zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -152,6 +152,7 @@ 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
@ -159,6 +160,7 @@ 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)
@ -174,6 +176,7 @@ 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
@ -182,6 +185,7 @@ 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)
@ -229,7 +233,9 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
maxAlleleCnt = curCnt; maxAlleleCnt = curCnt;
bestAltAllele = s; bestAltAllele = s;
} }
} // if (DEBUG)
// System.out.format("Key:%s, number: %d\n",s,consensusIndelStrings.get(s) );
} //gdebug-
if (maxAlleleCnt < minIndelCountForGenotyping) if (maxAlleleCnt < minIndelCountForGenotyping)
return aList; return aList;