From eeb3a3fffbe390ec98380b68a10523e1d21e58c7 Mon Sep 17 00:00:00 2001 From: depristo Date: Thu, 19 Nov 2009 12:56:04 +0000 Subject: [PATCH] comments for Aaron git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2081 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/papergenotyper/GATKPaperGenotyper.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java index 461b25197..a1f32b9da 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java @@ -51,8 +51,14 @@ public class GATKPaperGenotyper extends LocusWalker 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;