From 85cb1c281068e563c31e8bce00012586a40d5df9 Mon Sep 17 00:00:00 2001 From: Samuel Friedman Date: Wed, 26 Apr 2017 17:33:06 -0400 Subject: [PATCH] dont spam on NaNs --- .../variantrecalibration/GaussianMixtureModel.java | 3 --- .../variantrecalibration/MultivariateGaussian.java | 9 --------- 2 files changed, 12 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java index 59a5af92d..17b3a63d7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java @@ -195,9 +195,6 @@ public class GaussianMixtureModel { final double[] pVarInGaussianNormalized = MathUtils.normalizeFromLog10( pVarInGaussianLog10, false ); gaussianIndex = 0; for( final MultivariateGaussian gaussian : gaussians ) { - if (Double.isNaN(pVarInGaussianNormalized[gaussianIndex])){ - logger.info(" Got a NaN at gaussian:" + Integer.toString(gaussianIndex) + " datum:" + datum.toString()); - } gaussian.assignPVarInGaussian( pVarInGaussianNormalized[gaussianIndex++] ); } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java index 5e9d18ffd..51662dc92 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java @@ -272,13 +272,4 @@ public class MultivariateGaussian { resetPVarInGaussian(); // clean up some memory } - - public void setSumProb( final List data ) { - sumProb = 0.0; - - for( int datumIndex = 0; datumIndex < data.size(); datumIndex++ ) { - final double prob = pVarInGaussian.get(datumIndex); - if(!Double.isNaN(prob)) sumProb += prob; - } - } } \ No newline at end of file