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Corner case bug fix: if a read starts with an insertion, when computing the consensus allele for calling the insertion was only added to the last element in the consensus key hash map. Now, an insertion that partially overlaps with several candidate alleles will have their respective count increased for all of them

This commit is contained in:
Guillermo del Angel 2012-02-17 10:21:37 -05:00
parent 7dc6f73399
commit cd352f502d
1 changed files with 3 additions and 9 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -152,15 +152,13 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
// case 1: current insertion is prefix of indel in hash map
consensusIndelStrings.put(s,cnt+1);
foundKey = true;
break;
}
}
else if (indelString.startsWith(s)) {
// case 2: indel stored in hash table is prefix of current insertion
// In this case, new bases are new key.
consensusIndelStrings.remove(s);
consensusIndelStrings.put(indelString,cnt+1);
foundKey = true;
break;
}
}
if (!foundKey)
@ -176,8 +174,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
// case 1: current insertion is suffix of indel in hash map
consensusIndelStrings.put(s,cnt+1);
foundKey = true;
break;
}
}
else if (indelString.endsWith(s)) {
// case 2: indel stored in hash table is suffix of current insertion
// In this case, new bases are new key.
@ -185,7 +182,6 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
consensusIndelStrings.remove(s);
consensusIndelStrings.put(indelString,cnt+1);
foundKey = true;
break;
}
}
if (!foundKey)
@ -233,9 +229,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
maxAlleleCnt = curCnt;
bestAltAllele = s;
}
// if (DEBUG)
// System.out.format("Key:%s, number: %d\n",s,consensusIndelStrings.get(s) );
} //gdebug-
}
if (maxAlleleCnt < minIndelCountForGenotyping)
return aList;