diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java similarity index 93% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java index fec86460f..6806ace76 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java @@ -1,7 +1,6 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.utils.genotype.Variation; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicVariantAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/BasicVariantAnalysis.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicVariantAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/BasicVariantAnalysis.java index 2435a9f83..4630948c7 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicVariantAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/BasicVariantAnalysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CallableBasesAnalysis.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CallableBasesAnalysis.java index 9e3dffe3a..67282a1c1 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CallableBasesAnalysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ChipConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ChipConcordance.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ChipConcordance.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ChipConcordance.java index b4181d8b9..8c964cc62 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ChipConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ChipConcordance.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.Genotype; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ClusterCounterAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ClusterCounterAnalysis.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ClusterCounterAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ClusterCounterAnalysis.java index d7c717072..99884cb43 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ClusterCounterAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ClusterCounterAnalysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.IntervalRod; @@ -7,7 +7,6 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.genotype.Variation; import java.util.ArrayList; -import java.util.HashSet; import java.util.List; /** diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ConcordanceTruthTable.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ConcordanceTruthTable.java index aec483712..0d109c3b0 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ConcordanceTruthTable.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.utils.genotype.Genotype; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeAnalysis.java similarity index 86% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeAnalysis.java index 895f552d6..f781551a8 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeAnalysis.java @@ -1,7 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; - +package org.broadinstitute.sting.gatk.walkers.varianteval; /** * The Broad Institute diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java index a4e1ecd01..5260ee695 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.genotype.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java index 39b931b08..197a16e77 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import cern.jet.math.Arithmetic; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/Histogram.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/Histogram.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/Histogram.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/Histogram.java index ea37be6cb..3bf07cb63 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/Histogram.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/Histogram.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/IndelMetricsAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelMetricsAnalysis.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/IndelMetricsAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelMetricsAnalysis.java index 28842eafd..d3f76d3b3 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/IndelMetricsAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelMetricsAnalysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/NeighborDistanceAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/NeighborDistanceAnalysis.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/NeighborDistanceAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/NeighborDistanceAnalysis.java index f7fbc3723..2dfca15f8 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/NeighborDistanceAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/NeighborDistanceAnalysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.IntervalRod; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PoolAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PoolAnalysis.java similarity index 77% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PoolAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PoolAnalysis.java index a9ce647f1..fcf1d34cc 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PoolAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PoolAnalysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; /** * Created by IntelliJ IDEA. diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PooledConcordance.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledConcordance.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PooledConcordance.java index 2d4cd1a97..8a70ff0a2 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PooledConcordance.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.refdata.RodVCF; import org.broadinstitute.sting.utils.StingException; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledFrequencyAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PooledFrequencyAnalysis.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledFrequencyAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PooledFrequencyAnalysis.java index d1d7238c5..79d38c8d0 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledFrequencyAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PooledFrequencyAnalysis.java @@ -1,9 +1,8 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import java.util.List; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PopulationAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PopulationAnalysis.java similarity index 92% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PopulationAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PopulationAnalysis.java index 5e44df52b..34da97596 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PopulationAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PopulationAnalysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; /** * The Broad Institute diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/TransitionTranversionAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TransitionTranversionAnalysis.java similarity index 93% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/TransitionTranversionAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TransitionTranversionAnalysis.java index 29df63775..6162374a0 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/TransitionTranversionAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TransitionTranversionAnalysis.java @@ -1,9 +1,8 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.genotype.Variation; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ValidationDataAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationDataAnalysis.