library(mclust)
args<- commandArgs(TRUE)
chrf<-args[1]
outf<-args[2]
num<- 7
num<- ifelse(is.na(args[3]),num,args[3])
chr.data<-read.table(file=chrf,sep="\t",row.names=1,header=TRUE,comment.char='')
xydata<-chr.data[,1:3]
samples<-row.names(xydata)
xymod<- Mclust(xydata,num)
pdf(file="MBY2_M_chrXY_class.pdf")
plot(xymod, what = "classification")
dev.off()
nclass<-which.max(table(xymod$classification))
refs<-samples[xymod$classification==nclass]
write.table(file=outf,refs,quote=FALSE,row.names=FALSE,col.names=FALSE)