From 6790e103e00704640effc7710e1c0f819a2e8104 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 24 Jan 2013 11:42:49 -0500 Subject: [PATCH] Moving lots of walkers back from protected to public (along with several of the VA annotations). Let's see whether Mauricio's automatic git hook really works! --- .../sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java | 0 .../sting/gatk/walkers/annotator/AlleleBalance.java | 0 .../sting/gatk/walkers/annotator/AlleleBalanceBySample.java | 0 .../sting/gatk/walkers/annotator/AverageAltAlleleLength.java | 0 .../broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java | 0 .../org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java | 0 .../sting/gatk/walkers/annotator/MappingQualityZeroBySample.java | 0 .../sting/gatk/walkers/annotator/MappingQualityZeroFraction.java | 0 .../broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java | 0 .../org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java | 0 .../sting/gatk/walkers/annotator/TechnologyComposition.java | 0 .../sting/gatk/walkers/annotator/VariantAnnotator.java | 0 .../sting/gatk/walkers/annotator/VariantAnnotatorEngine.java | 0 .../walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java | 0 .../walkers/annotator/interfaces/AnnotationInterfaceManager.java | 0 .../sting/gatk/walkers/annotator/interfaces/AnnotationType.java | 0 .../gatk/walkers/annotator/interfaces/AnnotatorCompatible.java | 0 .../gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java | 0 .../gatk/walkers/annotator/interfaces/GenotypeAnnotation.java | 0 .../gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java | 0 .../gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java | 0 .../gatk/walkers/annotator/interfaces/StandardAnnotation.java | 0 .../walkers/annotator/interfaces/VariantAnnotatorAnnotation.java | 0 .../walkers/annotator/interfaces/WorkInProgressAnnotation.java | 0 .../sting/gatk/walkers/beagle/BeagleOutputToVCF.java | 0 .../sting/gatk/walkers/beagle/ProduceBeagleInput.java | 0 .../sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java | 0 .../sting/gatk/walkers/coverage/DepthOfCoverage.java | 0 .../sting/gatk/walkers/coverage/DepthOfCoverageStats.java | 0 .../sting/gatk/walkers/diffengine/BAMDiffableReader.java | 0 .../sting/gatk/walkers/diffengine/GATKReportDiffableReader.java | 0 .../sting/gatk/walkers/diffengine/VCFDiffableReader.java | 0 .../sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java | 0 .../sting/gatk/walkers/fasta/FastaReferenceMaker.java | 0 .../broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java | 0 .../broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java | 0 .../sting/gatk/walkers/filters/FiltrationContext.java | 0 .../sting/gatk/walkers/filters/FiltrationContextWindow.java | 0 .../sting/gatk/walkers/filters/VariantFiltration.java | 0 .../sting/gatk/walkers/validation/ValidationAmplicons.java | 0 .../sting/gatk/walkers/varianteval/VariantEval.java | 0 .../sting/gatk/walkers/varianteval/VariantEvalReportWriter.java | 0 .../sting/gatk/walkers/varianteval/evaluators/CompOverlap.java | 0 .../sting/gatk/walkers/varianteval/evaluators/CountVariants.java | 0 .../gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java | 0 .../sting/gatk/walkers/varianteval/evaluators/IndelSummary.java | 0 .../varianteval/evaluators/MendelianViolationEvaluator.java | 0 .../gatk/walkers/varianteval/evaluators/MultiallelicSummary.java | 0 .../gatk/walkers/varianteval/evaluators/PrintMissingComp.java | 0 .../sting/gatk/walkers/varianteval/evaluators/StandardEval.java | 0 .../walkers/varianteval/evaluators/ThetaVariantEvaluator.java | 0 .../gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java | 0 .../gatk/walkers/varianteval/evaluators/ValidationReport.java | 0 .../gatk/walkers/varianteval/evaluators/VariantEvaluator.java | 0 .../sting/gatk/walkers/varianteval/evaluators/VariantSummary.java | 0 .../gatk/walkers/varianteval/stratifications/AlleleCount.java | 0 .../gatk/walkers/varianteval/stratifications/AlleleFrequency.java | 0 .../sting/gatk/walkers/varianteval/stratifications/CompRod.java | 0 .../sting/gatk/walkers/varianteval/stratifications/Contig.java | 0 .../sting/gatk/walkers/varianteval/stratifications/CpG.java | 0 .../gatk/walkers/varianteval/stratifications/Degeneracy.java | 0 .../varianteval/stratifications/DynamicStratification.java | 0 .../sting/gatk/walkers/varianteval/stratifications/EvalRod.java | 0 .../sting/gatk/walkers/varianteval/stratifications/Filter.java | 0 .../gatk/walkers/varianteval/stratifications/FunctionalClass.java | 0 .../sting/gatk/walkers/varianteval/stratifications/IndelSize.java | 0 .../varianteval/stratifications/IntervalStratification.java | 0 .../gatk/walkers/varianteval/stratifications/JexlExpression.java | 0 .../sting/gatk/walkers/varianteval/stratifications/Novelty.java | 0 .../gatk/walkers/varianteval/stratifications/OneBPIndel.java | 0 .../varianteval/stratifications/RequiredStratification.java | 0 .../sting/gatk/walkers/varianteval/stratifications/Sample.java | 0 .../varianteval/stratifications/StandardStratification.java | 0 .../gatk/walkers/varianteval/stratifications/TandemRepeat.java | 0 .../walkers/varianteval/stratifications/VariantStratifier.java | 0 .../gatk/walkers/varianteval/stratifications/VariantType.java | 0 .../walkers/varianteval/stratifications/manager/StratNode.java | 0 .../varianteval/stratifications/manager/StratNodeIterator.java | 0 .../stratifications/manager/StratificationManager.java | 0 .../walkers/varianteval/stratifications/manager/Stratifier.java | 0 .../sting/gatk/walkers/varianteval/util/Analysis.java | 0 .../gatk/walkers/varianteval/util/AnalysisModuleScanner.java | 0 .../sting/gatk/walkers/varianteval/util/DataPoint.java | 0 .../sting/gatk/walkers/varianteval/util/EvaluationContext.java | 0 .../sting/gatk/walkers/varianteval/util/Molten.java | 0 .../gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java | 0 .../sting/gatk/walkers/varianteval/util/VariantEvalUtils.java | 0 .../gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java | 0 .../sting/gatk/walkers/variantutils/ConcordanceMetrics.java | 0 .../sting/gatk/walkers/variantutils/FilterLiftedVariants.java | 0 .../sting/gatk/walkers/variantutils/GenotypeConcordance.java | 0 .../sting/gatk/walkers/variantutils/LeftAlignVariants.java | 0 .../sting/gatk/walkers/variantutils/LiftoverVariants.java | 0 .../sting/gatk/walkers/variantutils/RandomlySplitVariants.java | 0 .../sting/gatk/walkers/variantutils/SelectHeaders.java | 0 .../sting/gatk/walkers/variantutils/ValidateVariants.java | 0 .../gatk/walkers/variantutils/VariantValidationAssessor.java | 0 .../sting/gatk/walkers/variantutils/VariantsToBinaryPed.java | 0 .../sting/gatk/walkers/variantutils/VariantsToTable.java | 0 .../sting/gatk/walkers/variantutils/VariantsToVCF.java | 0 .../sting/utils/genotyper/PerReadAlleleLikelihoodMap.java | 0 101 files changed, 0 insertions(+), 0 deletions(-) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java (100%) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/public/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java rename to public/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java diff --git a/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java rename to public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java