--- a/shm_csr.r	Mon Nov 07 03:04:07 2016 -0500
+++ b/shm_csr.r	Mon Nov 07 06:52:53 2016 -0500
@@ -175,6 +175,8 @@
 
 setwd(outputdir)
 
+write.table(dat, input, sep="\t",quote=F,row.names=F,col.names=T)
+
 base.order = data.frame(base=c("A", "T", "C", "G"), order=1:4)
 
 calculate_result = function(i, gene, dat, matrx, f, fname, name){
@@ -437,8 +439,6 @@
 
 write.table(dat[,c("Sequence.ID", "best_match", "VRegionMutations", "VRegionNucleotides", "percentage_mutations")], "scatter.txt", sep="\t",quote=F,row.names=F,col.names=T)
 
-write.table(dat, input, sep="\t",quote=F,row.names=F,col.names=T)
-
 print("Plotting frequency ranges plot")
 
 dat$best_match_class = substr(dat$best_match, 0, 3)