--- a/merge_and_filter.r	Thu Dec 08 04:51:09 2016 -0500
+++ b/merge_and_filter.r	Mon Dec 12 05:19:58 2016 -0500
@@ -119,22 +119,17 @@
 
 if(empty.region.filter == "leader"){
 	result = result[result$FR1.IMGT.seq != "" & result$CDR1.IMGT.seq != "" & result$FR2.IMGT.seq != "" & result$CDR2.IMGT.seq != "" & result$FR3.IMGT.seq != "", ]
-	print(paste("Number of sequences after empty FR1, CDR1, FR2, CDR2 and FR3 column filter:", nrow(result)))
-	filtering.steps = rbind(filtering.steps, c("After empty FR1, CDR1, FR2, CDR2, FR3 filter", nrow(result)))
 } else if(empty.region.filter == "FR1"){
 	result = result[result$CDR1.IMGT.seq != "" & result$FR2.IMGT.seq != "" & result$CDR2.IMGT.seq != "" & result$FR3.IMGT.seq != "", ]
-	print(paste("Number of sequences after empty CDR1, FR2, CDR2 and FR3 column filter:", nrow(result)))
-	filtering.steps = rbind(filtering.steps, c("After empty CDR1, FR2, CDR2, FR3 filter", nrow(result)))
 } else if(empty.region.filter == "CDR1"){
 	result = result[result$FR2.IMGT.seq != "" & result$CDR2.IMGT.seq != "" & result$FR3.IMGT.seq != "", ]
-	print(paste("Number of sequences after empty FR2, CDR2 and FR3 column filter:", nrow(result)))
-	filtering.steps = rbind(filtering.steps, c("After empty FR2, CDR2, FR3 filter", nrow(result)))
 } else if(empty.region.filter == "FR2"){
 	result = result[result$CDR2.IMGT.seq != "" & result$FR3.IMGT.seq != "", ]
-	print(paste("Number of sequences after empty CDR2 and FR3 column filter:", nrow(result)))
-	filtering.steps = rbind(filtering.steps, c("After empty CDR2, FR3 filter", nrow(result)))
 }
 
+print(paste("After removal sequences that are missing a gene region:", nrow(result)))
+filtering.steps = rbind(filtering.steps, c("After removal sequences that are missing a gene region", nrow(result)))
+
 if(empty.region.filter == "leader"){
 	result = result[!(grepl("n|N", result$FR1.IMGT.seq) | grepl("n|N", result$FR2.IMGT.seq) | grepl("n|N", result$FR3.IMGT.seq) | grepl("n|N", result$CDR1.IMGT.seq) | grepl("n|N", result$CDR2.IMGT.seq) | grepl("n|N", result$CDR3.IMGT.seq)),]
 } else if(empty.region.filter == "FR1"){