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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1524 348d0f76-0448-11de-a6fe-93d51630548a

This commit is contained in:
sjia 2009-09-03 19:34:42 +00:00
parent c849282e44
commit 043c97eede
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
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@ -198,7 +198,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
} }
//Calculate posterior probabilities! //Calculate posterior probabilities!
GenotypeLikelihoods gl = new ThreeStateErrorGenotypeLikelihoods(); GenotypeLikelihoods G = new EmpiricalSubstitutionGenotypeLikelihoods();
//I've tried simply adding the entire pileup to g, but quality scores are not checked, and 'N' bases throw an error //I've tried simply adding the entire pileup to g, but quality scores are not checked, and 'N' bases throw an error
//(GenotypeLikelihoods potentially has bug on line 57) //(GenotypeLikelihoods potentially has bug on line 57)
@ -217,7 +217,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
if (base == 'T'){numTs++;} if (base == 'T'){numTs++;}
if (base == 'g'){numGs++;} if (base == 'g'){numGs++;}
//consider base in likelihood calculations if it looks good and has high mapping score //consider base in likelihood calculations if it looks good and has high mapping score
gl.add(base, qual, read, offset); G.add(base, qual, read, offset);
} }
} }