Commit 8d999cf8 authored by Mathieu Giraud's avatar Mathieu Giraud

core/germline.cpp: the TRA/TRD locus is now named 'TRA+D'

This is a better name than 'VdJa', as we now also detect DdJa recombinations.
parent 78c4c9aa
......@@ -196,9 +196,9 @@ void MultiGermline::build_default_set(string path, int max_indexing)
void MultiGermline::build_incomplete_set(string path, int max_indexing)
{
// Should parse 'data/germlines.data'
// VdJa
add_germline(new Germline("VdJa", 'a', path + "/TRDV.fa", path + "/TRDD.fa", path + "/TRAJ.fa", -10, 80, max_indexing), SEED_S13);
add_germline(new Germline("VdJa", 'a', path + "/TRDD_upstream.fa", "", path + "/TRAJ.fa", -10, 80, max_indexing), SEED_S13);
// TRA+D
add_germline(new Germline("TRA+D", 'a', path + "/TRDV.fa", path + "/TRDD.fa", path + "/TRAJ.fa", -10, 80, max_indexing), SEED_S13);
add_germline(new Germline("TRA+D", 'a', path + "/TRDD_upstream.fa", "", path + "/TRAJ.fa", -10, 80, max_indexing), SEED_S13);
// DD-JD + DD2-DD3
add_germline(new Germline("TRD+", 'd', path + "/TRDD_upstream.fa", "", path + "/TRDJ.fa", -10, 60, max_indexing), SEED_9);
......@@ -240,7 +240,7 @@ void MultiGermline::build_with_one_index(string seed, bool set_index)
/* Mark k-mers common to several germlines as ambiguous */
void MultiGermline::mark_cross_germlines_as_ambiguous()
{
string VdJa = "VdJa";
string VdJa = "TRA+D";
for (list<Germline*>::const_iterator it = germlines.begin(); it != germlines.end(); ++it)
{
......
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