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!
2013-01-24 11:42:49 -05:00 · 2013-01-24 11:42:49 -05:00 · 6790e103e0
parent 9e003b3296
commit 6790e103e0
101 changed files with 0 additions and 0 deletions
--- a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
--- a/protected/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
--- a/protected/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
--- a/protected/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
--- a/protected/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
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
--- a/Show More
+++ b/Show More