From 7e3cb45093f86a29537c3475b46ca3b919f95f96 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Wed, 28 Sep 2011 16:27:28 -0400 Subject: [PATCH] Further performance optim in banded hmm, about 60% speed improvement over current implementation now --- .../sting/gatk/walkers/indels/PairHMMIndelErrorModel.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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) {