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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
This commit is contained in:
kiran 2011-01-31 17:42:08 +00:00
parent c59b2a8296
commit cab426f86f
40 changed files with 110 additions and 112 deletions
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24
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -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<Integer, Integer> implements TreeReducible<Integer> {
public class VariantEvalWalker extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
// Output arguments
@Output
protected PrintStream out;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CompEvalGenotypes.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
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@ -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;

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CompOverlap.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
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@ -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

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/CountVariants.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
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@ -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")

8
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
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@ -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;

18
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypePhasingEvaluator.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
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@ -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)

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelLengthHistogram.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
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@ -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;
/**

10
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelMetricsByAC.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
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@ -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();
}

10
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/IndelStatistics.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
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@ -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();
}

10
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/MendelianViolationEvaluator.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
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@ -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();
}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/PhaseStats.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PhaseStats.java
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@ -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

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/PrintMissingComp.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
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@ -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 {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/SamplePreviousGenotypes.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
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@ -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;

16
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/SimpleMetricsByAC.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
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@ -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);
}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/StandardEval.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java
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@ -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 {}

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/ThetaVariantEvaluator.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
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@ -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;

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/TiTvVariantEvaluator.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
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@ -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 {

10
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/VariantEvaluator.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
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@ -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();

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/VariantQualityScore.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/CompRod.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/CpG.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Degeneracy.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/EvalRod.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Filter.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/FunctionalClass.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/JexlExpression.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Novelty.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
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@ -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;

3
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java 100755
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@ -0,0 +1,3 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
public interface RequiredStratification {}

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/Sample.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
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@ -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<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
samples = new ArrayList<String>();
samples.add(NewVariantEvalWalker.ALL_SAMPLE_NAME);
samples.add(VariantEvalWalker.ALL_SAMPLE_NAME);
samples.addAll(sampleNames);
}

4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java 100755
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@ -0,0 +1,4 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
public interface StandardStratification {
}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/VariantStratifier.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/Analysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/DataPoint.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/tags/Param.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Param.java
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@ -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;

8
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/AnalysisModuleScanner.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
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@ -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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/ComplexDataUtils.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/ComplexDataUtils.java
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@ -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;

10
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/NewEvaluationContext.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
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@ -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<VariantStratifier, String> {
return value;
}
public void addEvaluationClassList(NewVariantEvalWalker walker, StateKey stateKey, Set<Class<? extends VariantEvaluator>> evaluationClasses) {
public void addEvaluationClassList(VariantEvalWalker walker, StateKey stateKey, Set<Class<? extends VariantEvaluator>> evaluationClasses) {
evaluationInstances = new TreeMap<String, VariantEvaluator>();
for ( Class<? extends VariantEvaluator> c : evaluationClasses ) {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/StateKey.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/StateKey.java
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@ -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;

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/RequiredStratification.java
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@ -1,3 +0,0 @@
package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications;
public interface RequiredStratification {}

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/StandardStratification.java
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@ -1,4 +0,0 @@
package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications;
public interface StandardStratification {
}