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Putting my changes from earlier in the day back in after someone (rhymes with 'Dark') trounced on them with his last commit... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4687 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-11-16 01:55:50 +00:00
parent 8ff4e4cb25
commit f1b0f3bc49
1 changed files with 6 additions and 3 deletions
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9
java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
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@ -92,11 +92,14 @@ public class AnnotatorInputTableCodec implements ReferenceDependentFeatureCodec<
GenomeLoc loc; GenomeLoc loc;
String chr = st.nextToken(); String chr = st.nextToken();
if ( chr.indexOf(":") != -1 ) if ( chr.indexOf(":") != -1 ) {
loc = genomeLocParser.parseGenomeInterval(chr); loc = genomeLocParser.parseGenomeInterval(chr);
else } else {
if ( st.countTokens() < 3 )
throw new CodecLineParsingException("Couldn't parse GenomeLoc out of the following line because there aren't enough tokens.\nLine: " + line);
loc = genomeLocParser.createGenomeLoc(chr, Integer.valueOf(st.nextToken()), Integer.valueOf(st.nextToken())); loc = genomeLocParser.createGenomeLoc(chr, Integer.valueOf(st.nextToken()), Integer.valueOf(st.nextToken()));
return new AnnotatorInputTableFeature(loc.getContig(), (int)loc.getStart(), (int)loc.getStop()); }
return new AnnotatorInputTableFeature(loc.getContig(), loc.getStart(), loc.getStop());
} }