From 67ea66c8663f87b2729163acd804bf5f9ed80c02 Mon Sep 17 00:00:00 2001 From: aaron Date: Wed, 15 Apr 2009 19:12:18 +0000 Subject: [PATCH] Bug fix git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@434 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/dataSources/shards/LocusShardStrategy.java | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShardStrategy.java index 817cd7d05..5ddfaebaa 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShardStrategy.java @@ -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) {