diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java index ff3a51c92..449c58479 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java @@ -982,6 +982,19 @@ public class VariantContextUtils { } } + public static Integer getIntegerAttribute(Map attribs, String attribName) { + Object val = attribs.get(attribName); + if (val == null || val.equals(VCFConstants.MISSING_VALUE_v4)) + return null; + + try { + return new Integer(val.toString()); + } + catch (Exception e) {// IGNORE unparseable data + return null; + } + } + private static boolean mergeIntoMNPvalidationCheck(GenomeLocParser genomeLocParser,VariantContext vc1, VariantContext vc2) { GenomeLoc loc1 = VariantContextUtils.getLocation(genomeLocParser,vc1); GenomeLoc loc2 = VariantContextUtils.getLocation(genomeLocParser,vc2);