From cab426f86f667271ac81f302c74828978c138fc3 Mon Sep 17 00:00:00 2001 From: kiran Date: Mon, 31 Jan 2011 17:42:08 +0000 Subject: [PATCH] VariantEval 3.0 is now in core. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5139 348d0f76-0448-11de-a6fe-93d51630548a --- .../varianteval/VariantEvalWalker.java} | 24 +++++++++---------- .../evaluators/CompEvalGenotypes.java | 2 +- .../varianteval}/evaluators/CompOverlap.java | 6 ++--- .../evaluators/CountVariants.java | 6 ++--- .../evaluators/GenotypeConcordance.java | 8 +++---- .../evaluators/GenotypePhasingEvaluator.java | 18 +++++++------- .../evaluators/IndelLengthHistogram.java | 6 ++--- .../evaluators/IndelMetricsByAC.java | 10 ++++---- .../evaluators/IndelStatistics.java | 10 ++++---- .../MendelianViolationEvaluator.java | 10 ++++---- .../varianteval}/evaluators/PhaseStats.java | 2 +- .../evaluators/PrintMissingComp.java | 6 ++--- .../evaluators/SamplePreviousGenotypes.java | 2 +- .../evaluators/SimpleMetricsByAC.java | 16 ++++++------- .../varianteval}/evaluators/StandardEval.java | 2 +- .../evaluators/ThetaVariantEvaluator.java | 6 ++--- .../evaluators/TiTvVariantEvaluator.java | 6 ++--- .../evaluators/VariantEvaluator.java | 10 ++++---- .../evaluators/VariantQualityScore.java | 6 ++--- .../varianteval}/stratifications/CompRod.java | 2 +- .../varianteval}/stratifications/CpG.java | 2 +- .../stratifications/Degeneracy.java | 2 +- .../varianteval}/stratifications/EvalRod.java | 2 +- .../varianteval}/stratifications/Filter.java | 2 +- .../stratifications/FunctionalClass.java | 2 +- .../stratifications/JexlExpression.java | 2 +- .../varianteval}/stratifications/Novelty.java | 2 +- .../RequiredStratification.java | 3 +++ .../varianteval}/stratifications/Sample.java | 6 ++--- .../StandardStratification.java | 4 ++++ .../stratifications/VariantStratifier.java | 2 +- .../walkers/varianteval}/tags/Analysis.java | 2 +- .../walkers/varianteval}/tags/DataPoint.java | 2 +- .../walkers/varianteval}/tags/Param.java | 2 +- .../util/AnalysisModuleScanner.java | 8 +++---- .../varianteval}/util/ComplexDataUtils.java | 2 +- .../util/NewEvaluationContext.java | 10 ++++---- .../walkers/varianteval}/util/StateKey.java | 2 +- .../RequiredStratification.java | 3 --- .../StandardStratification.java | 4 ---- 40 files changed, 110 insertions(+), 112 deletions(-) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java => gatk/walkers/varianteval/VariantEvalWalker.java} (96%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/CompEvalGenotypes.java (90%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/CompOverlap.java (92%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/CountVariants.java (95%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/GenotypeConcordance.java (98%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/GenotypePhasingEvaluator.java (95%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/IndelLengthHistogram.java (93%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/IndelMetricsByAC.java (94%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/IndelStatistics.java (97%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/MendelianViolationEvaluator.java (94%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/PhaseStats.java (95%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/PrintMissingComp.java (90%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/SamplePreviousGenotypes.java (91%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/SimpleMetricsByAC.java (89%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/StandardEval.java (90%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/ThetaVariantEvaluator.java (95%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/TiTvVariantEvaluator.java (89%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/VariantEvaluator.java (81%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/evaluators/VariantQualityScore.java (97%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/stratifications/CompRod.java (92%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/stratifications/CpG.java (95%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/stratifications/Degeneracy.java (97%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/stratifications/EvalRod.java (92%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/stratifications/Filter.java (93%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/stratifications/FunctionalClass.java (96%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/stratifications/JexlExpression.java (94%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/stratifications/Novelty.java (93%) create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/stratifications/Sample.java (81%) create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/stratifications/VariantStratifier.java (91%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/tags/Analysis.java (77%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/tags/DataPoint.java (73%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/tags/Param.java (88%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/util/AnalysisModuleScanner.java (92%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/util/ComplexDataUtils.java (98%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/util/NewEvaluationContext.java (86%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/newvarianteval => gatk/walkers/varianteval}/util/StateKey.java (88%) delete mode 100755 java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/RequiredStratification.java delete mode 100755 java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/StandardStratification.java diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index c062dbe22..f8af762e1 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.VCFConstants; @@ -17,18 +17,18 @@ import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.Window; +import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.StandardEval; +import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; +import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.RequiredStratification; +import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.StandardStratification; +import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.AnalysisModuleScanner; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey; import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche; import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators.StandardEval; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators.VariantEvaluator; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications.RequiredStratification; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications.StandardStratification; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications.VariantStratifier; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.AnalysisModuleScanner; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.NewEvaluationContext; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.StateKey; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.classloader.PluginManager; @@ -46,7 +46,7 @@ import java.util.