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unfortunately samrecord pileup also uses zero length intervals to indicate deletions; this will have to be a BED specific exception. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4964 348d0f76-0448-11de-a6fe-93d51630548a
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aaron 2011-01-07 22:32:50 +00:00
parent b34e2f733f
commit b24e1134f9
1 changed files with 0 additions and 3 deletions
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3
java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
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@ -75,9 +75,6 @@ public abstract class GATKFeature implements Feature {
} }
public GenomeLoc getLocation() { public GenomeLoc getLocation() {
if (position == null) position = genomeLocParser.createGenomeLoc(feature.getChr(), feature.getStart(), feature.getEnd()); if (position == null) position = genomeLocParser.createGenomeLoc(feature.getChr(), feature.getStart(), feature.getEnd());
if (position.getStart() > position.getStop()) {
throw new UserException.BadInput("A feature produced by the reference metadata track named \"" + this.name + "\" at position " + position + " has a start greater than the stop; this is an invalid this is an invalid position");
}
return position; return position;
} }