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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
This commit is contained in:
kiran 2010-09-09 19:56:00 +00:00
parent f5c295b6b2
commit dfdd0b69a9
1 changed files with 2 additions and 3 deletions
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5
R/VariantRecalibratorReport/VariantRecalibratorReport.R
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@ -1,6 +1,5 @@
library(ellipse); library(ellipse);
library(hexbin); library(hexbin);
library(rgl);
getAnnIndex <- function(d, ann) { getAnnIndex <- function(d, ann) {
index = -1; index = -1;
@ -231,8 +230,8 @@ print("Greedy reading")
d = read.table(vcfTable, header=TRUE, nrows = greedy); d = read.table(vcfTable, header=TRUE, nrows = greedy);
c = read.clusters(clusterFile); c = read.clusters(clusterFile);
d.known = d[which(d$DB == 1),]; d.known = d[which(d$DB == 1 | d$ID != "."),];
d.novel = d[which(d$DB == 0),]; d.novel = d[which(d$DB == 0 | d$ID == "."),];
d.loci = NA; d.loci = NA;
if (length(l) > 0) { if (length(l) > 0) {
d.loci = d[which(d$POS %in% l),]; d.loci = d[which(d$POS %in% l),];