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Reverting last commit until I learn how to effectively replicate and debug pipeline test failures, and until I also learn how to effectively remove a kep from a HashMap that's being iterated on

This commit is contained in:
Guillermo del Angel 2012-02-17 17:15:53 -05:00
parent cd352f502d
commit f2ef8d1d23
1 changed files with 9 additions and 3 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -152,13 +152,15 @@ 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)
@ -174,7 +176,8 @@ 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.
@ -182,6 +185,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
consensusIndelStrings.remove(s);
consensusIndelStrings.put(indelString,cnt+1);
foundKey = true;
break;
}
}
if (!foundKey)
@ -229,7 +233,9 @@ 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;