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An additional safety check to ensure that we only walk over coordinate-sorted 

data when doing locus traversals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3053 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-21 23:31:45 +00:00
parent b4b4e8d672
commit 6cd97b78ab
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -667,8 +667,11 @@ public class GenomeAnalysisEngine {
throw new StingException("The GATK cannot currently process unindexed BAM files");
Shard.ShardType shardType;
if(walker instanceof LocusWalker)
if(walker instanceof LocusWalker) {
if(readsDataSource != null && readsDataSource.getSortOrder() != SAMFileHeader.SortOrder.coordinate)
Utils.scareUser("Locus walkers can only walk over coordinate-sorted data. Please resort your input BAM file.");
shardType = Shard.ShardType.LOCUS;
}
else if(walker instanceof ReadWalker || walker instanceof DuplicateWalker || walker instanceof ReadPairWalker)
shardType = Shard.ShardType.READ;
else