diff --git a/src/junction.h b/src/junction.h
index 9c6f492..26acc09 100644
--- a/src/junction.h
+++ b/src/junction.h
@@ -303,6 +303,7 @@ inline void
 	  svRec.svEndBeg = std::max(itSV->svEnd - consLen, 0);
 	  svRec.svEnd = itSV->svEnd;
 	  svRec.svEndEnd = std::min(itSV->svEnd + consLen, references[itSV->chr2].RefLength);
+	  svRec.ct = itSV->ct;
 	  if ((itSV->chr != itSV->chr2) && (itSV->chr2 == refIndex)) {
             refProbes[itSV->id] = _getSVRef(seq->seq.s, svRec, refIndex, svType);
           }
diff --git a/src/version.h b/src/version.h
index 5ce501a..6847222 100644
--- a/src/version.h
+++ b/src/version.h
@@ -27,7 +27,7 @@ Contact: Tobias Rausch (rausch@embl.de)
 namespace torali
 {
 
-  std::string dellyVersionNumber = "0.5.8";
+  std::string dellyVersionNumber = "0.5.9";
 
   inline 
     void printTitle(std::string const& title)