From 87c18603984cba7cc1a83a3dcf7c712d14809ea5 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Nov 2009 17:00:32 +0000
Subject: [PATCH] I'm not sure I believe it, but JProfiler claims that calling
 FourBaseProbs.isVerbose() was taking 5% of my runtime...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2142 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/GenotypeLikelihoods.java | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
index 30b7b49cb..dfde2038e 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
@@ -43,6 +43,7 @@ public class GenotypeLikelihoods implements Cloneable {
     protected final static int MAX_PLOIDY = FIXED_PLOIDY + 1;
 
     protected boolean enableCacheFlag = true;
+    protected boolean VERBOSE = false;
 
     //
     // The fundamental data arrays associated with a Genotype Likelhoods object
@@ -123,11 +124,12 @@ public class GenotypeLikelihoods implements Cloneable {
     }
 
     public void setVerbose(boolean v) {
+        VERBOSE = v;
         fourBaseLikelihoods.setVerbose(v);
     }
 
     public boolean isVerbose() {
-        return fourBaseLikelihoods.isVerbose();
+        return VERBOSE;
     }
 
     public int getMinQScoreToInclude() {
@@ -314,7 +316,7 @@ public class GenotypeLikelihoods implements Cloneable {
         for ( DiploidGenotype g : DiploidGenotype.values() ) {
             double likelihood = likelihoods[g.ordinal()];
             
-            if ( isVerbose() ) {
+            if ( VERBOSE ) {
                 boolean fwdStrand = ! read.getReadNegativeStrandFlag();
                 System.out.printf("  L(%c | G=%s, Q=%d, S=%s) = %f / %f%n",
                         observedBase, g, qualityScore, fwdStrand ? "+" : "-", pow(10,likelihood) * 100, likelihood);
@@ -397,7 +399,7 @@ public class GenotypeLikelihoods implements Cloneable {
                 gl.log10Posteriors[g.ordinal()] += likelihood;
             }
 
-            if ( fourBaseLikelihoods.isVerbose() ) {
+            if ( VERBOSE ) {
                 for ( DiploidGenotype g : DiploidGenotype.values() ) { System.out.printf("%s\t", g); }
                 System.out.println();
                 for ( DiploidGenotype g : DiploidGenotype.values() ) { System.out.printf("%.2f\t", gl.log10Likelihoods[g.ordinal()]); }