args<- commandArgs(TRUE)
sam <- args[1]
sam_data <- read.table(file=paste(sam,".cov",sep=""),header = TRUE,sep="\t",as.is=TRUE)
ncols<-dim(sam_data)[2]
if (ncols ==5 ) {
    sam_data <- sam_data[,c(1,5)]
}else if (ncols ==10 ) {
    sam_data <- sam_data[,c(1,7)]
}else{
    q(save = FALSE)
}

names(sam_data) <- c('contig',sam)
sam_m <- mean(sam_data[,2])
sam_sd<- sd(sam_data[,2])

vals<-sam_data[,sam]
vals=vals/sam_m
vals[vals < 0.07] <- 0.07
sam_data$Mean <- vals
Y_median<-fivenum(sam_data[sam_data$contig=='Y',sam])[3]
fivenum(sam_data[sam_data$contig=='Y',sam])
y_mean <- mean(sam_data[sam_data$contig=='Y','Mean'])
y_mean
sex <- 'F'
if(y_mean > 0.5){
  sex <- 'M'
}

pdf(file=paste(sam,sex,"QC_plot.pdf",sep="_"),width = 10)

hist(sam_data[,sam],breaks=1000,xlim=c(0,500),col='lightblue',
     xlab='Counts',main=paste(sam,' Counts/Bin. Mean= ',
     round(sam_m,0),' SD=',round(sam_sd,0),sep=''),freq = F)

hist(sam_data[,'Mean'],breaks=1000,xlim=c(0,3),col='lightblue',
     xlab='Copy-Ratio',main=paste(sam,' Bin Copy-Ratio Distributions',sep=''),freq = F)
hist(sam_data[sam_data$contig =='X' |sam_data$contig =='Y',sam],breaks=1000,xlim=c(0,500),col='lightblue',
     xlab='Counts',main=paste(sam,' XY Counts/Bin. Mean= ',
     round(sam_m,0),' SD=',round(sam_sd,0),sep=''),freq = F)
hist(sam_data[sam_data$contig =='X' |sam_data$contig =='Y','Mean'],breaks=1000,xlim=c(0,3),col='lightblue',
     xlab='Copy-Ratio',main=paste(sam,' XY Bin Copy-Ratio Distributions',sep=''),freq = F)

boxplot(sam_data[,sam] ~ ordered(sam_data$contig,levels=c(1:22,'X','Y')),ylim=c(0,500),
        main=paste(sam,'-Boxplot of Counts/Bin. Mean=',round(sam_m,0),
        'SD/Mean=',round(sam_sd/sam_m,2),sep=' ') )

lines(rep(sam_m,24),col='red')

boxplot(sam_data[,'Mean'] ~ ordered(sam_data$contig,levels=c(1:22,'X','Y')),ylim=c(0,3),
        main=paste(sam,'-Boxplot of Copy-Ratio.',sep=' '))
lines(rep(1,24),col='red')

dev.off()