diff --git a/merge.R b/merge.R
deleted file mode 100644
index cfa5f03..0000000
--- a/merge.R
+++ /dev/null
@@ -1,60 +0,0 @@
-#!/home/jhamp/.conda/envs/tfbs/bin/Rscript
-#library(data.table)
-#args=commandArgs(TRUE)
-#min=as.numeric(args[1])
-#max=as.numeric(args[2])
-#folder=args[3]
-#splitted = fread(paste(folder, "/pass2Tr.bed", sep=''), header=FALSE)
-#colnames(splitted) = c("chromosome", "start", "stop", "id", "score", "length", "maxpos", "bonus_info")
-#p1 = fread(paste(folder, "/pass1Tr.bed", sep=''), header=TRUE)
-#colnames(p1) = c("chromosome", "start", "stop", "id", "score", "length", "maxpos", "bonus_info")
-#p1$maxpos = p1$start + p1$maxpos
-
-#splitted=rbind(splitted, p1)
-
-#splitted=splitted[which(splitted$stop - splitted$start >= min),]
-#splitted=splitted[which(splitted$stop - splitted$start <= max),]
-#splitted$id=make.unique(as.character(splitted$id))
-#splitted$length=splitted$stop - splitted$start
-
-#splitted=cbind(splitted, containsMaxpos=0)
-#splitted$containsMaxpos[intersect(which(splitted$start <= splitted$maxpos), which(splitted$stop > splitted$maxpos))] = 1
-#splitted$maxpos = splitted$maxpos - splitted$start
-#fwrite(splitted, paste(folder, "/merged.bed", sep=''), row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t')
-
-#!/bin/Rscript
-library(data.table)
-args=commandArgs(TRUE)
-min=as.numeric(args[1])
-max=as.numeric(args[2])
-folder=args[3]
-
-splitted = fread(paste(folder, "/pass2Tr.bed", sep=''))
-colnames(splitted) = c("chromosome", "start", "stop", "id", "score", "length", "maxpos", "info")
-p1 = fread(paste(folder, "/pass1Tr.bed", sep=''))
-colnames(p1) = c("chromosome", "start", "stop", "id", "score", "length", "maxpos", "info")
-
-p1$maxpos = p1$start + p1$maxpos
-
-splitted=rbind(splitted, p1)
-
-splitted=splitted[which(splitted$stop - splitted$start >= min),]
-splitted=splitted[which(splitted$stop - splitted$start <= max),]
-splitted$id=make.unique(as.character(splitted$id))
-splitted$length=splitted$stop - splitted$start
-
-splitted=cbind(splitted, containsMaxpos=0)
-splitted$containsMaxpos[intersect(which(splitted$start <= splitted$maxpos), which(splitted$stop > splitted$maxpos))] = 1
-splitted$maxpos = splitted$maxpos - splitted$start
-data.table::fwrite(splitted, paste(folder, "/merged.bed", sep=''), row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t')
-
-before = fread(args[4], header=FALSE)
-
-sumb=sum(before$V3-before$V2)
-suma=sum(splitted$length)
-difference = formatC(sumb/suma, digits=4)
-loss = formatC(1 - suma/sumb, digits=2)
-lengthb = formatC(mean(before$V3-before$V2), digits=4)
-lengtha = formatC(mean(splitted$length), digits=4)
-stats=data.frame(sum_nt_input=sumb, sum_nt_filtered=suma, factor=difference, loss=loss, mean_length_input=lengthb, mean_length_filtered=lengtha)
-write.table(stats, "./FilterMotifs.stats", row.names=FALSE, quote=FALSE, sep='\t')