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Better error message as per Mark 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4953 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-06 15:44:02 +00:00
parent e0d091b3db
commit 2ac5c52281
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -331,7 +331,7 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
int i = BaseUtils.simpleBaseToBaseIndex(observedBase);
int j = qualityScore;
if ( j > SAMUtils.MAX_PHRED_SCORE )
throw new UserException.MalformedBam(read, String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s", SAMUtils.MAX_PHRED_SCORE, j, read.getReadName()));
throw new UserException.MalformedBam(read, 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, j, read.getReadName()));
int k = ploidy;
int x = strandIndex(! read.getReadNegativeStrandFlag() );
@ -343,7 +343,7 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
int i = BaseUtils.simpleBaseToBaseIndex(observedBase);
int j = qualityScore;
if ( j > SAMUtils.MAX_PHRED_SCORE )
throw new UserException.MalformedBam(read, String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s", SAMUtils.MAX_PHRED_SCORE, j, read.getReadName()));
throw new UserException.MalformedBam(read, 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, j, read.getReadName()));
int k = ploidy;
int x = strandIndex(! read.getReadNegativeStrandFlag() );
return cache[i][j][k][x];