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Rewrote warning message to discourage use of unsafe mode. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5003 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2011-01-14 21:32:53 +00:00
parent 2355a55067
commit 579e0d59fa
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -377,7 +377,7 @@ public class GenomeAnalysisEngine {
// sharding system; it's required with the new sharding system only for locus walkers.
if(readsDataSource != null && !readsDataSource.hasIndex() ) {
if(!exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM))
throw new UserException.CommandLineException("The GATK cannot currently process unindexed BAM files without the -U ALLOW_UNINDEXED_BAM");
throw new UserException.CommandLineException("Cannot process the provided BAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.");
if(intervals != null)
throw new UserException.CommandLineException("Cannot perform interval processing when reads are present but no index is available.");