*; * General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ts/Tv ratios, and a lot more) */ @Reference(window=@Window(start=-50, stop=50)) -public class NewVariantEvalWalker extends RodWalker implements TreeReducible { +public class VariantEvalWalker extends RodWalker implements TreeReducible { // Output arguments @Output protected PrintStream out; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CompEvalGenotypes.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java similarity index 90% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CompEvalGenotypes.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java index e08b8555c..00c997a67 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CompEvalGenotypes.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.Genotype; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CompOverlap.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java similarity index 92% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CompOverlap.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java index d96a135a1..0097395ff 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CompOverlap.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java @@ -1,12 +1,12 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; /** * The Broad Institute diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CountVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CountVariants.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java index bb357da5a..6340ab813 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CountVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java @@ -1,12 +1,12 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @Analysis(description = "Counts different classes of variants in the sample") diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java index da54034ab..26fa3baab 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java @@ -1,16 +1,14 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.apache.commons.lang.ArrayUtils; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.refdata.*; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.NewEvaluationContext; import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.apache.log4j.Logger; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypePhasingEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypePhasingEvaluator.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java index e71e2a458..a2b548404 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypePhasingEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.apache.log4j.Logger; import org.broad.tribble.util.variantcontext.Genotype; @@ -9,10 +9,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.phasing.AllelePair; import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.NewEvaluationContext; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.report.utils.TableType; @@ -59,7 +59,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator { double minPhaseQuality = 10.0; - public void initialize(NewVariantEvalWalker walker) { + public void initialize(VariantEvalWalker walker) { this.samplePhasingStatistics = new SamplePhasingStatistics(walker.getMinPhaseQuality()); this.samplePrevGenotypes = new SamplePreviousGenotypes(); } @@ -253,9 +253,9 @@ public class GenotypePhasingEvaluator extends VariantEvaluator { sb = new StringBuilder(); } - public void addReason(String category, String sample, VariantEvalWalker.EvaluationContext evalGroup, GenomeLoc prevLoc, String reason) { - sb.append(category + "(" + sample + ", previous: " + prevLoc + " [" + evalGroup.compTrackName + ", " + evalGroup.evalTrackName + "]): " + reason + ";"); - } +// public void addReason(String category, String sample, VariantEvalWalker.EvaluationContext evalGroup, GenomeLoc prevLoc, String reason) { +// sb.append(category + "(" + sample + ", previous: " + prevLoc + " [" + evalGroup.compTrackName + ", " + evalGroup.evalTrackName + "]): " + reason + ";"); +// } public String toString() { if (sb.length() == 0) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelLengthHistogram.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java similarity index 93% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelLengthHistogram.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java index 7c3f55825..840b94a15 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelLengthHistogram.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -1,12 +1,12 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.report.utils.TableType; /** diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java similarity index 94% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelMetricsByAC.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java index b98413af3..82c95a4ba 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelMetricsByAC.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java @@ -1,13 +1,13 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.report.utils.TableType; import java.util.ArrayList; @@ -50,7 +50,7 @@ public class IndelMetricsByAC extends VariantEvaluator { int numSamples = 0; - public void initialize(NewVariantEvalWalker walker) { + public void initialize(VariantEvalWalker walker) { numSamples = walker.getNumSamples(); } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelStatistics.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelStatistics.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java index 1dd5c2237..03fa2f7c6 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelStatistics.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java @@ -1,13 +1,13 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.report.utils.TableType; import java.util.Arrays; @@ -48,7 +48,7 @@ public class IndelStatistics extends VariantEvaluator { int numSamples = 0; - public void initialize(NewVariantEvalWalker walker) { + public void initialize(VariantEvalWalker walker) { numSamples = walker.getNumSamples(); } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java similarity index 94% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/MendelianViolationEvaluator.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index 01b711d7b..1eee21fe5 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/MendelianViolationEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype; @@ -6,9 +6,9 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.List; @@ -84,7 +84,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator { } // todo: fix - public void initialize(NewVariantEvalWalker walker) { + public void initialize(VariantEvalWalker walker) { trio = parseTrioDescription(walker.getFamilyStructure()); mendelianViolationQualThreshold = walker.getMendelianViolationQualThreshold(); } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/PhaseStats.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PhaseStats.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/PhaseStats.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PhaseStats.java index 50addd946..ab1f410f9 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/PhaseStats.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PhaseStats.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; /** * Created by IntelliJ IDEA. User: kiran Date: Nov 29, 2010 Time: 3:25:59 PM To change this template use File | Settings diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/PrintMissingComp.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java similarity index 90% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/PrintMissingComp.