored
-    //
-    // --------------------------------------------------------------------------------------------------------------
-
-    @Test
-    public void testContaminationDownsampling() {
-        if ( !GATKLiteUtils.isGATKLite() )
-            throw new SkipException("Only want to test for GATK lite");
-
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("9addd225a985178339a0c49dc5fdc220"));
-        executeTest("test contamination_percentage_to_filter gets ignored", spec);
-    }
-
-}
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/FlagStatIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/FlagStatIntegrationTest.java
similarity index 92%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/FlagStatIntegrationTest.java
rename to public/java/test/org/broadinstitute/sting/gatk/walkers/qc/FlagStatIntegrationTest.java
index d2acaa588..aaebfc588 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/FlagStatIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/FlagStatIntegrationTest.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.WalkerTest;
 import org.testng.annotations.Test;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java
similarity index 98%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java
rename to public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java
index b457698e9..05c82806d 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.WalkerTest;
 import org.testng.annotations.Test;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java
similarity index 98%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java
rename to public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java
index ade9bda16..a19b3724f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.readutils;
 
 import org.broadinstitute.sting.WalkerTest;
 import org.testng.annotations.Test;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java
similarity index 97%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java
rename to public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java
index 717d9d953..247000431 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.readutils;
 
 import org.broadinstitute.sting.WalkerTest;
 import org.testng.annotations.DataProvider;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsLargeScaleTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsLargeScaleTest.java
similarity index 92%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsLargeScaleTest.java
rename to public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsLargeScaleTest.java
index ad7ac56f9..81a3082a2 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsLargeScaleTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsLargeScaleTest.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.readutils;
 
 import org.broadinstitute.sting.WalkerTest;
 import org.testng.annotations.Test;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java
similarity index 94%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java
rename to public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java
index 1aaa00aee..0da3b6b1f 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.readutils;
 
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
@@ -59,7 +59,7 @@ public class PrintReadsUnitTest extends BaseTest {
     private ReferenceContext bases = null;
     //private ReferenceContext ref = new ReferenceContext()
 
-    PrintReads walker;
+    org.broadinstitute.sting.gatk.walkers.readutils.PrintReads walker;
     ArtificialSAMFileWriter writer;
 
     @BeforeMethod
@@ -67,7 +67,7 @@ public class PrintReadsUnitTest extends BaseTest {
         trav = new ArtificialReadsTraversal();
         readTotal = ( ( trav.endingChr - trav.startingChr ) + 1 ) * trav.readsPerChr + trav.unMappedReads;
 
-        walker = new PrintReads();
+        walker = new org.broadinstitute.sting.gatk.walkers.readutils.PrintReads();
         writer = new ArtificialSAMFileWriter();
         walker.out = writer;
         walker.initialize();