From 8a57c52005de5c2516bf83979d29c38992fa457c Mon Sep 17 00:00:00 2001
From: corin <corin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 26 May 2011 19:57:49 +0000
Subject: [PATCH] Produces a more throurough tearsheet with detailed metrics
 and information

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5882 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/DataProcessingReport/tearsheetMaker.r | 34 +++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 R/DataProcessingReport/tearsheetMaker.r

diff --git a/R/DataProcessingReport/tearsheetMaker.r b/R/DataProcessingReport/tearsheetMaker.r
new file mode 100644
index 000000000..68cfe30e1
--- /dev/null
+++ b/R/DataProcessingReport/tearsheetMaker.r
@@ -0,0 +1,34 @@
+source("/humgen/gsa-pipeline/.repository/R/DataProcessingReport/Tearsheet.R")
+cmdargs = gsa.getargs(
+    list(
+        title = list(value=NA, doc="Title for the tearsheet"),
+        tsv = list(value=NA, doc="pipeline tsv file"),
+        evalroot = list(value=NA, doc="VariantEval file base (everything before the .eval)"),
+        tearout = list(value=NA, doc="Output path for tearsheet PDF")#,
+    ),
+    doc="Creates a tearsheet"
+);
+
+read.delim(cmdargs$tsv, header=FALSE)->settable
+
+squids<-unique(settable[,1])
+
+lane<-data.frame()
+samp<-data.frame()
+for(squid in squids){
+  gsa.read.squidmetrics(squid, TRUE)->lanemetrics 
+  addlanes<-lanemetrics[which(lanemetrics$"External ID" %in% settable[,2]),]
+  gsa.read.squidmetrics(squid, FALSE)->samplemetrics 
+  addsamps<-samplemetrics[which(samplemetrics$"Sample" %in% settable[,2]),]
+  lane<-rbind(lane, addlanes)
+  samp<-rbind(samp, addsamps)
+}
+print("Picard Data Obtained...")
+gsa.read.gatkreport(paste(cmdargs$evalroot, ".eval", sep=""))->basiceval 
+gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraFC.eval", sep=""))->FCeval 
+gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraSA.eval", sep=""))->SAeval 
+print("Evals read")
+  pdf(file= cmdargs$tearout, width=22, height=17, pagecentre=TRUE, pointsize=24) 
+    print("PDF created...")
+tearsheet()
+dev.off()
\ No newline at end of file