--- a/RScript.r	Mon Oct 12 10:48:32 2015 -0400
+++ b/RScript.r	Tue Oct 13 09:13:24 2015 -0400
@@ -67,7 +67,7 @@
 
 patient.merge.list = list() #cache the 'both' table, 2x speedup for more memory...
 patient.merge.list.second = list()
-
+cat(paste("<table border='0'>", sep=""), file="multiple_matches.html", append=T)
 patientCountOnColumn <- function(x, product, interval, on, appendtxt=F){
   if (!is.data.frame(x) & is.list(x)){
     x = x[[1]]
@@ -175,7 +175,6 @@
 
     merge.list[["second"]] = vector()
 
-
     while(nrow(patient.fuzzy) > 1){
       first.merge = patient.fuzzy[1,"merge"]
       first.clone.sequence = patient.fuzzy[1,"Clone_Sequence"]
@@ -234,7 +233,7 @@
         second.rows.j = table(second.rows$J_Segment_Major_Gene)
         second.rows.j = names(second.rows.j[which.max(second.rows.j)])
 
-        second.sum = data.frame(merge = first.clone.sequence,
+        second.sum = data.frame(merge = paste(first.clone.sequence, "*", sep=""),
                                Patient = patient,
                                Receptor = second.rows[1,"Receptor"],
                                Sample = second.rows[1,"Sample"],
@@ -270,7 +269,7 @@
         }
 
         if(nrow(first.rows) > 1 | nrow(second.rows) > 1){
-
+          cat(paste("<tr><td>", patient, ": ", nrow(first.rows), " ", nrow(second.rows), " ", first.clone.sequence,  "</td></tr>", sep=""), file="multiple_matches.html", append=T)
         }
 
       } else {