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Added getIntegerAttribute() 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4697 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2010-11-17 16:33:07 +00:00
parent d492eb94ad
commit e2f7f33ce7
1 changed files with 13 additions and 0 deletions
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13
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -982,6 +982,19 @@ public class VariantContextUtils {
} }
} }
public static Integer getIntegerAttribute(Map<String, Object> 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) { private static boolean mergeIntoMNPvalidationCheck(GenomeLocParser genomeLocParser,VariantContext vc1, VariantContext vc2) {
GenomeLoc loc1 = VariantContextUtils.getLocation(genomeLocParser,vc1); GenomeLoc loc1 = VariantContextUtils.getLocation(genomeLocParser,vc1);
GenomeLoc loc2 = VariantContextUtils.getLocation(genomeLocParser,vc2); GenomeLoc loc2 = VariantContextUtils.getLocation(genomeLocParser,vc2);