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silly bug fix: if I'm to do a short term hack to avoid -infinity likelihoods I might as well do it right. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4403 348d0f76-0448-11de-a6fe-93d51630548a
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delangel 2010-10-01 18:39:45 +00:00
parent 8d25a5f9f2
commit d4398f2686
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
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@ -47,7 +47,7 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo
private final double insertionEndProbability = 0.5; private final double insertionEndProbability = 0.5;
private final double alphaDeletionProbability = 1e-3; private final double alphaDeletionProbability = 1e-3;
private final int HAPLOTYPE_SIZE = 80; private final int HAPLOTYPE_SIZE = 80;
private static final double MINUS_INFINITY = -1e200; private static final double MINUS_LOG_INFINITY = -300;
// todo - the following need to be exposed for command line argument control // todo - the following need to be exposed for command line argument control
private final double indelHeterozygosity = 1.0/8000; private final double indelHeterozygosity = 1.0/8000;
@ -130,7 +130,7 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo
for (int k=0; k < 3; k++) { for (int k=0; k < 3; k++) {
genotypeLikelihoods[k] = Math.log10(genotypeLikelihoods[k]); genotypeLikelihoods[k] = Math.log10(genotypeLikelihoods[k]);
if (Double.isInfinite(genotypeLikelihoods[k])) if (Double.isInfinite(genotypeLikelihoods[k]))
genotypeLikelihoods[k] = -MINUS_INFINITY; genotypeLikelihoods[k] = MINUS_LOG_INFINITY;
} }
GLs.put(sample.getKey(), new BiallelicGenotypeLikelihoods(sample.getKey(),vc.getReference(), GLs.put(sample.getKey(), new BiallelicGenotypeLikelihoods(sample.getKey(),vc.getReference(),
vc.getAlternateAllele(0), vc.getAlternateAllele(0),