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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
This commit is contained in:
ebanks 2010-12-16 05:18:12 +00:00
parent 9f3e56e487
commit 8ab4704b4c
1 changed files with 8 additions and 1 deletions
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9
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -72,6 +72,9 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
@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) @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"; 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 // JEXL expressions for the filters
List<VariantContextUtils.JexlVCMatchExp> filterExps; List<VariantContextUtils.JexlVCMatchExp> filterExps;
List<VariantContextUtils.JexlVCMatchExp> genotypeFilterExps; List<VariantContextUtils.JexlVCMatchExp> genotypeFilterExps;
@ -221,7 +224,11 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
try { try {
if ( VariantContextUtils.match(vc, exp) ) if ( VariantContextUtils.match(vc, exp) )
filters.add(exp.name); 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; VariantContext filteredVC;