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java index 616b1a30c..3085e358c 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/PrintMissingComp.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java @@ -22,14 +22,14 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; @Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites") public class PrintMissingComp extends VariantEvaluator { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/SamplePreviousGenotypes.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java similarity index 91% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/SamplePreviousGenotypes.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java index 100f374b4..c1ba8cccb 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/SamplePreviousGenotypes.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.Genotype; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/SimpleMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java similarity index 89% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/SimpleMetricsByAC.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java index 0a24f829e..bf1c54c3b 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/SimpleMetricsByAC.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java @@ -1,16 +1,16 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications.Degeneracy; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications.Sample; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.StateKey; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Degeneracy; +import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Sample; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey; import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -128,7 +128,7 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval } } - public void initialize(NewVariantEvalWalker walker) { + public void initialize(VariantEvalWalker walker) { numSamples = walker.getNumSamples(); metrics = new MetricsByAc(2*numSamples); } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/StandardEval.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java similarity index 90% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/StandardEval.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java index 787def0d0..ae2060776 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/StandardEval.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java @@ -23,6 +23,6 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; public interface StandardEval {} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/ThetaVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/ThetaVariantEvaluator.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index 676d62183..0d4f4df77 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/ThetaVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype; @@ -6,8 +6,8 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ConcurrentMap; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/TiTvVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java similarity index 89% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/TiTvVariantEvaluator.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index 52fbe5cc9..5ab6d7741 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/TiTvVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -1,12 +1,12 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; @Analysis(description = "Ti/Tv Variant Evaluator") public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/VariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java similarity index 81% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/VariantEvaluator.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java index 8593a0d5c..2180bb732 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/VariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java @@ -1,15 +1,15 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.NewEvaluationContext; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.StateKey; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey; public abstract class VariantEvaluator { - public void initialize(NewVariantEvalWalker walker) {} + public void initialize(VariantEvalWalker walker) {} public abstract boolean enabled(); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/VariantQualityScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/VariantQualityScore.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java index e6b53e3b2..f79211d62 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/VariantQualityScore.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.VariantContext; @@ -32,8 +32,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.report.utils.TableType; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/CompRod.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java similarity index 92% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/CompRod.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java index 622fb8569..ab423bc86 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/CompRod.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/CpG.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/CpG.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java index 3763519aa..98da6a3b9 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/CpG.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Degeneracy.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Degeneracy.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java index 92d67df94..0cc7b91ae 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Degeneracy.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/EvalRod.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java similarity index 92% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/EvalRod.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java index b6a3d6ebf..16e4aa8cc 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/EvalRod.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Filter.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java similarity index 93% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Filter.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java index 3a58b2675..718f73831 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Filter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/FunctionalClass.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/FunctionalClass.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java index 9eb73d99f..a86bdf861 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/FunctionalClass.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/JexlExpression.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java similarity index 94% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/JexlExpression.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java index b521d65ce..842b2a1eb 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/JexlExpression.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Novelty.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java similarity index 93% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Novelty.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java index 330b3236d..5d0422a39 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Novelty.