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Bug fix for logging likelihoods in new read allele map: reads which were filtered out were being excluded from map, but they should be included in annotations

This commit is contained in:
Guillermo del Angel 2012-09-09 20:35:45 -04:00
parent 8ca205f1a9
commit 2d4b00833b
1 changed files with 5 additions and 10 deletions
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15
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
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@ -346,20 +346,15 @@ public class LikelihoodCalculationEngine {
} }
} }
} }
/* // add all filtered reads to the NO_CALL list because they weren't given any likelihoods // add all filtered reads to the NO_CALL list because they weren't given any likelihoods
List<GATKSAMRecord> readList = alleleReadMap.get(Allele.NO_CALL); for( final GATKSAMRecord read : perSampleFilteredReadList.get(sample.getKey()) ) {
if( readList == null ) {
readList = new ArrayList<GATKSAMRecord>();
alleleReadMap.put(Allele.NO_CALL, readList);
}
*/
/* for( final GATKSAMRecord read : perSampleFilteredReadList.get(sample.getKey()) ) {
// only count the read if it overlaps the event, otherwise it is not added to the output read list at all // only count the read if it overlaps the event, otherwise it is not added to the output read list at all
if( callLoc.overlapsP(parser.createGenomeLoc(read)) ) { if( callLoc.overlapsP(parser.createGenomeLoc(read)) ) {
readList.add(read); for( final Allele a : call.getFirst().getAlleles() )
likelihoodMap.add(read,a,0.0);
} }
} }
*/
returnMap.put(sample.getKey(), likelihoodMap); returnMap.put(sample.getKey(), likelihoodMap);
} }