Commit 47968b3e authored by Mikaël Salson's avatar Mikaël Salson

pedantic: Remove unused variables/declarations

parent 01d65bc7
......@@ -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 ;
////////////////////////
......
......@@ -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);
......
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