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don't run off the end of the list of loci. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@134 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-03-22 16:47:29 +00:00
parent 4e0cd6ab84
commit 096f0dbc68
1 changed files with 3 additions and 1 deletions
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4
core/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
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@ -560,7 +560,7 @@ public class TraversalEngine {
//System.out.format("DEBUG Seeking from %s to %s\n", locus.getLocation().toString(), this.locs[current_interval_index].toString());
while ((!locus.getLocation().overlapsP(this.locs[current_interval_index])) && (iter.hasNext()))
while ((this.locs.length > current_interval_index) && (!locus.getLocation().overlapsP(this.locs[current_interval_index])) && (iter.hasNext()))
{
switch (locus.getLocation().compareTo(this.locs[current_interval_index]))
{
@ -573,10 +573,12 @@ public class TraversalEngine {
case 1 :
current_interval_index += 1;
current_interval_offset = 0;
if (this.locs.length <= current_interval_index) { done = true; break; }
//System.out.format("DEBUG Giving up on old locus, Seeking from %s to %s\n", locus.getLocation().toString(), this.locs[current_interval_index].toString());
break;
}
}
if (this.locs.length <= current_interval_index) { done = true; break; }
//System.out.format("DEBUG Got there.\n");
}