Commit c3f5de7f authored by Mathieu Giraud's avatar Mathieu Giraud

core/germline.{h,cpp}: remove hard-coded build_{default,incomplete}_set functions

We now use germlines.data
parent d4eff037
......@@ -265,38 +265,6 @@ void MultiGermline::build_from_json(string path, string json_filename, int filte
}
void MultiGermline::build_default_set(string path, int max_indexing)
{
// Should parse 'data/germlines.data'
add_germline(new Germline("TRA", 'A', path + "/TRAV.fa", "", path + "/TRAJ.fa", -10, max_indexing), SEED_S13);
add_germline(new Germline("TRB", 'B', path + "/TRBV.fa", path + "/TRBD.fa", path + "/TRBJ.fa", 0, max_indexing), SEED_S12);
add_germline(new Germline("TRG", 'G', path + "/TRGV.fa", "", path + "/TRGJ.fa", -10, max_indexing), SEED_S10);
add_germline(new Germline("TRD", 'D', path + "/TRDV.fa", path + "/TRDD.fa", path + "/TRDJ.fa", 0, max_indexing), SEED_S10);
add_germline(new Germline("IGH", 'H', path + "/IGHV.fa", path + "/IGHD.fa", path + "/IGHJ.fa", 0, max_indexing), SEED_S12);
add_germline(new Germline("IGK", 'K', path + "/IGKV.fa", "", path + "/IGKJ.fa", -10, max_indexing), SEED_S10);
add_germline(new Germline("IGL", 'L', path + "/IGLV.fa", "", path + "/IGLJ.fa", -10, max_indexing), SEED_S10);
}
void MultiGermline::build_incomplete_set(string path, int max_indexing)
{
// Should parse 'data/germlines.data'
// TRA+D
add_germline(new Germline("TRA+D", 'a', path + "/TRDV.fa", path + "/TRDD.fa", path + "/TRAJ.fa", -10, max_indexing), SEED_S13);
add_germline(new Germline("TRA+D", 'a', path + "/TRDD_upstream.fa", "", path + "/TRAJ.fa", -10, max_indexing), SEED_S13);
// DD-JD + DD2-DD3
add_germline(new Germline("TRD+", 'd', path + "/TRDD2_upstream.fa", "", path + "/TRDJ.fa", -10, max_indexing), SEED_9);
add_germline(new Germline("TRD+", 'd', path + "/TRDV.fa", "", path + "/TRDD3_downstream.fa", -10, max_indexing), SEED_9);
add_germline(new Germline("TRD+", 'd', path + "/TRDD2_upstream.fa", "", path + "/TRDD3_downstream.fa", -10, max_indexing), SEED_9);
// DH-JH
add_germline(new Germline("IGH+", 'h', path + "/IGHD_upstream.fa", "", path + "/IGHJ.fa", -10, max_indexing), SEED_S12);
// IGK: KDE, INTRON
add_germline(new Germline("IGK+", 'k', path + "/IGK-INTRON.fa", "", path + "/IGK-KDE.fa", -10, max_indexing), SEED_S10);
add_germline(new Germline("IGK+", 'k', path + "/IGKV.fa", "", path + "/IGK-KDE.fa", -10, max_indexing), SEED_S10);
}
/* if 'one_index_per_germline' was not set, this should be called once all germlines have been loaded */
void MultiGermline::insert_in_one_index(IKmerStore<KmerAffect> *_index, bool set_index)
......
......@@ -106,8 +106,6 @@ class MultiGermline {
void insert(Germline *germline);
void add_germline(Germline *germline, string seed);
void build_default_set(string path, int max_indexing);
void build_incomplete_set(string path, int max_indexing);
void build_from_json(string path, string json_filename, int filter, int max_indexing);
// Creates and update an unique index for all the germlines
......
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment