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comments for Aaron 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2081 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-11-19 12:56:04 +00:00
parent 7997455f38
commit eeb3a3fffb
1 changed files with 6 additions and 0 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java
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@ -51,8 +51,14 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, SimpleCallList>
for (GENOTYPE genotype : GENOTYPE.values())
for (byte pileupBase : pileup.getBases()) {
// todo -- epsilon isn't a constant variable, it's the de-phred error probabilities of the base
// you need to grab the qual score associated with this base and calcluate
// epsilon = pow(10, qual / -10.0)
// Also, only do the calculations below for bases with qual > 0
for (char genotypeBase : genotype.toString().toCharArray())
// todo -- all of these calculations should be in log10 space (like the priors are)
if (genotypeBase == pileupBase)
// todo -- potential int flow problems there. Needs parens
likelihoods[genotype.ordinal()] += 1 / 2 * (1 - EPSILON) + EPSILON / 3;
else
likelihoods[genotype.ordinal()] += EPSILON / 3;