diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java index 87c636a8b..2c6afaa04 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java @@ -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.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java index 319a58a6f..867972f71 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java @@ -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.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java index 274a447cd..f43059d13 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java @@ -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.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java index 1fab3ccc0..a53d1d87b 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java @@ -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.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java index 561086f15..fb8f6ef3c 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java @@ -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.ReferenceContext; @@ -86,9 +86,9 @@ public class VariantEval2Walker extends RodWalker { private class EvaluationContext extends HashMap> { // useful for typing 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.contextName = contextName; this.selectExp = selectExp; @@ -117,11 +117,11 @@ public class VariantEval2Walker extends RodWalker { public void initialize() { determineAllEvalations(); - List selectExps = VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS); + List selectExps = VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS); for ( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) { 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() + ".all", null); @@ -171,7 +171,7 @@ public class VariantEval2Walker extends RodWalker { 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); for ( String filteredName : Arrays.asList(RAW_SET_NAME, RETAINED_SET_NAME, FILTERED_SET_NAME) ) { @@ -288,7 +288,7 @@ public class VariantEval2Walker extends RodWalker { if ( rodList != null ) { for ( ReferenceOrderedDatum rec : rodList.getRecords() ) { if ( rec.getLocation().getStart() == context.getLocation().getStart() ) { - VariantContext vc = VariantContextAdaptors.convertToVariantContext(name, rec); + VariantContext vc = VariantContextAdaptors.toVariantContext(name, rec); if ( vc != null ) { return vc; } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java index 522d1a538..289aab923 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java @@ -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.gatk.refdata.RefMetaDataTracker; @@ -15,7 +15,7 @@ import java.util.ArrayList; * Time: 3:38:02 PM * To change this template use File | Settings | File Templates. */ -public abstract class VariantEvaluator { +abstract class VariantEvaluator { protected boolean accumulateInterestingSites = false, printInterestingSites = false; protected String interestingSitePrefix = null; protected boolean processedASite = false;