--- a/tmp/igat.r	Wed Jun 22 10:07:28 2016 -0400
+++ b/tmp/igat.r	Thu Jun 23 03:58:03 2016 -0400
@@ -13,14 +13,14 @@
 merged = merged[!grepl("unmatched", merged$best_match),]
 
 for(f in list.files(imgt.dir, pattern="*.txt$")){
-	print(paste("filtering", f))
+	#print(paste("filtering", f))
 	path = paste(imgt.dir, f, sep="")
 	dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F)
 	
 	dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
 	
-	if(nrow(dat) > 0 &  "FR1.IMGT" %in% colnames(dat)){
-		dat$FR1.IMGT = ""
+	if(nrow(dat) > 0 & grepl("^8_", f)){ #change the FR1 columns to 0 in the "8_..." file
+		dat[,grepl("^FR1", names(dat))] = 0
 	}
 	
 	write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T)