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Bug fix 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@434 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-04-15 19:12:18 +00:00
parent 1edfe48194
commit 67ea66c866
1 changed files with 6 additions and 3 deletions
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9
java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShardStrategy.java
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@ -96,8 +96,11 @@ public abstract class LocusShardStrategy implements ShardStrategy {
this.dic = dic;
this.intervals = intervals;
this.currentInterval = 0;
mLoc = new GenomeLoc(0, 0, 0);
// set the starting point to the beginning interval
if (intervals.size() < 1) {
throw new IllegalArgumentException("Interval files must contain at least one interval");
}
mLoc = new GenomeLoc(intervals.get(0).getContig(),intervals.get(0).getStart()-1,intervals.get(0).getStart()-1);
if (dic.getSequences().size() > 0) {
nextContig = true;
}
@ -162,7 +165,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
lastGenomeLocSize = proposedSize;
// the next sequence should start at the begining of the next contig
Shard ret = LocusShard.toShard(new GenomeLoc(intervals.get(currentInterval).getContigIndex(), nextStart, nextStart + proposedSize - 1));
Shard ret = LocusShard.toShard(new GenomeLoc(intervals.get(currentInterval).getContigIndex(), nextStart, nextStart + proposedSize));
++currentInterval;
if (intervals.size() > currentInterval) {