--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge.r	Mon Dec 12 05:22:37 2016 -0500
@@ -0,0 +1,27 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+input.1 = args[1]
+input.2 = args[2]
+
+fields.1 = args[3]
+fields.2 = args[4]
+
+field.1 = args[5]
+field.2 = args[6]
+
+output = args[7]
+
+dat1 = read.table(input.1, header=T, sep="\t", quote="", stringsAsFactors=F, fill=T, row.names=NULL)
+if(fields.1 != "all"){
+	fields.1 = unlist(strsplit(fields.1, ","))
+	dat1 = dat1[,fields.1]
+}
+dat2 = read.table(input.2, header=T, sep="\t", quote="", stringsAsFactors=F, fill=T, row.names=NULL)
+if(fields.2 != "all"){
+	fields.2 = unlist(strsplit(fields.2, ","))
+	dat2 = dat2[,fields.2]
+}
+
+dat3 = merge(dat1, dat2, by.x=field.1, by.y=field.2)
+
+write.table(dat3, output, sep="\t",quote=F,row.names=F,col.names=T)