--- a/tmp/igat.r	Thu Jun 16 05:05:47 2016 -0400
+++ b/tmp/igat.r	Thu Jun 16 10:01:54 2016 -0400
@@ -2,9 +2,14 @@
 
 imgt.dir = args[1]
 merged.file = args[2]
+gene = args[3]
 
 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
 
+if(gene != "-"){
+	merged = merged[grepl(gene, merged$best_match),]
+}
+
 merged = merged[!grepl("unmatched", merged$best_match),]
 
 for(f in list.files(imgt.dir, pattern="*.txt$")){
@@ -14,7 +19,7 @@
 	
 	dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
 	
-	if("FR1.IMGT" %in% colnames(dat)){
+	if(nrow(dat) > 0 &  "FR1.IMGT" %in% colnames(dat)){
 		dat$FR1.IMGT = ""
 	}