From 92c63fb53099114438cadd0e8ced3f6a6d79ac13 Mon Sep 17 00:00:00 2001 From: jmaguire Date: Mon, 17 Aug 2009 18:44:09 +0000 Subject: [PATCH] It's just "lod" not discovery_lod now. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1427 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java index f883a134f..d3f44faa0 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java @@ -40,7 +40,7 @@ public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes { public double getMAF() { return Double.parseDouble(this.get("EM_alt_freq")); } public double getHeterozygosity() { return 2 * getMAF() * (1 - getMAF()); } public boolean isGenotype() { return false; } - public double getVariationConfidence() { return Double.parseDouble(this.get("discovery_lod")); } + public double getVariationConfidence() { return Double.parseDouble(this.get("lod")); } public double getConsensusConfidence() { return -1; } public List getGenotype() throws IllegalStateException { throw new IllegalStateException(); } public int getPloidy() throws IllegalStateException { return 2; }