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dont spam on NaNs

This commit is contained in:
Samuel Friedman 2017-04-26 17:33:06 -04:00
parent 57c064eaa3
commit 85cb1c2810
2 changed files with 0 additions and 12 deletions
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3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java
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@ -195,9 +195,6 @@ public class GaussianMixtureModel {
final double[] pVarInGaussianNormalized = MathUtils.normalizeFromLog10( pVarInGaussianLog10, false ); final double[] pVarInGaussianNormalized = MathUtils.normalizeFromLog10( pVarInGaussianLog10, false );
gaussianIndex = 0; gaussianIndex = 0;
for( final MultivariateGaussian gaussian : gaussians ) { 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++] ); gaussian.assignPVarInGaussian( pVarInGaussianNormalized[gaussianIndex++] );
} }
} }

9
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java
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@ -272,13 +272,4 @@ public class MultivariateGaussian {
resetPVarInGaussian(); // clean up some memory resetPVarInGaussian(); // clean up some memory
} }
public void setSumProb( final List<VariantDatum> data ) {
sumProb = 0.0;
for( int datumIndex = 0; datumIndex < data.size(); datumIndex++ ) {
final double prob = pVarInGaussian.get(datumIndex);
if(!Double.isNaN(prob)) sumProb += prob;
}
}
} }