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Bug fix for reduced read; only adds regular bases for calculation 

-- No longer passes on deletions for genotyping
This commit is contained in:
Mark DePristo 2011-09-20 15:07:06 -04:00
parent 83bb91020f
commit bffd3cca6f
1 changed files with 5 additions and 2 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -276,8 +276,11 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
if ( elt.isReducedRead() ) {
// reduced read representation
byte qual = elt.getReducedQual();
add(obsBase, qual, (byte)0, (byte)0, elt.getReducedCount()); // fast calculation of n identical likelihoods
return elt.getReducedCount(); // we added nObs bases here
if ( BaseUtils.isRegularBase( elt.getBase() )) {
add(obsBase, qual, (byte)0, (byte)0, elt.getReducedCount()); // fast calculation of n identical likelihoods
return elt.getReducedCount(); // we added nObs bases here
} else // odd bases or deletions => don't use them
return 0;
} else {
byte qual = qualToUse(elt, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual);
return qual > 0 ? add(obsBase, qual, (byte)0, (byte)0, 1) : 0;