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java new file mode 100755 index 000000000..60e6f714f --- /dev/null +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java @@ -0,0 +1,3 @@ +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; + +public interface RequiredStratification {} diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Sample.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java similarity index 81% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Sample.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java index 02fb2b165..d30484f6d 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Sample.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java @@ -1,9 +1,9 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import java.util.ArrayList; import java.util.Set; @@ -15,7 +15,7 @@ public class Sample extends VariantStratifier { @Override public void initialize(Set jexlExpressions, Set compNames, Set knownNames, Set evalNames, Set sampleNames) { samples = new ArrayList(); - samples.add(NewVariantEvalWalker.ALL_SAMPLE_NAME); + samples.add(VariantEvalWalker.ALL_SAMPLE_NAME); samples.addAll(sampleNames); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java new file mode 100755 index 000000000..9ea399859 --- /dev/null +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java @@ -0,0 +1,4 @@ +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; + +public interface StandardStratification { +} diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/VariantStratifier.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java similarity index 91% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/VariantStratifier.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java index 8eb88dfaf..c3fccd1b8 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/VariantStratifier.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/Analysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java similarity index 77% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/Analysis.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java index 8e6a6f682..129d5a95d 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/Analysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags; +package org.broadinstitute.sting.gatk.walkers.varianteval.tags; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/DataPoint.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java similarity index 73% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/DataPoint.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java index abdce9736..3ba448049 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/DataPoint.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags; +package org.broadinstitute.sting.gatk.walkers.varianteval.tags; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/Param.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Param.java similarity index 88% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/Param.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Param.java index 3c3fb91a2..544dfae0a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/Param.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Param.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags; +package org.broadinstitute.sting.gatk.walkers.varianteval.tags; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/AnalysisModuleScanner.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java similarity index 92% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/AnalysisModuleScanner.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java index fa6d2bee1..e7179427b 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/AnalysisModuleScanner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java @@ -21,11 +21,11 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util; +package org.broadinstitute.sting.gatk.walkers.varianteval.util; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Param; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Param; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.annotation.Annotation; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/ComplexDataUtils.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/ComplexDataUtils.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/ComplexDataUtils.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/ComplexDataUtils.java index 7f74abcd6..aa8dfcc10 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/ComplexDataUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/ComplexDataUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util; +package org.broadinstitute.sting.gatk.walkers.varianteval.util; import java.lang.reflect.Field; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/NewEvaluationContext.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java similarity index 86% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/NewEvaluationContext.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java index 23aebff99..3d76ffb4a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/NewEvaluationContext.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java @@ -1,12 +1,12 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util; +package org.broadinstitute.sting.gatk.walkers.varianteval.util; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators.VariantEvaluator; -import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications.VariantStratifier; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; +import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; @@ -27,7 +27,7 @@ public class NewEvaluationContext extends HashMap { return value; } - public void addEvaluationClassList(NewVariantEvalWalker walker, StateKey stateKey, Set> evaluationClasses) { + public void addEvaluationClassList(VariantEvalWalker walker, StateKey stateKey, Set> evaluationClasses) { evaluationInstances = new TreeMap(); for ( Class c : evaluationClasses ) { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/StateKey.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/StateKey.java similarity index 88% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/StateKey.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/StateKey.java index 2c61b7163..2cccb0d35 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/StateKey.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/StateKey.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util; +package org.broadinstitute.sting.gatk.walkers.varianteval.util; import java.util.TreeMap; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/RequiredStratification.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/RequiredStratification.java deleted file mode 100755 index d6213f3c6..000000000 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/RequiredStratification.java +++ /dev/null @@ -1,3 +0,0 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; - -public interface RequiredStratification {} diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/StandardStratification.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/StandardStratification.java deleted file mode 100755 index e4b58c739..000000000 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/StandardStratification.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications; - -public interface StandardStratification { -}