# HG changeset patch
# User davidvanzessen
# Date 1446652921 18000
# Node ID 39ea37070e904a9e2329989812d6079c6e989b8c
# Parent  b1ad6f515338086818bad078859ee703d1abb303
Uploaded

diff -r b1ad6f515338 -r 39ea37070e90 RScript.r
--- a/RScript.r	Tue Nov 03 10:49:26 2015 -0500
+++ b/RScript.r	Wed Nov 04 11:02:01 2015 -0500
@@ -714,6 +714,10 @@
         hidden.clone.sequences = c(rows.1[-1,"Clone_Sequence"], rows.3[rows.3$Clone_Sequence != first.clone.sequence,"Clone_Sequence"])
         merge.list[["second"]] = append(merge.list[["second"]], hidden.clone.sequences)
 
+      } else if(nrow(rows.1) > 1){
+        patient1 = patient1[!(patient1$Clone_Sequence %in% rows.1$Clone_Sequence),]
+        patient1 = rbind(patient1, sum.1)
+        patient.fuzzy = patient.fuzzy[-match.filter.1,]
       } else {
         patient.fuzzy = patient.fuzzy[-1,]
       }
@@ -745,9 +749,9 @@
   patientMerge13$thresholdValue = pmax(patientMerge13[,onx], patientMerge13[,ony])
   patientMerge23$thresholdValue = pmax(patientMerge23[,onx], patientMerge23[,ony])
 
-  patient1 = patient1[!(patient1$Clone_Sequence %in% patient.merge.list.second[[label1]]),]
-  patient2 = patient2[!(patient2$Clone_Sequence %in% patient.merge.list.second[[label1]]),]
-  patient2 = patient3[!(patient3$Clone_Sequence %in% patient.merge.list.second[[label1]]),]
+  patient1 = patient1[!(patient1$Clone_Sequence %in% merge.list[["second"]]),]
+  patient2 = patient2[!(patient2$Clone_Sequence %in% merge.list[["second"]]),]
+  patient3 = patient3[!(patient3$Clone_Sequence %in% merge.list[["second"]]),]
 
   if(F){
     patientMerge = merge(patient1, patient2, by="merge")