From 8ab4704b4ce1c0251b584f0ae5b0cd64d15f734b Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 16 Dec 2010 05:18:12 +0000 Subject: [PATCH] Adding a command-line argument to allow missing values to evaluate as false instead of true git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4854 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/filters/VariantFiltrationWalker.java | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) 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 2e1cb17b1..0d8b99d48 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -72,6 +72,9 @@ public class VariantFiltrationWalker extends RodWalker { @Argument(fullName="maskName", shortName="mask", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']", required=false) protected String MASK_NAME = "Mask"; + @Argument(fullName="missingValuesInExpressionsShouldEvaluateAsFailing", doc="When evaluating the JEXL expressions, should missing values be considered failing the expression (by default they are considered passing)?", required=false) + protected Boolean FAIL_MISSING_VALUES = false; + // JEXL expressions for the filters List filterExps; List genotypeFilterExps; @@ -221,7 +224,11 @@ public class VariantFiltrationWalker extends RodWalker { 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 + } catch (Exception e) { + // do nothing unless specifically asked to; it just means that the expression isn't defined for this context + if ( FAIL_MISSING_VALUES ) + filters.add(exp.name); + } } VariantContext filteredVC;