zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Changed method name from applyFourBaseDistributionPrior to applySecondBaseDistributionPrior. 'Cause that's how I roll. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@960 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-10 08:21:22 +00:00
parent 3adb4239e4
commit a12ed404ce
1 changed files with 20 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

31
java/src/org/broadinstitute/sting/playground/utils/GenotypeLikelihoods.java
View File

@ -197,7 +197,7 @@ public class GenotypeLikelihoods {
this.sort();
}
public void applyFourBaseDistributionPrior(String primaryBases, String secondaryBases) {
public void applySecondBaseDistributionPrior(String primaryBases, String secondaryBases) {
for (int genotypeIndex = 0; genotypeIndex < genotypes.length; genotypeIndex++) {
char firstAllele = genotypes[genotypeIndex].charAt(0);
char secondAllele = genotypes[genotypeIndex].charAt(1);
@ -210,24 +210,33 @@ public class GenotypeLikelihoods {
for (int pileupIndex = 0; pileupIndex < primaryBases.length(); pileupIndex++) {
char primaryBase = primaryBases.charAt(pileupIndex);
char secondaryBase = secondaryBases.charAt(pileupIndex);
if (primaryBase != firstAllele && primaryBase != secondAllele) {
if (secondaryBase == firstAllele || secondaryBase == secondAllele) {
offIsGenotypic++;
if (secondaryBases != null) {
char secondaryBase = secondaryBases.charAt(pileupIndex);
if (primaryBase != firstAllele && primaryBase != secondAllele) {
if (secondaryBase == firstAllele || secondaryBase == secondAllele) {
offIsGenotypic++;
}
offTotal++;
} else {
if (secondaryBase == firstAllele || secondaryBase == secondAllele) {
onIsGenotypic++;
}
onTotal++;
}
offTotal++;
} else {
if (secondaryBase == firstAllele || secondaryBase == secondAllele) {
onIsGenotypic++;
}
onTotal++;
}
}
double offPrior = MathUtils.binomialProbability(offIsGenotypic, offTotal, offNextBestBasePriors.get(genotypes[genotypeIndex]));
double onPrior = MathUtils.binomialProbability(onIsGenotypic, onTotal, onNextBestBasePriors.get(genotypes[genotypeIndex]));
//System.out.printf("%c%c [%d %d %f %e] [%d %d %f %e]\n",
// firstAllele, secondAllele,
// offIsGenotypic, offTotal, offNextBestBasePriors.get(genotypes[genotypeIndex]), offPrior,
// onIsGenotypic, onTotal, onNextBestBasePriors.get(genotypes[genotypeIndex]), onPrior);
//System.out.printf("%f\n", (new cern.jet.random.Binomial(onTotal, onNextBestBasePriors.get(genotypes[genotypeIndex]), cern.jet.random.engine.RandomEngine.makeDefault())).pdf(onIsGenotypic));
likelihoods[genotypeIndex] += Math.log10(offPrior) + Math.log10(onPrior);
//System.out.println(genotypes[genotypeIndex] + " " + offNextBestBasePriors.get(genotypes[genotypeIndex]) + " " + offIsGenotypic + " " + offTotal + " " + (((double) offIsGenotypic)/((double) offTotal)) + " " + offPrior);