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Further performance optim in banded hmm, about 60% speed improvement over current implementation now

This commit is contained in:
Guillermo del Angel 2011-09-28 16:27:28 -04:00
parent fe23e4d10c
commit 7e3cb45093
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -260,7 +260,7 @@ public class PairHMMIndelErrorModel {
currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray); currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray);
// update max in diagonal // update max in diagonal
if (bandedLikelihoods) { 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 // check if we've fallen off diagonal value by threshold
if (bestMetric > maxElementInDiag) { if (bestMetric > maxElementInDiag) {
@ -294,7 +294,7 @@ public class PairHMMIndelErrorModel {
updateCell(indI, indJ, X_METRIC_LENGTH, Y_METRIC_LENGTH, readBases, readQuals, haplotypeBases, updateCell(indI, indJ, X_METRIC_LENGTH, Y_METRIC_LENGTH, readBases, readQuals, haplotypeBases,
currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray); currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray);
// update max in diagonal // 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 // check if we've fallen off diagonal value by threshold
if (bestMetric > maxElementInDiag) { if (bestMetric > maxElementInDiag) {