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Reverting bad exact model changes

This commit is contained in:
Mark DePristo 2011-11-21 16:14:40 -05:00
parent 1561af22af
commit ab2efe3bd3
1 changed files with 54 additions and 43 deletions
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97
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -339,7 +339,8 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
} }
} }
final GenotypesContext calls = GenotypesContext.create(); GenotypesContext calls = GenotypesContext.create();
int startIdx = AFofMaxLikelihood; int startIdx = AFofMaxLikelihood;
for (int k = sampleIdx; k > 0; k--) { for (int k = sampleIdx; k > 0; k--) {
int bestGTguess; int bestGTguess;
@ -353,49 +354,59 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
double[] likelihoods = g.getLikelihoods().getAsVector(); double[] likelihoods = g.getLikelihoods().getAsVector();
if (MathUtils.sum(likelihoods) <= SUM_GL_THRESH_NOCALL) { if (SIMPLE_GREEDY_GENOTYPER || !vc.isBiallelic()) {
if (SIMPLE_GREEDY_GENOTYPER || !vc.isBiallelic()) { bestGTguess = Utils.findIndexOfMaxEntry(likelihoods);
bestGTguess = Utils.findIndexOfMaxEntry(likelihoods);
}
else {
int newIdx = tracebackArray[k][startIdx];;
bestGTguess = startIdx - newIdx;
startIdx = newIdx;
}
// likelihoods are stored row-wise in lower triangular matrix. IE
// for 2 alleles they have ordering AA,AB,BB
// for 3 alleles they are ordered AA,AB,BB,AC,BC,CC
// Get now alleles corresponding to best index
int kk=0;
boolean done = false;
for (int j=0; j < vc.getNAlleles(); j++) {
for (int i=0; i <= j; i++){
if (kk++ == bestGTguess) {
if (i==0)
myAlleles.add(vc.getReference());
else
myAlleles.add(vc.getAlternateAllele(i-1));
if (j==0)
myAlleles.add(vc.getReference());
else
myAlleles.add(vc.getAlternateAllele(j-1));
done = true;
break;
}
}
if (done)
break;
}
final double qual = GenotypeLikelihoods.getQualFromLikelihoods(bestGTguess, likelihoods);
calls.add(new Genotype(sample, myAlleles, qual, null, g.getAttributes(), false));
} else {
final double qual = Genotype.NO_LOG10_PERROR;
calls.add(new Genotype(sample, NO_CALL_ALLELES, qual, null, g.getAttributes(), false));
} }
else {
int newIdx = tracebackArray[k][startIdx];;
bestGTguess = startIdx - newIdx;
startIdx = newIdx;
}
// likelihoods are stored row-wise in lower triangular matrix. IE
// for 2 alleles they have ordering AA,AB,BB
// for 3 alleles they are ordered AA,AB,BB,AC,BC,CC
// Get now alleles corresponding to best index
int kk=0;
boolean done = false;
for (int j=0; j < vc.getNAlleles(); j++) {
for (int i=0; i <= j; i++){
if (kk++ == bestGTguess) {
if (i==0)
myAlleles.add(vc.getReference());
else
myAlleles.add(vc.getAlternateAllele(i-1));
if (j==0)
myAlleles.add(vc.getReference());
else
myAlleles.add(vc.getAlternateAllele(j-1));
done = true;
break;
}
}
if (done)
break;
}
final double qual = GenotypeLikelihoods.getQualFromLikelihoods(bestGTguess, likelihoods);
//System.out.println(myAlleles.toString());
calls.add(new Genotype(sample, myAlleles, qual, null, g.getAttributes(), false));
}
for ( final Genotype genotype : GLs.iterateInSampleNameOrder() ) {
if ( !genotype.hasLikelihoods() )
continue;
Genotype g = GLs.get(genotype.getSampleName());
double[] likelihoods = genotype.getLikelihoods().getAsVector();
if (MathUtils.sum(likelihoods) <= SUM_GL_THRESH_NOCALL)
continue; // regular likelihoods
final double qual = Genotype.NO_LOG10_PERROR;
calls.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, qual, null, g.getAttributes(), false));
} }
return calls; return calls;