diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 4eaed4840..cad3569e5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -55,6 +55,9 @@ public class VariantFiltrationWalker extends RodWalker { @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; + @Input(fullName="mask", doc="Input ROD mask", required=false) + public RodBinding 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 { 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 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;