--- a/naive_output.r	Wed Apr 20 10:16:25 2016 -0400
+++ b/naive_output.r	Fri Apr 22 05:07:10 2016 -0400
@@ -2,7 +2,9 @@
 
 naive.file = args[1]
 shm.file = args[2]
-output.file = args[3]
+output.file.ca = args[3]
+output.file.cg = args[4]
+output.file.cm = args[5]
 
 naive = read.table(naive.file, sep="\t", header=T, quote="", fill=T)
 shm.merge = read.table(shm.file, sep="\t", header=T, quote="", fill=T)
@@ -14,10 +16,19 @@
 final.numeric = final[,sapply(final, is.numeric)]
 final.numeric[is.na(final.numeric)] = 0
 final[,sapply(final, is.numeric)] = final.numeric
-print(paste("nrow final:", nrow(final)))
-final2 = final
-final2$Sample = gsub("[0-9]", "", final2$Sample)
-final = rbind(final, final2)
-final$Replicate = 1
+
+final.ca = final[grepl("ca", final$Sample),]
+final.cg = final[grepl("cg", final$Sample),]
+final.cm = final[grepl("cm", final$Sample),]
+
+
 
-write.table(final, output.file, quote=F, sep="\t", row.names=F, col.names=T)
+#print(paste("nrow final:", nrow(final)))
+#final2 = final
+#final2$Sample = gsub("[0-9]", "", final2$Sample)
+#final = rbind(final, final2)
+#final$Replicate = 1
+
+write.table(final.ca, output.file.ca, quote=F, sep="\t", row.names=F, col.names=T)
+write.table(final.cg, output.file.cg, quote=F, sep="\t", row.names=F, col.names=T)
+write.table(final.cm, output.file.cm, quote=F, sep="\t", row.names=F, col.names=T)