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Ensure that active region extensions stay on contig

This commit is contained in:
Joel Thibault 2013-01-02 14:10:55 -05:00
parent dcb7735d3c
commit c515175313
2 changed files with 6 additions and 1 deletions
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5
public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
View File

@ -287,6 +287,11 @@ public final class GenomeLocParser {
return new GenomeLoc(contig, index, start, stop);
}
public GenomeLoc createGenomeLocOnContig(final String contig, final int start, final int stop) {
GenomeLoc contigLoc = createOverEntireContig(contig);
return new GenomeLoc(contig, getContigIndex(contig), start, stop).intersect(contigLoc);
}
/**
* validate a position or interval on the genome as valid
*

2
public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
View File

@ -31,7 +31,7 @@ public class ActiveRegion implements HasGenomeLocation {
this.isActive = isActive;
this.genomeLocParser = genomeLocParser;
this.extension = extension;
extendedLoc = genomeLocParser.createGenomeLoc(activeRegionLoc.getContig(), activeRegionLoc.getStart() - extension, activeRegionLoc.getStop() + extension);
extendedLoc = genomeLocParser.createGenomeLocOnContig(activeRegionLoc.getContig(), activeRegionLoc.getStart() - extension, activeRegionLoc.getStop() + extension);
fullExtentReferenceLoc = extendedLoc;
}