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updating back names 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2786 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-02-05 13:53:45 +00:00
parent 777617b6c7
commit e0af3bf761
6 changed files with 13 additions and 13 deletions
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2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext.varianteval2; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext.varianteval2; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext.varianteval2; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext.varianteval2; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

14
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext.varianteval2; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -86,9 +86,9 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
private class EvaluationContext extends HashMap<String, Set<VariantEvaluator>> { private class EvaluationContext extends HashMap<String, Set<VariantEvaluator>> {
// useful for typing // useful for typing
public String trackName, contextName; public String trackName, contextName;
VariantContextUtils.MatchExp selectExp; VariantContextUtils.JexlVCMatchExp selectExp;
public EvaluationContext(String trackName, String contextName, VariantContextUtils.MatchExp selectExp) { public EvaluationContext(String trackName, String contextName, VariantContextUtils.JexlVCMatchExp selectExp) {
this.trackName = trackName; this.trackName = trackName;
this.contextName = contextName; this.contextName = contextName;
this.selectExp = selectExp; this.selectExp = selectExp;
@ -117,11 +117,11 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
public void initialize() { public void initialize() {
determineAllEvalations(); determineAllEvalations();
List<VariantContextUtils.MatchExp> selectExps = VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS); List<VariantContextUtils.JexlVCMatchExp> selectExps = VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS);
for ( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) { for ( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) {
if ( d.getName().startsWith("eval") ) { if ( d.getName().startsWith("eval") ) {
for ( VariantContextUtils.MatchExp e : selectExps ) { for ( VariantContextUtils.JexlVCMatchExp e : selectExps ) {
addNewContext(d.getName(), d.getName() + "." + e.name, e); addNewContext(d.getName(), d.getName() + "." + e.name, e);
} }
addNewContext(d.getName(), d.getName() + ".all", null); addNewContext(d.getName(), d.getName() + ".all", null);
@ -171,7 +171,7 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
return evals; return evals;
} }
private void addNewContext(String trackName, String contextName, VariantContextUtils.MatchExp selectExp) { private void addNewContext(String trackName, String contextName, VariantContextUtils.JexlVCMatchExp selectExp) {
EvaluationContext group = new EvaluationContext(trackName, contextName, selectExp); EvaluationContext group = new EvaluationContext(trackName, contextName, selectExp);
for ( String filteredName : Arrays.asList(RAW_SET_NAME, RETAINED_SET_NAME, FILTERED_SET_NAME) ) { for ( String filteredName : Arrays.asList(RAW_SET_NAME, RETAINED_SET_NAME, FILTERED_SET_NAME) ) {
@ -288,7 +288,7 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
if ( rodList != null ) { if ( rodList != null ) {
for ( ReferenceOrderedDatum rec : rodList.getRecords() ) { for ( ReferenceOrderedDatum rec : rodList.getRecords() ) {
if ( rec.getLocation().getStart() == context.getLocation().getStart() ) { if ( rec.getLocation().getStart() == context.getLocation().getStart() ) {
VariantContext vc = VariantContextAdaptors.convertToVariantContext(name, rec); VariantContext vc = VariantContextAdaptors.toVariantContext(name, rec);
if ( vc != null ) { if ( vc != null ) {
return vc; return vc;
} }

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.variantcontext.varianteval2; package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext; import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -15,7 +15,7 @@ import java.util.ArrayList;
* Time: 3:38:02 PM * Time: 3:38:02 PM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public abstract class VariantEvaluator { abstract class VariantEvaluator {
protected boolean accumulateInterestingSites = false, printInterestingSites = false; protected boolean accumulateInterestingSites = false, printInterestingSites = false;
protected String interestingSitePrefix = null; protected String interestingSitePrefix = null;
protected boolean processedASite = false; protected boolean processedASite = false;