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Likelihood engine now gives non-zero likelihoods. Using HMM function that can handle context specific gap open and gap continuation penalties

This commit is contained in:
Ryan Poplin 2011-08-23 13:43:07 -04:00
parent 3c37d841db
commit a1a1fac9e4
2 changed files with 3 additions and 4 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -156,7 +156,7 @@ public class UnifiedArgumentCollection {
public boolean OUTPUT_DEBUG_INDEL_INFO = false;
@Hidden
@Argument(fullName = "dovit", shortName = "dovit", doc = "Output indel debug info", required = false)
@Argument(fullName = "dovit", shortName = "dovit", doc = "Perform full Viterbi calculation when evaluating the HMM", required = false)
public boolean dovit = false;
@Hidden

1
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -1055,7 +1055,6 @@ public class PairHMMIndelErrorModel {
genotypeLikelihoods[i] -= maxElement;
return genotypeLikelihoods;
}
/**