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We really don't want to be advising the user to use an unsafe option - really, they should fix their busted bam file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5949 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-06-05 05:18:16 +00:00
parent 7e49e1668f
commit 27dfb53d26
1 changed files with 1 additions and 1 deletions
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java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -83,7 +83,7 @@ public class GATKSAMRecord extends SAMRecord {
// sanity check that the lengths of the base and quality strings are equal
if ( getBaseQualities().length != getReadLength() )
throw new UserException.MalformedBAM(this, String.format("Error: the number of base qualities does not match the number of bases in %s. Use -DBQ x to set a default base quality score to all reads so GATK can proceed.", mRecord.getReadName()));
throw new UserException.MalformedBAM(this, String.format("Error: the number of base qualities does not match the number of bases in %s.", mRecord.getReadName()));
}
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