From 5bd99fc1c4461f5ba4f85933f7476c6f5c43925b Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 3 Sep 2009 15:41:41 +0000 Subject: [PATCH] VariantFiltration moved to core. Another win for the team. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1517 348d0f76-0448-11de-a6fe-93d51630548a --- .../variants => gatk/walkers/filters}/IVFBinomialStrand.java | 2 +- .../gatk/walkers/variants => gatk/walkers/filters}/IVFNull.java | 2 +- .../variants => gatk/walkers/filters}/IVFPrimaryBases.java | 2 +- .../variants => gatk/walkers/filters}/IVFSecondaryBases.java | 2 +- .../walkers/filters}/IndependentVariantFeature.java | 2 +- .../walkers/variants => gatk/walkers/filters}/RatioFilter.java | 2 +- .../variants => gatk/walkers/filters}/VECAlleleBalance.java | 2 +- .../variants => gatk/walkers/filters}/VECClusteredSnps.java | 2 +- .../variants => gatk/walkers/filters}/VECDepthOfCoverage.java | 2 +- .../variants => gatk/walkers/filters}/VECFisherStrand.java | 2 +- .../variants => gatk/walkers/filters}/VECHomopolymer.java | 2 +- .../variants => gatk/walkers/filters}/VECIndelArtifact.java | 2 +- .../variants => gatk/walkers/filters}/VECLodThreshold.java | 2 +- .../variants => gatk/walkers/filters}/VECMappingQuality.java | 2 +- .../walkers/filters}/VECMappingQualityZero.java | 2 +- .../gatk/walkers/variants => gatk/walkers/filters}/VECNull.java | 2 +- .../walkers/filters}/VECOnOffGenotypeRatio.java | 2 +- .../variants => gatk/walkers/filters}/VariantContextWindow.java | 2 +- .../walkers/filters}/VariantExclusionCriterion.java | 2 +- .../walkers/filters}/VariantFiltrationWalker.java | 2 +- 20 files changed, 20 insertions(+), 20 deletions(-) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/IVFBinomialStrand.java (97%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/IVFNull.java (86%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/IVFPrimaryBases.java (97%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/IVFSecondaryBases.java (98%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/IndependentVariantFeature.java (93%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/RatioFilter.java (98%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECAlleleBalance.java (97%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECClusteredSnps.java (96%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECDepthOfCoverage.java (95%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECFisherStrand.java (99%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECHomopolymer.java (98%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECIndelArtifact.java (95%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECLodThreshold.java (93%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECMappingQuality.java (95%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECMappingQualityZero.java (95%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECNull.java (88%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VECOnOffGenotypeRatio.java (97%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VariantContextWindow.java (98%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VariantExclusionCriterion.java (83%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variants => gatk/walkers/filters}/VariantFiltrationWalker.java (99%) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFBinomialStrand.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFBinomialStrand.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFBinomialStrand.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFBinomialStrand.java index 65fecd298..51bea790b 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFBinomialStrand.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFBinomialStrand.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.VariantContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFNull.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFNull.java similarity index 86% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFNull.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFNull.java index d51ae9e94..7ddbea3c8 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFNull.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFNull.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; public class IVFNull implements IndependentVariantFeature { public void initialize(String arguments) {} diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFPrimaryBases.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFPrimaryBases.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFPrimaryBases.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFPrimaryBases.java index 8d89bb919..8dc5636ea 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFPrimaryBases.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFPrimaryBases.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.utils.MathUtils; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFSecondaryBases.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFSecondaryBases.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFSecondaryBases.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFSecondaryBases.java index 3ffaa5f77..f4d0f54ae 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFSecondaryBases.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFSecondaryBases.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.utils.MathUtils; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IndependentVariantFeature.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/IndependentVariantFeature.java similarity index 93% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IndependentVariantFeature.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/IndependentVariantFeature.java index 82919e081..f9fd63c75 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IndependentVariantFeature.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/IndependentVariantFeature.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; /** * Interface for conditionally independent variant features. diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java index b3235dd73..4e54caa0a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.refdata.rodVariants; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECAlleleBalance.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECAlleleBalance.java index c7024dd02..8966abba7 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECAlleleBalance.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.refdata.rodVariants; import org.broadinstitute.sting.utils.ReadBackedPileup; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECClusteredSnps.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECClusteredSnps.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECClusteredSnps.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECClusteredSnps.java index 6e53c9a84..d1ad57ba0 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECClusteredSnps.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECClusteredSnps.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECDepthOfCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECDepthOfCoverage.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECDepthOfCoverage.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECDepthOfCoverage.java index 551f1ce27..56e0f0693 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECDepthOfCoverage.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECDepthOfCoverage.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.VariantContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECFisherStrand.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECFisherStrand.java index 66e4642dd..7d7fbfc99 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECFisherStrand.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.VariantContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECHomopolymer.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECHomopolymer.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECHomopolymer.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECHomopolymer.java index 6f025b3a7..28b8528c5 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECHomopolymer.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECHomopolymer.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.VariantContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECIndelArtifact.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECIndelArtifact.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECIndelArtifact.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECIndelArtifact.java index 0496d0d48..e8166411a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECIndelArtifact.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECIndelArtifact.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.refdata.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECLodThreshold.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECLodThreshold.java similarity index 93% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECLodThreshold.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECLodThreshold.java index 9010eb494..b376c47a3 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECLodThreshold.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECLodThreshold.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.VariantContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQuality.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECMappingQuality.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQuality.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECMappingQuality.java index 56179722f..5afe79b48 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQuality.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECMappingQuality.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.utils.MathUtils; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQualityZero.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECMappingQualityZero.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQualityZero.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECMappingQualityZero.java index d8fc22ce5..8b6c15abc 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQualityZero.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECMappingQualityZero.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.VariantContext; import net.sf.samtools.SAMRecord; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECNull.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECNull.java similarity index 88% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECNull.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECNull.java index 3889bdcc0..3f2397f24 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECNull.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECNull.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; public class VECNull implements VariantExclusionCriterion { public void initialize(String arguments) { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECOnOffGenotypeRatio.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VECOnOffGenotypeRatio.java index 54d0e1bec..594f4d3a0 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECOnOffGenotypeRatio.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.refdata.rodVariants; import org.broadinstitute.sting.utils.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantContextWindow.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantContextWindow.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantContextWindow.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantContextWindow.java index d70220715..d248c9364 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantContextWindow.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantContextWindow.java @@ -23,7 +23,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.utils.StingException; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantExclusionCriterion.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantExclusionCriterion.java similarity index 83% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantExclusionCriterion.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantExclusionCriterion.java index 959a27395..2d2f5b174 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantExclusionCriterion.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantExclusionCriterion.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; public interface VariantExclusionCriterion { public void initialize(String arguments); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 7645bc840..274ee48a9 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variants; +package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.refdata.*;