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ValidationDataAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationDataAnalysis.java index dfacb6a20..3dae63bf2 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ValidationDataAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationDataAnalysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.gatk.refdata.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantAnalysis.java similarity index 94% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantAnalysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantAnalysis.java index 4f5c31b58..f06723823 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantAnalysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantCounter.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantCounter.java index 3fcb87edb..a585f9fc2 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantCounter.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantDBCoverage.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantDBCoverage.java index 5ce0f5339..a7bc3ef01 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantDBCoverage.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index f5a33042e..76cb51aac 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantMatcher.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantMatcher.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantMatcher.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantMatcher.java index c831bad37..0636ccfd4 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantMatcher.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantMatcher.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java index 1ad28eaee..7547bbd0c 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java @@ -13,7 +13,7 @@ import org.broadinstitute.sting.utils.genotype.Genotype; import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype; import org.broadinstitute.sting.playground.gatk.walkers.poolseq.PowerBelowFrequencyWalker; -import org.broadinstitute.sting.playground.gatk.walkers.varianteval.ConcordanceTruthTable; +import org.broadinstitute.sting.gatk.walkers.varianteval.ConcordanceTruthTable; import java.io.*; import java.util.LinkedList; diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java similarity index 92% rename from java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java rename to java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java index b3be55ce8..f69a7103b 100644 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.WalkerTest; import org.junit.Test; @@ -18,8 +18,8 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalVariantROD() { HashMap md5 = new HashMap(); - md5.put("", "4b5a43cb4fa1b82e1bb361632754eaa1"); - md5.put("-A", "7dd6aa5379ea5422fe7db4e79baad1f7"); + md5.put("", "9cfda40f521d75a3e8bafc44a663c14a"); + md5.put("-A", "8fea7cc25f551ce170636fc35c5ae0fe"); /** * the above MD5 was calculated from running the following command: @@ -52,7 +52,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalVariantRODConfSix() { List md5 = new ArrayList(); - md5.add("cfcc2a8e0587cb288f0472118a9bdc1d"); + md5.add("11d636d105f902680c46b9f2e330d922"); /** * the above MD5 was calculated from running the following command: @@ -84,7 +84,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalVariantRODOutputViolations() { List md5 = new ArrayList(); - md5.add("ce708258676bbd4e71e8714828e7d695"); + md5.add("12ecd457d62329e9d4e593de904a457d"); /** * the above MD5 was calculated from running the following command: @@ -116,7 +116,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalGenotypeROD() { List md5 = new ArrayList(); - md5.add("4df6a9c9d09a7bf034f29db24fb7a923"); + md5.add("cbe45debc69e83d2b90988ee72042074"); /** * the above MD5 was calculated after running the following command: * @@ -150,7 +150,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalMarksGenotypingExample() { List md5 = new ArrayList(); - md5.add("f79448f380cfb56be3585547b794a48c"); + md5.add("2694cf3eb73a9fecdda8cf5b76d0135d"); /** * Run with the following commands: * @@ -177,7 +177,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalRuntimeWithLotsOfIntervals() { List md5 = new ArrayList(); - md5.add("4d01485ed2d3cb5edbff24cc0c05b205"); + md5.add("6a90341517fc3c5026529301d9970c7b"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T VariantEval -R " + oneKGLocation + "reference/human_b36_both.fasta " + "-B eval,Variants," + validationDataLocation + "NA12878.pilot_3.all.geli.calls " + @@ -193,11 +193,11 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testVCFVariantEvals() { HashMap md5 = new HashMap(); - md5.put("", "9702cba801cf216324607c8ecb7871e4"); - md5.put("-A", "e9e02eba2e3423bde18ddb0a33a50e34"); - md5.put("-A --includeFilteredRecords", "f0cb51e2c7917e502ca510cc9a3382a9"); - md5.put("-A --sampleName NA12878", "b936723b0de69ed2698ab2af4b70a1e8"); - md5.put("-A -vcfInfoSelector AF=0.50", "a8299c6ba370bf9334327ec03e8885b7"); + md5.put("", "a1c5c8e9b185108969528e8c9fbef15e"); + md5.put("-A", "2ae1456de2375502689c4af8f40b8693"); + md5.put("-A --includeFilteredRecords", "9b2f446f0f42ab10d9d27f5221748f5e"); + md5.put("-A --sampleName NA12878", "38deda8ab3816f083f0aeb97ccf8c347"); + md5.put("-A -vcfInfoSelector AF=0.50", "715ea2da250f58aa35004386a890f5ba"); for ( Map.Entry e : md5.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableTest.java index 08d32d71c..cebeaf484 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableTest.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.utils.genotype.Genotype; import org.broadinstitute.sting.utils.genotype.BasicGenotype; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Pair; -import org.broadinstitute.sting.playground.gatk.walkers.varianteval.ConcordanceTruthTable; +import org.broadinstitute.sting.gatk.walkers.varianteval.ConcordanceTruthTable; import org.broadinstitute.sting.BaseTest; import java.util.List;