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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; public boolean OUTPUT_DEBUG_INDEL_INFO = false;
@Hidden @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; public boolean dovit = false;
@Hidden @Hidden

5
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -274,7 +274,7 @@ public class PairHMMIndelErrorModel {
this.doViterbi = dovit; this.doViterbi = dovit;
} }
public PairHMMIndelErrorModel(double indelGOP, double indelGCP, boolean deb, boolean doCDP) { public PairHMMIndelErrorModel(double indelGOP, double indelGCP, boolean deb, boolean doCDP) {
this.logGapOpenProbability = -indelGOP/10.0; // QUAL to log prob this.logGapOpenProbability = -indelGOP/10.0; // QUAL to log prob
@ -754,7 +754,7 @@ public class PairHMMIndelErrorModel {
// check if we've already computed likelihoods for this pileup element (i.e. for this read at this location) // check if we've already computed likelihoods for this pileup element (i.e. for this read at this location)
if (indelLikelihoodMap.containsKey(p)) { if (indelLikelihoodMap.containsKey(p)) {
HashMap<Allele,Double> el = indelLikelihoodMap.get(p); HashMap<Allele,Double> el = indelLikelihoodMap.get(p);
int j=0; int j=0;
for (Allele a: haplotypeMap.keySet()) { for (Allele a: haplotypeMap.keySet()) {
readLikelihoods[readIdx][j++] = el.get(a); readLikelihoods[readIdx][j++] = el.get(a);
@ -1055,7 +1055,6 @@ public class PairHMMIndelErrorModel {
genotypeLikelihoods[i] -= maxElement; genotypeLikelihoods[i] -= maxElement;
return genotypeLikelihoods; return genotypeLikelihoods;
} }
/** /**