diff --git a/R/isize.R b/R/isize.R
deleted file mode 100644
index b4eb280..0000000
--- a/R/isize.R
+++ /dev/null
@@ -1,36 +0,0 @@
-library(ggplot2)
-library(scales)
-library(grid)
-
-args=commandArgs(trailingOnly=TRUE)
-orient=c("F+", "F-", "R+", "R-")
-ins=read.table(args[1], header=T)
-maxSize = max(ins$Size)
-if ((length(args)>1) & (as.integer(args[2])<maxSize)) {  maxSize = as.integer(args[2]); }
-count=c()
-titleVal="Insert Size ("
-for (o in orient) {
-    s=sum(ins[ins$Orient==o,]$Count)
-    count=c(count, s)
-    lab=paste("#", o, ":", s, sep="")
-    titleVal=paste(titleVal, lab, sep="  ")
-}
-countTotal=sum(count)
-titleVal=paste0(titleVal, "  )")
-
-# Theme
-txtFontSize=10; axisFontSize=16; axisTtlFontSize=18; lgdTtlFontSize=18; lgdFontSize=16;
-sth=theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank(), legend.key=element_blank(), legend.background=element_blank(), panel.background = element_blank(), panel.border=element_blank(), strip.background = element_blank(), axis.line=element_line(size=0.7, color="black"), axis.text.x=element_text(size=axisFontSize), axis.text.y=element_text(size=axisFontSize), axis.title.x=element_text(size=axisTtlFontSize), axis.title.y=element_text(size=axisTtlFontSize), legend.title=element_text(size=lgdTtlFontSize, face="bold"), legend.text=element_text(size=lgdFontSize), text=element_text(size=txtFontSize), plot.title=element_text(size=axisTtlFontSize), strip.text.x=element_text(size=axisTtlFontSize))
-
-png(paste(args[1], "png", sep="."), height=800, width=800)
-#pdf(paste(args[1], "pdf", sep="."), height=8, width=8)
-grid.newpage()
-pushViewport(viewport(layout=grid.layout(4,2)))
-p1=ggplot(data=ins, aes(x=Size, y=Count)) + geom_freqpoly(aes(colour=Orientation), size=1.2, stat="identity") + scale_y_continuous(labels=comma) + xlim(0, maxSize) + ggtitle(titleVal) + sth
-#p1=ggplot(data=ins, aes(x=Size, y=Count)) + geom_freqpoly(aes(colour=Orientation), size=1.2, stat="identity") + scale_y_log10(labels=comma) + xlim(0, maxSize) + ggtitle(titleVal) + sth
-p2=ggplot(data=ins, aes(x=Size, y=Count)) + geom_freqpoly(aes(colour=Orientation), size=1.2, stat="identity") + scale_y_continuous(labels=comma) + xlim(0, maxSize) + facet_wrap(~ Orientation, nrow=2, ncol=2) + sth
-print(p1, vp = viewport(layout.pos.row=1:2, layout.pos.col=1:2))
-print(p2, vp = viewport(layout.pos.row=3:4, layout.pos.col=1:2))
-dev.off()
-print(warnings())
-
diff --git a/R/rd.R b/R/rd.R
deleted file mode 100644
index 97589b5..0000000
--- a/R/rd.R
+++ /dev/null
@@ -1,91 +0,0 @@
-library(optparse)
-
-optl = list(
-     	    make_option(c("-f", "--file"), type="character", default=NULL, help="input coverage file"),
-	    make_option(c("-r", "--region"), type="character", default=NULL, help="region chr:start-end"),
-	    make_option(c("-v", "--vcf"), type="character", default=NULL, help="SV vcf file"),
-	    make_option(c("-s", "--sample"), type="character", default=NULL, help="sample ID")
-	    )
-
-opt_parser = OptionParser(option_list=optl)
-opt = parse_args(opt_parser)
-
-if (is.null(opt$file)) {
-   print_help(opt_parser)
-   stop("Input coverage file is missing!", call.=FALSE)
-}
-
-
-library(ggplot2)
-library(reshape2)
-library(scales)
-library(VariantAnnotation)
-
-gg_color_hue = function(n) {
-  hues=seq(15,375,length=n+1)
-  hcl(h=hues, l=65, c=100)[1:n]
-}
-
-cov = read.table(opt$file, header=T)
-col = 5
-if (!is.null(opt$sample) && (opt$sample %in% colnames(cov))) {  col = which(colnames(cov) == opt$sample); }
-chr = NULL
-if (!is.null(opt$region)) {
-   s=unlist(strsplit(opt$region, ":"))
-   chr=s[1]
-   minStart = 0
-   maxStart = max(cov[cov$chr==chr,]$start) + 1
-   if (length(s) > 1) {
-      v=unlist(strsplit(s[2], "-"))
-      minStart = as.integer(v[1])
-      maxStart = as.integer(v[2])
-   }
-}
-sv = NULL
-if (!is.null(opt$vcf)) {
-  vcf = readVcf(opt$vcf, "hg19")
-  svChr = as.vector(seqnames(rowRanges(vcf)))
