From 7a8b85dd15130cca5a5e51e62b70e440ebe7e612 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 24 Nov 2010 05:00:41 +0000 Subject: [PATCH] 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 --- .../sting/gatk/walkers/filters/VariantFiltrationWalker.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index e8d6bc76c..136285d3f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -211,8 +211,10 @@ public class VariantFiltrationWalker extends RodWalker { 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;