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Merge pull request #53 from broadinstitute/rp_pcrfree_bad_mappingquality_GSA-780 

Bug fix in LikelihoodCalculationEngine: Mapping quality was being cast t...
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depristo 2013-02-22 05:52:50 -08:00
parent 48c699eec6 62e14f5b58
commit c8a01e6569
2 changed files with 2 additions and 2 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -427,7 +427,7 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
if ( qual > SAMUtils.MAX_PHRED_SCORE ) if ( qual > SAMUtils.MAX_PHRED_SCORE )
throw new UserException.MisencodedBAM(p.getRead(), "we encountered an extremely high quality score (" + (int)qual + ")"); 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( 0xff & qual, p.getMappingQual());
if ( (int)qual < minBaseQual ) if ( (int)qual < minBaseQual )
qual = (byte)0; qual = (byte)0;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
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@ -137,7 +137,7 @@ public class LikelihoodCalculationEngine {
final byte[] readInsQuals = read.getBaseInsertionQualities(); final byte[] readInsQuals = read.getBaseInsertionQualities();
final byte[] readDelQuals = read.getBaseDeletionQualities(); final byte[] readDelQuals = read.getBaseDeletionQualities();
for( int kkk = 0; kkk < readQuals.length; kkk++ ) { for( int kkk = 0; kkk < readQuals.length; kkk++ ) {
readQuals[kkk] = ( readQuals[kkk] > (byte) read.getMappingQuality() ? (byte) read.getMappingQuality() : readQuals[kkk] ); // cap base quality by mapping quality readQuals[kkk] = (byte) Math.min( 0xff & readQuals[kkk], read.getMappingQuality()); // cap base quality by mapping quality, as in UG
//readQuals[kkk] = ( readQuals[kkk] > readInsQuals[kkk] ? readInsQuals[kkk] : readQuals[kkk] ); // cap base quality by base insertion quality, needs to be evaluated //readQuals[kkk] = ( readQuals[kkk] > readInsQuals[kkk] ? readInsQuals[kkk] : readQuals[kkk] ); // cap base quality by base insertion quality, needs to be evaluated
//readQuals[kkk] = ( readQuals[kkk] > readDelQuals[kkk] ? readDelQuals[kkk] : readQuals[kkk] ); // cap base quality by base deletion quality, needs to be evaluated //readQuals[kkk] = ( readQuals[kkk] > readDelQuals[kkk] ? readDelQuals[kkk] : readQuals[kkk] ); // cap base quality by base deletion quality, needs to be evaluated
// TODO -- why is Q18 hard-coded here??? // TODO -- why is Q18 hard-coded here???