From f76e2791a945ec0243f9851f074b9ee2c936533c Mon Sep 17 00:00:00 2001 From: corin Date: Mon, 2 May 2011 13:44:50 +0000 Subject: [PATCH] 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 --- R/DataProcessingReport/GetTearsheetStats.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/DataProcessingReport/GetTearsheetStats.R b/R/DataProcessingReport/GetTearsheetStats.R index 119cf64bb..032ff9f84 100644 --- a/R/DataProcessingReport/GetTearsheetStats.R +++ b/R/DataProcessingReport/GetTearsheetStats.R @@ -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