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Deal with screwy reads by changing logic to determine whether we are 

past the last interval


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@409 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-04-14 19:13:16 +00:00
parent 0629f79049
commit b363eedd2c
1 changed files with 1 additions and 6 deletions
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7
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -281,12 +281,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
* @return true if we are past the last location to process * @return true if we are past the last location to process
*/ */
public static boolean pastFinalLocation(GenomeLoc curr, ArrayList<GenomeLoc> locs) { public static boolean pastFinalLocation(GenomeLoc curr, ArrayList<GenomeLoc> locs) {
if ( locs.size() == 0 ) return (locs.size() > 0 && curr.isPast(locs.get(locs.size() - 1)));
return false;
else {
GenomeLoc last = locs.get(locs.size() - 1);
return last.compareTo(curr) == -1 && ! last.overlapsP(curr);
}
} }
/** /**