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Better error message for bad qual

This commit is contained in:
Eric Banks 2013-01-17 10:30:04 -05:00
parent 953592421b
commit 6db3e473af
1 changed files with 1 additions and 1 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -425,7 +425,7 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
byte qual = p.getQual(); byte qual = p.getQual();
if ( qual > SAMUtils.MAX_PHRED_SCORE ) if ( qual > SAMUtils.MAX_PHRED_SCORE )
throw new UserException.MalformedBAM(p.getRead(), String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s. Perhaps your BAM incorrectly encodes the quality scores in Sanger format; see http://en.wikipedia.org/wiki/FASTQ_format for more details", SAMUtils.MAX_PHRED_SCORE, qual, p.getRead().getReadName())); throw new UserException.MisencodedBAM(p.getRead(), "we encountered an extremely high quality score (" + (int)qual + ")");
if ( capBaseQualsAtMappingQual ) if ( capBaseQualsAtMappingQual )
qual = (byte)Math.min((int)qual, p.getMappingQual()); qual = (byte)Math.min((int)qual, p.getMappingQual());
if ( (int)qual < minBaseQual ) if ( (int)qual < minBaseQual )