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Bug fix for mask RodBinding

This commit is contained in:
Mark DePristo 2011-08-03 14:58:18 -04:00
parent b25140db83
commit 38efd3066c
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -55,6 +55,9 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Input(fullName="mask", doc="Input ROD mask", required=false)
public RodBinding<Feature> mask = RodBinding.makeUnbound(Feature.class);
@Output(doc="File to which variants should be written", required=true)
protected VCFWriter writer = null;
@ -77,8 +80,6 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
protected Integer MASK_EXTEND = 0;
@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";
@Input(fullName="mask", doc="Input ROD mask", required=false)
public RodBinding<Feature> 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;