pedantic: Remove unused variables/declarations

algo/core/cluster-junctions.cpp

@@ -40,8 +40,6 @@ void comp_matrix::compare(ostream &out, Cost cluster_cost)
   // DEBUG // out << "  DEBUT COMPARE JUNCTION" << endl ;
   //     clock_t start = clock();
    
-  typedef map<junction,list<Sequence> > mjs ;
-  
   Cost compareCost = cluster_cost;
   out << "  Using cost " << compareCost << endl ;
   
@@ -124,8 +122,6 @@ list<list<junction> >  comp_matrix::cluster(string forced_edges, int w, ostream
   // out << "  eps: " << epsilon << " / minPts: " << minPts << endl ;
     
     
-  typedef map<junction,list<Sequence> > mjs ;
-
   map <string, map <string, bool> > graph ;
   
 ////////////////////////

algo/core/germline.cpp

@@ -170,8 +170,6 @@ void MultiGermline::add_germline(Germline *germline, string seed)
 void MultiGermline::build_default_set(string path)
 {
   // Should parse 'data/germlines.data'
-  Germline *germline;
-
   add_germline(new Germline("TRA", 'A', path + "/TRAV.fa", "",                path + "/TRAJ.fa", -10, 20), SEED_S13);
   add_germline(new Germline("TRB", 'B', path + "/TRBV.fa", path + "/TRBD.fa", path + "/TRBJ.fa",   0, 80), SEED_S12);
   add_germline(new Germline("TRG", 'G', path + "/TRGV.fa", "",                path + "/TRGJ.fa", -10, 30), SEED_S10);
@@ -185,8 +183,6 @@ void MultiGermline::build_default_set(string path)
 void MultiGermline::build_incomplete_set(string path)
 {
   // Should parse 'data/germlines.data'
-  Germline *germline;
-
   // VdJa
   add_germline(new Germline("VdJa", 'a', path + "/TRDV.fa", path + "/TRDD.fa", path + "/TRAJ.fa", -10, 80), SEED_S13);