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When evaluating JEXL expressions, on't blow up if the eval VC is null 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5085 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-01-26 18:25:03 +00:00
parent 22e599ec76
commit a9d0772516
2 changed files with 2 additions and 2 deletions
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1
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java
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@ -461,6 +461,7 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
* @param trackNames the list of track names to process * @param trackNames the list of track names to process
* @param sampleNames the list of samples to include * @param sampleNames the list of samples to include
* @param allowableTypes a set of allowable variation types * @param allowableTypes a set of allowable variation types
* @param byFilter if false, only accept PASSing VariantContexts. Otherwise, accept both PASSing and filtered sites
* @return a mapping of track names to a list of VariantContext objects * @return a mapping of track names to a list of VariantContext objects
*/ */
private HashMap<String, HashMap<String, VariantContext>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> trackNames, Set<String> sampleNames, EnumSet<VariantContext.Type> allowableTypes, boolean byFilter) { private HashMap<String, HashMap<String, VariantContext>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> trackNames, Set<String> sampleNames, EnumSet<VariantContext.Type> allowableTypes, boolean byFilter) {

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/JexlExpression.java
View File

@ -32,8 +32,7 @@ public class JexlExpression extends VariantStratifier implements StandardStratif
relevantStates.add("none"); relevantStates.add("none");
for ( VariantContextUtils.JexlVCMatchExp jexlExpression : jexlExpressions ) { for ( VariantContextUtils.JexlVCMatchExp jexlExpression : jexlExpressions ) {
System.out.println(jexlExpression.name + " " + jexlExpression.exp.getExpression()); if (eval != null && VariantContextUtils.match(eval, jexlExpression)) {
if (VariantContextUtils.match(eval, jexlExpression)) {
relevantStates.add(jexlExpression.name); relevantStates.add(jexlExpression.name);
} }
} }