--- a/RScript.r	Wed Oct 14 10:21:13 2015 -0400
+++ b/RScript.r	Thu Oct 15 05:34:17 2015 -0400
@@ -276,6 +276,21 @@
           }
         }
 
+      } else if(nrow(first.rows) > 1) {
+        if(patient1[1,"Sample"] == first.sample){
+          patient1 = patient1[!(patient1$Clone_Sequence %in% first.rows$Clone_Sequence),]
+          patient1 = rbind(patient1, first.sum)
+        } else {
+          patient2 = patient2[!(patient2$Clone_Sequence %in% first.rows$Clone_Sequence),]
+          patient2 = rbind(patient2, first.sum)
+        }
+
+        hidden.clone.sequences = c(first.rows[-1,"Clone_Sequence"])
+        merge.list[["second"]] = append(merge.list[["second"]], hidden.clone.sequences)
+
+        patient.fuzzy = patient.fuzzy[-first.match.filter,]
+
+        cat(paste("<tr bgcolor='#DDF'><td>", patient, " row ", 1:nrow(first.rows), "</td><td>", first.rows$Sample, ":</td><td>", first.rows$Clone_Sequence, "</td><td>", first.rows$normalized_read_count, "</td></tr>", sep=""), file="single_matches.html", append=T)
       } else {
         patient.fuzzy = patient.fuzzy[-1,]
       }