-  svStart = start(rowRanges(vcf))
-  svEnd = info(vcf)$END
-  svId = names(rowRanges(vcf))
-  svType = info(vcf)$SVTYPE
-  sv = data.frame(svChr, svStart, svEnd, svId, svType)
-  sv[sv$svType=="TRA",]$svEnd = sv[sv$svType=="TRA",]$svStart
-  sv$middle = as.integer( (sv$svStart + sv$svEnd) / 2 )
-  sv$yv = 4
-  sv = melt(sv, id.vars=c("svChr", "svType", "svId", "yv"))
-  sv[sv$variable=="middle",]$yv = sv[sv$variable=="middle",]$yv + 1.5
-}
-
-
-  
-
-cov=cov[cov[,col]!=0,]
-md=median(cov[,col])
-cov$cn=(cov[,col]/md)*2
-lab=colnames(cov)[col]
-
-if (is.null(chr)) { chrs = unique(cov$chr); } else { chrs = c(chr); }
-
-# Plot individual chromosomes
-for (cr in chrs) {
-    chrCov = cov[cov$chr==cr,]
-    if (!is.null(chr)) chrCov = chrCov[(chrCov$start>=minStart) & (chrCov$start < maxStart),]
-    maxcn = ceiling(quantile(chrCov$cn, 0.999))
-    if (maxcn < 6) maxcn = 6
-    if (max(chrCov$cn) > maxcn) { chrCov[chrCov$cn>maxcn,]$cn = maxcn; }
-    
-    p1=ggplot(data=chrCov, aes(x=start, y=cn)) + geom_point(alpha=1/4, size=0.5)
-    p1=p1 + xlab(paste0(lab, " - ", cr)) + ylab("CN estimate")
-    p1=p1 + scale_y_continuous(breaks=0:maxcn, labels=as.character(0:maxcn), limits=c(0,maxcn))
-    p1=p1 + scale_x_continuous(labels=comma)
-    if (!is.null(sv)) {
-       svChr = sv[sv$svChr==cr,]
-       if (nrow(svChr)) {
-              p1=p1 + geom_line(data=svChr, aes(x=value, y=yv, group=svId, colour=svType));
-       }
-    }
-    ggsave(paste0(lab, ".", cr, ".png"), width=16, height=6)
-}
-print(warnings())
-quit()
diff --git a/R/replication.R b/R/replication.R
deleted file mode 100644
index 6b70205..0000000
--- a/R/replication.R
+++ /dev/null
@@ -1,69 +0,0 @@
-library(ggplot2)
-library(reshape2)
-library(scales)
-
-# Read data
-args=commandArgs(trailingOnly=TRUE)
-cov = read.table(args[1], header=T)
-chr=NA
-if (length(args) > 1) {
-   s=unlist(strsplit(args[2], ":"))
-   chr=s[1]
-   minStart = 0
-   maxStart = max(cov[cov$chr==chr,]$start) + 1
-   if (length(s) > 1) {
-      v=unlist(strsplit(s[2], "-"))
-      minStart = as.integer(v[1])
-      maxStart = as.integer(v[2])
-   }
-}
-cov=cov[cov[,5]!=0,]
-s=boxplot(cov[,5], plot=F)$stats
-lq=s[2,1]
-uq=s[4,1]
-iqrcov=cov[cov[,5]>=lq & cov[,5]<=uq,5]
-mu=mean(iqrcov)
-sdev=sd(cov[,5])
-cov=cov[cov[,5]>=(mu - 3*sdev) & cov[,5]<=(mu+3*sdev),]
-cov$zscores=(cov[,5] - mu)/sdev
-lab=colnames(cov)[5]
-
-if (is.na(chr)) { chrs = unique(cov$chr); } else { chrs = c(chr); }
-
-# Plot individual chromosomes
-plot = T
-for (cr in chrs) {
-    chrCov = cov[cov$chr==cr,]
-    if (!is.na(chr)) chrCov = chrCov[(chrCov$start>=minStart) & (chrCov$start < maxStart),]
-    chrCov$spl = fitted(with(chrCov, smooth.spline(start, zscores, spar=0.3)))
-
-    # Find contiguous blocks
-    medDist = median(chrCov$start[-1] - chrCov$start[1:nrow(chrCov)-1])
-    runs = rle((chrCov$start[-1] - chrCov$start[1:nrow(chrCov)-1]) == medDist)
-    idx = 1
-    rd = data.frame()
-    for(i in 1:length(runs$values)) {
-    	  if ((runs$values[i]==T) && (runs$length[i]>20)) {
-	     subset = chrCov[idx:(idx+runs$length[i]),]
-	     subset$grp = idx
-	     rd = rbind(rd, subset)
-	  }
-	  idx = idx + runs$length[i]
-    }
-
-    # Plot segments
-    if (plot) {
-        p1=ggplot(data=rd, aes(x=start, y=zscores)) + geom_point(alpha=1/4, size=1)
-    	p1=p1 + xlab(paste0(lab, " - ", cr)) + ylab("Read depth")
-	p1=p1 + scale_y_continuous(labels=comma) 
-	p1=p1 + scale_x_continuous(labels=comma)
-	p1=p1 + geom_line(data=rd, aes(x=start, y=spl, group=grp), color="darkblue", size=1.5)
-	ggsave(paste0(lab, ".", cr, ".png"), width=16, height=6)
-    } else {
-      	colnames(rd)[colnames(rd)=="spl"] = paste0(lab, "spl");
-        write.table(rd[,c("chr", "start", paste0(lab, "spl"))], file=paste0(lab, ".", cr, ".spl.tsv"), sep="\t", quote=FALSE, row.names=FALSE)
-    }
-}
-print(warnings())
-quit()
-