From 9ef391706cdbb494b4e295c2c1e64a95f91fb58e Mon Sep 17 00:00:00 2001 From: kiran Date: Wed, 17 Jun 2009 21:31:46 +0000 Subject: [PATCH] Added outputting of genotype posteriors to geli.calls file. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1035 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/utils/AlleleFrequencyEstimate.java | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java b/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java index 20e89feda..05afdf8ce 100755 --- a/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java +++ b/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java @@ -171,7 +171,8 @@ public class AlleleFrequencyEstimate { // chr1 7764136 A 48 99 CC 83.650421 9.18159 -92.83638 -18.367548 -96.91729 -96.614204 -9.185958 -23.33643 -23.033337 -101.282059 -101.583092 -101.279999 // chr pos ref Nreads maxMapQ genotype BtrLod BtnbLod dbSNP AA AC AG AT CC CG CT GG GT TT - return String.format("%s %16d %c %8d %d %s %.6f %.6f 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0", + //public double[] posteriors; + return String.format("%s %16d %c %8d %d %s %.6f %.6f %6.6f %6.6f %6.6f %6.6f %6.6f %6.6f %6.6f %6.6f %6.6f %6.6f", location.getContig(), location.getStart(), ref, @@ -179,7 +180,17 @@ public class AlleleFrequencyEstimate { -1, genotype(), lodVsRef, - lodVsNextBest); + lodVsNextBest, + posteriors[0], + posteriors[1], + posteriors[2], + posteriors[3], + posteriors[4], + posteriors[5], + posteriors[6], + posteriors[7], + posteriors[8], + posteriors[9]); } public String asTabularString()