From ff6386c29bcd2cff432338efcee4dab8c6d2eb0f Mon Sep 17 00:00:00 2001 From: droazen Date: Wed, 22 Jun 2011 22:54:55 +0000 Subject: [PATCH] binomial coefficient was in log2, changed to log10. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6052 348d0f76-0448-11de-a6fe-93d51630548a --- .../replication_validation/ReplicationValidationWalker.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java index b9bc50030..3e3a97ac8 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.playground.gatk.walkers.replication_validation; +import cern.jet.math.Arithmetic; import com.google.common.collect.ArrayListMultimap; import com.sun.xml.internal.ws.client.BindingProviderProperties; import net.sf.samtools.SAMFileHeader; @@ -102,7 +103,7 @@ public class ReplicationValidationWalker extends LocusWalker impl for (byte q=0; q<=maxQualityScore; q++) { double probMismatch = MathUtils.phredScaleToProbability(q); model[q] = MathUtils.phredScaleToLog10Probability(phredScaledPrior) + - org.apache.commons.math.util.MathUtils.binomialCoefficientLog(coverage, mismatches) + + Math.log10(Arithmetic.binomial(coverage, mismatches)) + mismatches * Math.log10(probMismatch) + matches * Math.log10(1-probMismatch); }