--- a/new_imgt.r	Mon Dec 12 05:19:58 2016 -0500
+++ b/new_imgt.r	Tue Dec 13 10:06:49 2016 -0500
@@ -4,7 +4,7 @@
 merged.file = args[2]
 gene = args[3]
 
-merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
+merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F, comment.char="")
 
 if(gene != "-"){
 	merged = merged[grepl(paste("^", gene, sep=""), merged$best_match),]
@@ -17,7 +17,7 @@
 for(f in list.files(imgt.dir, pattern="*.txt$")){
 	#print(paste("filtering", f))
 	path = paste(imgt.dir, f, sep="")
-	dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F, check.names=FALSE)
+	dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F, check.names=FALSE, comment.char="")
 	
 	dat = dat[dat[,"Sequence ID"] %in% merged$Sequence.ID,]