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Temp. to PairHMM to avoid bad likelihoods 

-- Simply caps PairHMM likelihoods from rising above 0 by taking the min of the likelihood and 0.  Will be properly fixed in GATK 2.5 with better PairHMM implementation.
This commit is contained in:
Mark DePristo 2013-03-18 12:34:51 -04:00
parent 5e89f01e10
commit 7ab7c873a1
1 changed files with 4 additions and 1 deletions
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5
public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
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@ -122,7 +122,10 @@ public abstract class PairHMM {
if ( overallGCP.length != readBases.length ) throw new IllegalArgumentException("Read bases and overall GCP aren't the same size: " + readBases.length + " vs " + overallGCP.length);
if ( hapStartIndex < 0 || hapStartIndex > haplotypeBases.length ) throw new IllegalArgumentException("hapStartIndex is bad, must be between 0 and haplotype length " + haplotypeBases.length + " but got " + hapStartIndex);
final double result = subComputeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals, insertionGOP, deletionGOP, overallGCP, hapStartIndex, recacheReadValues);
double result = subComputeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals, insertionGOP, deletionGOP, overallGCP, hapStartIndex, recacheReadValues);
// TODO -- remove max when PairHMM no longer returns likelihoods >= 0
result = Math.min(result, 0.0);
if ( MathUtils.goodLog10Probability(result) )
return result;