34 lines
1.3 KiB
R
34 lines
1.3 KiB
R
|
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()
|