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Update to work with latest eval format 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5720 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2011-05-02 13:44:50 +00:00
parent 139ae79d9e
commit f76e2791a9
1 changed files with 3 additions and 3 deletions
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6
R/DataProcessingReport/GetTearsheetStats.R
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@ -18,7 +18,7 @@ cmdargs = gsa.getargs(
list(
yaml = list(value=NA, doc="pipeline YAML file"),
bamlist = list(value=NA, doc="list of BAM files"),
evalroot = list(value=NA, doc="VariantEval root"),
evalroot = list(value=NA, doc="VariantEval file"),
tearout = list(value=NA, doc="Output path for tearsheet PDF")#,
plotout = list(value=NA, doc="Output path for PDF")
),
@ -102,7 +102,7 @@ tearsheet<-function(){
#plot title bar
par(mar=c(0,0,0,0))
plot(drop)
text(155, 50, "NonAutism_Walsh", family="serif", adj=c(0,0), cex=3, col=gray(.25))
text(155, 50, "testing", family="serif", adj=c(0,0), cex=3, col=gray(.25))
# Project summary
@ -249,7 +249,7 @@ tearsheet<-function(){
textplot(table3, rmar=1, col.rownames="dark blue", show.colnames=FALSE, cex=1.25, valign="top")
title(main="Sequencing Summary", family="sans", cex.main=1.25, line=0)
eval = gsa.read.gatkreport("NonAutism_Walsh.cleaned.snps_and_indels.filtered.annotated.eval")
eval = gsa.read.gatkreport(cmdargs$evalroot)
# Variant summary