# HG changeset patch
# User davidvanzessen
# Date 1503067411 14400
# Node ID 275e759e7985085af2f6a94babb5c5e7565a3adb
# Parent  3b5fe323f563061f1322cf46e46ec9874bc3fa5a
Uploaded

diff -r 3b5fe323f563 -r 275e759e7985 merge_and_filter.r
--- a/merge_and_filter.r	Wed Jul 26 10:24:49 2017 -0400
+++ b/merge_and_filter.r	Fri Aug 18 10:43:31 2017 -0400
@@ -220,7 +220,7 @@
 if(filter.unique != "no"){
 	clmns = names(result)
 	if(filter.unique == "remove_vjaa"){
-		result$unique.def = paste(result$V.GENE.and.allele, result$J.GENE.and.allele, result$CDR3.IMGT.seq)
+		result$unique.def = paste(result$VGene, result$JGene, result$CDR3.IMGT.AA)
 	} else if(empty.region.filter == "leader"){
 		result$unique.def = paste(result$FR1.IMGT.seq, result$CDR1.IMGT.seq, result$FR2.IMGT.seq, result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq)
 	} else if(empty.region.filter == "FR1"){
@@ -238,7 +238,9 @@
 		result = result[result$unique.def %in% unique.defs$Var1,]
 	}
 
-	result$unique.def = paste(result$unique.def, gsub(",.*", "", result$best_match)) #keep the unique sequences that are in multiple classes, gsub so the unmatched don't have a class after it
+	if(filter.unique != "remove_vjaa"){
+		result$unique.def = paste(result$unique.def, gsub(",.*", "", result$best_match)) #keep the unique sequences that are in multiple classes, gsub so the unmatched don't have a class after it
+	}
 
 	result = result[!duplicated(result$unique.def),]
 }