diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java index 1da0f8221..e03f21334 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java @@ -47,7 +47,7 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo private final double insertionEndProbability = 0.5; private final double alphaDeletionProbability = 1e-3; 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 private final double indelHeterozygosity = 1.0/8000; @@ -130,7 +130,7 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo for (int k=0; k < 3; k++) { genotypeLikelihoods[k] = Math.log10(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(), vc.getAlternateAllele(0),