args <- commandArgs(TRUE)
if(length(args)!=3){
  stop('usage:Rscript $0 <sample_prefix> <insertsize.plot from bamdst> <depth_distribution.plot from bamddst>')
}
sample<-args[1]
png(paste0(sample,".png"),width=1024,height=768)
layout(matrix(c(1,1,2,3),2,2,byrow=T))
insert<-read.table(args[2])
depth<-read.table(args[3])
par(cex=1.5)
plot(insert[,1],insert[,3],type="h",xlim=c(0,1000),col="red",main="Insert size distribution",xlab="Insert size",ylab="Read percent",xaxt="n")
axis(1,seq(0,1000,100))
a<-ceiling(weighted.mean(depth[,1],depth[,2])*3/100)*100
plot(depth[,1],depth[,5],xlim=c(0,a),type="l",col="red",xlab="Base depth",ylab="Cumulative base",main="Base depth cumulative distribution")
plot(depth[,1],depth[,3],xlim=c(0,a),type="h",col="red",xlab="Base depth",ylab="Base percent",main="Base depth distribution")
dev.off()