From dfdd0b69a9116051b48a682f72cdf782773d3f6f Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 9 Sep 2010 19:56:00 +0000
Subject: [PATCH] Removed unused dependency (it was causing a problem by
 looking for an X11 connection that didn't necessarily exist).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4244 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/VariantRecalibratorReport/VariantRecalibratorReport.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/VariantRecalibratorReport/VariantRecalibratorReport.R b/R/VariantRecalibratorReport/VariantRecalibratorReport.R
index 20f67de2c..aa4622f01 100644
--- a/R/VariantRecalibratorReport/VariantRecalibratorReport.R
+++ b/R/VariantRecalibratorReport/VariantRecalibratorReport.R
@@ -1,6 +1,5 @@
 library(ellipse);
 library(hexbin);
-library(rgl);
 
 getAnnIndex <- function(d, ann) {
     index = -1;
@@ -231,8 +230,8 @@ print("Greedy reading")
 d = read.table(vcfTable, header=TRUE, nrows = greedy);
 c = read.clusters(clusterFile);
 
-d.known = d[which(d$DB == 1),];
-d.novel = d[which(d$DB == 0),];
+d.known = d[which(d$DB == 1 | d$ID != "."),];
+d.novel = d[which(d$DB == 0 | d$ID == "."),];
 d.loci = NA;
 if (length(l) > 0) {
     d.loci = d[which(d$POS %in% l),];