Commit c853dbf6 authored by Marc Duez's avatar Marc Duez

c++ : germline.cpp : germline object always have code/shortcut

parent 7314fdfa
......@@ -22,12 +22,13 @@ Germline::Germline(string _code, char _shortcut,
}
Germline::Germline(Fasta _rep_5, Fasta _rep_4, Fasta _rep_3,
Germline::Germline(string _code, char _shortcut,
Fasta _rep_5, Fasta _rep_4, Fasta _rep_3,
string seed,
int _delta_min, int _delta_max)
{
code = "" ;
shortcut = 'X' ;
code = _code ;
shortcut = _shortcut ;
// affect_5 = KmerAffect("", "V", 0) ;
// affect_3 = KmerAffect("", "J", 0) ;
......@@ -88,7 +89,8 @@ MultiGermline::MultiGermline(string f_germlines_json)
Fasta rep_3(f_rep_3, 2, "|", cout);
Germline *germline;
germline = new Germline(rep_5, rep_4, rep_3,
germline = new Germline("TRG", 'G',
rep_5, rep_4, rep_3,
seed,
delta_min, delta_max);
......
......@@ -29,7 +29,8 @@ class Germline {
string seed,
int _delta_min, int _delta_max);
Germline(Fasta _rep_5, Fasta _rep_4, Fasta _rep_3,
Germline(string _code, char _shortcut,
Fasta _rep_5, Fasta _rep_4, Fasta _rep_3,
string seed,
int _delta_min, int _delta_max);
......
......@@ -790,7 +790,8 @@ int main (int argc, char **argv)
else
{
Germline *germline;
germline = new Germline(rep_V, rep_D, rep_J, seed,
germline = new Germline(germline_system, 'X',
rep_V, rep_D, rep_J, seed,
delta_min, delta_max);
multigermline->insert(germline);
......@@ -1284,7 +1285,8 @@ int main (int argc, char **argv)
Germline *germline;
// Here, it could be run without building the index
germline = new Germline(rep_V, rep_D, rep_J, seed,
germline = new Germline(germline_system, 'X',
rep_V, rep_D, rep_J, seed,
delta_min, delta_max);
while (reads->hasNext())
......
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