From c36069355e2eef66d352e54c199e5be1cc409ff7 Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 1 Dec 2009 20:48:10 +0000 Subject: [PATCH] Trivial change to verbose git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2203 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/genotyper/FourBaseProbabilities.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/FourBaseProbabilities.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/FourBaseProbabilities.java index fb5fbaa07..1ad2a798f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/FourBaseProbabilities.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/FourBaseProbabilities.java @@ -154,7 +154,7 @@ public abstract class FourBaseProbabilities implements Cloneable { log10Likelihoods[BaseUtils.simpleBaseToBaseIndex(base)] += likelihood; } - if ( isVerbose() ) { + if ( verbose ) { for ( char base : BaseUtils.BASES ) { System.out.printf("%s\t", base); } System.out.println(); for ( char base : BaseUtils.BASES ) { System.out.printf("%.2f\t", log10Likelihoods[BaseUtils.simpleBaseToBaseIndex(base)]); } @@ -188,7 +188,7 @@ public abstract class FourBaseProbabilities implements Cloneable { for ( char base : BaseUtils.BASES ) { double likelihood = log10PofObservingBaseGivenChromosome(observedBase, base, qualityScore, read, offset); - if ( isVerbose() ) { + if ( verbose ) { boolean fwdStrand = ! read.getReadNegativeStrandFlag(); System.out.printf(" L(%c | b=%s, Q=%d, S=%s) = %f / %f%n", observedBase, base, qualityScore, fwdStrand ? "+" : "-", pow(10,likelihood) * 100, likelihood);