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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
This commit is contained in:
ebanks 2009-11-24 17:00:32 +00:00
parent b3f561710f
commit 87c1860398
1 changed files with 5 additions and 3 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
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@ -43,6 +43,7 @@ public class GenotypeLikelihoods implements Cloneable {
protected final static int MAX_PLOIDY = FIXED_PLOIDY + 1; protected final static int MAX_PLOIDY = FIXED_PLOIDY + 1;
protected boolean enableCacheFlag = true; protected boolean enableCacheFlag = true;
protected boolean VERBOSE = false;
// //
// The fundamental data arrays associated with a Genotype Likelhoods object // The fundamental data arrays associated with a Genotype Likelhoods object
@ -123,11 +124,12 @@ public class GenotypeLikelihoods implements Cloneable {
} }
public void setVerbose(boolean v) { public void setVerbose(boolean v) {
VERBOSE = v;
fourBaseLikelihoods.setVerbose(v); fourBaseLikelihoods.setVerbose(v);
} }
public boolean isVerbose() { public boolean isVerbose() {
return fourBaseLikelihoods.isVerbose(); return VERBOSE;
} }
public int getMinQScoreToInclude() { public int getMinQScoreToInclude() {
@ -314,7 +316,7 @@ public class GenotypeLikelihoods implements Cloneable {
for ( DiploidGenotype g : DiploidGenotype.values() ) { for ( DiploidGenotype g : DiploidGenotype.values() ) {
double likelihood = likelihoods[g.ordinal()]; double likelihood = likelihoods[g.ordinal()];
if ( isVerbose() ) { if ( VERBOSE ) {
boolean fwdStrand = ! read.getReadNegativeStrandFlag(); boolean fwdStrand = ! read.getReadNegativeStrandFlag();
System.out.printf(" L(%c | G=%s, Q=%d, S=%s) = %f / %f%n", System.out.printf(" L(%c | G=%s, Q=%d, S=%s) = %f / %f%n",
observedBase, g, qualityScore, fwdStrand ? "+" : "-", pow(10,likelihood) * 100, likelihood); observedBase, g, qualityScore, fwdStrand ? "+" : "-", pow(10,likelihood) * 100, likelihood);
@ -397,7 +399,7 @@ public class GenotypeLikelihoods implements Cloneable {
gl.log10Posteriors[g.ordinal()] += likelihood; gl.log10Posteriors[g.ordinal()] += likelihood;
} }
if ( fourBaseLikelihoods.isVerbose() ) { if ( VERBOSE ) {
for ( DiploidGenotype g : DiploidGenotype.values() ) { System.out.printf("%s\t", g); } for ( DiploidGenotype g : DiploidGenotype.values() ) { System.out.printf("%s\t", g); }
System.out.println(); System.out.println();
for ( DiploidGenotype g : DiploidGenotype.values() ) { System.out.printf("%.2f\t", gl.log10Likelihoods[g.ordinal()]); } for ( DiploidGenotype g : DiploidGenotype.values() ) { System.out.printf("%.2f\t", gl.log10Likelihoods[g.ordinal()]); }