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Cheap optimization: don't keep calculating the log of a constant. (How did I not catch this before?) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4791 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-12-05 04:36:21 +00:00
parent 0944184832
commit 8901e63879
1 changed files with 1 additions and 2 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -69,6 +69,7 @@ import static java.lang.Math.pow;
public class DiploidSNPGenotypeLikelihoods implements Cloneable { public class DiploidSNPGenotypeLikelihoods implements Cloneable {
protected final static int FIXED_PLOIDY = 2; protected final static int FIXED_PLOIDY = 2;
protected final static int MAX_PLOIDY = FIXED_PLOIDY + 1; protected final static int MAX_PLOIDY = FIXED_PLOIDY + 1;
protected final static double ploidyAdjustment = log10(FIXED_PLOIDY);
protected boolean enableCacheFlag = true; protected boolean enableCacheFlag = true;
protected boolean VERBOSE = false; protected boolean VERBOSE = false;
@ -407,8 +408,6 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
gl.setToZero(); gl.setToZero();
// we need to adjust for ploidy. We take the raw p(obs | chrom) / ploidy, which is -log10(ploidy) in log space // we need to adjust for ploidy. We take the raw p(obs | chrom) / ploidy, which is -log10(ploidy) in log space
double ploidyAdjustment = log10(FIXED_PLOIDY);
for ( DiploidGenotype g : DiploidGenotype.values() ) { for ( DiploidGenotype g : DiploidGenotype.values() ) {
// todo assumes ploidy is 2 -- should be generalized. Obviously the below code can be turned into a loop // todo assumes ploidy is 2 -- should be generalized. Obviously the below code can be turned into a loop