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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 17:18:43 -05:00
parent 3e031a540f f2ef8d1d23
commit e724c63f2b
1 changed files with 4 additions and 0 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -150,12 +150,14 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
// case 1: current insertion is prefix of indel in hash map // case 1: current insertion is prefix of indel in hash map
consensusIndelStrings.put(s, cnt + 1); consensusIndelStrings.put(s, cnt + 1);
foundKey = true; foundKey = true;
break;
} else if (indelString.startsWith(s)) { } else if (indelString.startsWith(s)) {
// case 2: indel stored in hash table is prefix of current insertion // case 2: indel stored in hash table is prefix of current insertion
// In this case, new bases are new key. // In this case, new bases are new key.
consensusIndelStrings.remove(s); consensusIndelStrings.remove(s);
consensusIndelStrings.put(indelString, cnt + 1); consensusIndelStrings.put(indelString, cnt + 1);
foundKey = true; foundKey = true;
break;
} }
} }
if (!foundKey) if (!foundKey)
@ -170,6 +172,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
// case 1: current insertion is suffix of indel in hash map // case 1: current insertion is suffix of indel in hash map
consensusIndelStrings.put(s, cnt + 1); consensusIndelStrings.put(s, cnt + 1);
foundKey = true; foundKey = true;
break;
} else if (indelString.endsWith(s)) { } else if (indelString.endsWith(s)) {
// case 2: indel stored in hash table is suffix of current insertion // case 2: indel stored in hash table is suffix of current insertion
// In this case, new bases are new key. // In this case, new bases are new key.
@ -177,6 +180,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
consensusIndelStrings.remove(s); consensusIndelStrings.remove(s);
consensusIndelStrings.put(indelString, cnt + 1); consensusIndelStrings.put(indelString, cnt + 1);
foundKey = true; foundKey = true;
break;
} }
} }
if (!foundKey) if (!foundKey)