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Catch the JEXL exception when trying to match a variable that's not in the context - and don't filter in these cases. Now everyone can happily go back to using the stupid (and hopefully temporary) AlleleBalance filter. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4727 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-11-24 05:00:41 +00:00
parent caf2c21f61
commit 7a8b85dd15
1 changed files with 4 additions and 2 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -211,8 +211,10 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
filters.add(CLUSTERED_SNP_FILTER_NAME);
for ( VariantContextUtils.JexlVCMatchExp exp : filterExps ) {
if ( VariantContextUtils.match(vc, exp) )
filters.add(exp.name);
try {
if ( VariantContextUtils.match(vc, exp) )
filters.add(exp.name);
} catch (Exception e) {} // do nothing; it just means that the expression isn't defined for this context
}
VariantContext filteredVC;