--- a/report_clonality/RScript.r	Tue Dec 20 09:06:51 2016 -0500
+++ b/report_clonality/RScript.r	Wed Dec 21 05:57:31 2016 -0500
@@ -594,7 +594,10 @@
         res = merge(res, clone_table, by="paste", all=T)
       }
       
-      res[is.na(res)] = 0      
+      res[is.na(res)] = 0
+      
+      write.table(res, file=paste("raw_clonality_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=F)
+      
       infer.result = infer.clonality(as.matrix(res[,2:ncol(res)]))
       
       #print(infer.result)
@@ -607,7 +610,7 @@
       colnames(coincidence.table) = c("Coincidence Type",  "Raw Coincidence Freq")
       write.table(coincidence.table, file=paste("lymphclon_coincidences_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=T)
     }
-  } else {
+  } else if(clonality_method == "old") {
     clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "clonaltype")])
     
     #write files for every coincidence group of >1