Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/vidjil/vidjil

algo/core/segment.cpp

@@ -142,6 +142,7 @@ ostream &operator<<(ostream &out, const Segmenter &s)
   out << ">" << s.label << " " ;
   out << (s.segmented ? "" : "! ") << s.info ;
   out << " " << s.info_extra ;
+  out << " " << s.segmented_germline->code ;
   out << endl ;
 
   if (s.segmented)
@@ -461,7 +462,7 @@ string format_del(int deletions)
 
 FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
 {
-
+  segmented_germline = germline ;
   info_extra = "" ;
   label = seq.label ;
   sequence = seq.sequence ;

algo/core/segment.h

@@ -53,6 +53,7 @@ protected:
   bool finishSegmentationD();
 
  public:
+  Germline *segmented_germline;
   string code;
   string code_short;
   string code_light;
@@ -140,8 +141,6 @@ class KmerSegmenter : public Segmenter
   string affects;
 
  public:
-  Germline *segmented_germline;
-  
   /**
    * Build a segmenter based on KmerSegmentation
    * @param seq: An object read from a FASTA/FASTQ file