# HG changeset patch
# User davidvanzessen
# Date 1438941141 14400
# Node ID b45a7424862863b1646340dedc11f0176e3da50b
# Parent  010402c959aad9f8d7e4d2f3ff2543814d3356a6
Uploaded

diff -r 010402c959aa -r b45a74248628 report_clonality/RScript.r
--- a/report_clonality/RScript.r	Tue Aug 04 10:00:20 2015 -0400
+++ b/report_clonality/RScript.r	Fri Aug 07 05:52:21 2015 -0400
@@ -114,6 +114,14 @@
 
 # ---------------------- Counting the productive/unproductive and unique sequences ----------------------
 
+if(!("Functionality" %in% inputdata)){ #add a functionality column to the igblast data
+  inputdata$Functionality = "unproductive"
+  search = (inputdata$VDJ.Frame != "In-frame with stop codon" & inputdata$VDJ.Frame != "Out-of-frame" & inputdata$CDR3.Found.How != "NOT_FOUND")
+  if(sum(search) > 0){
+    inputdata[search,]$Functionality = "productive"
+  }
+}
+
 inputdata.dt = data.table(inputdata) #for speed
 
 if(clonaltype == "none"){