1 files changed, 42 insertions, 0 deletions
diff --git a/0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch b/0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch
new file mode 100644
index 000000000000..b386599ea2e3
--- /dev/null
+++ b/0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch
@@ -0,0 +1,42 @@
+From 02ebdb357913d9c07021e156768e504ef5e27950 Mon Sep 17 00:00:00 2001
+From: Ronny Lorenz <ronny@tbi.univie.ac.at>
+Date: Tue, 28 Jan 2014 17:00:00 +0100
+Subject: [PATCH 6/8] fix bug for co-transcriptional folding with dangles != 0
+
+---
+ Node.cpp | 4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/Node.cpp b/Node.cpp
+index 3f33123..bdc092c 100644
+--- a/Node.cpp
++++ b/Node.cpp
+@@ -581,6 +581,7 @@ Node::FindLocalExtrema()
+ {
+   int *f5, *c, *fML, *fM1, *indx; char *ptype;
+   export_fold_arrays(&f5,&c,&fML,&fM1,&indx,&ptype);
++  if(verbose>=2) Cout("#extrema: "+Str((int)extrema.size())+"\n");
+   int n = matrix_size;
+   for (int i=1; i<=n-TURN-1; i++) {
+     for (int j=i+TURN+1; j<=n; j++) {
+@@ -598,8 +599,8 @@ Node::FindLocalExtrema()
+   // (1,n) is in general not a pair. You can't include it in the list
+   //Node node2=Node(1,n,energy);
+   extrema.push_back(new Node(1,n,energy));//& node2);
+-  sort(extrema.begin(), extrema.end(), Node::LessThan);  
+   if(verbose>=3) Cout("#extrema: "+Str((int)Node::extrema.size())+"\n");
++  stable_sort(extrema.begin(), extrema.end(), Node::LessThan);  
+ }
+ 
+ 
+@@ -941,6 +942,7 @@ void Node::Transcribe(){
+   pair_table[0]=Node::transcribed;
+   Node::front_structure+=".";
+   MakePairTableFromFrontStructure();
++  Node::front_energy=Evaluate(Node::front_structure);
+ }
+ 
+ bool Node::IsTranscribed(){
+-- 
+2.5.2
+