diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index 55cc38e04..c8328771b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -260,7 +260,7 @@ public class PairHMMIndelErrorModel { currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray); // update max in diagonal if (bandedLikelihoods) { - final double bestMetric = MathUtils.softMax(matchMetricArray[indI][indJ], XMetricArray[indI][indJ], YMetricArray[indI][indJ]); + final double bestMetric = MathUtils.max(matchMetricArray[indI][indJ], XMetricArray[indI][indJ], YMetricArray[indI][indJ]); // check if we've fallen off diagonal value by threshold if (bestMetric > maxElementInDiag) { @@ -294,7 +294,7 @@ public class PairHMMIndelErrorModel { updateCell(indI, indJ, X_METRIC_LENGTH, Y_METRIC_LENGTH, readBases, readQuals, haplotypeBases, currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray); // update max in diagonal - final double bestMetric = MathUtils.softMax(matchMetricArray[indI][indJ], XMetricArray[indI][indJ], YMetricArray[indI][indJ]); + final double bestMetric = MathUtils.max(matchMetricArray[indI][indJ], XMetricArray[indI][indJ], YMetricArray[indI][indJ]); // check if we've fallen off diagonal value by threshold if (bestMetric > maxElementInDiag) {