Commit 7ca20a8d authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: do not open f_rep_{V,D,J} if '-g' option is set

If there a '-g' option, we do not have to open default '-V'/'-D'/'-J' files.
parent 0f1e495e
......@@ -749,9 +749,6 @@ int main (int argc, char **argv)
if (!segment_D) // TODO: add other constructor to Fasta, and do not load rep_D in this case
f_rep_D = "";
Fasta rep_V(f_rep_V, 2, "|", cout);
Fasta rep_D(f_rep_D, 2, "|", cout);
Fasta rep_J(f_rep_J, 2, "|", cout);
OnlineFasta *reads;
......@@ -791,6 +788,10 @@ int main (int argc, char **argv)
}
else
{
Fasta rep_V(f_rep_V, 2, "|", cout);
Fasta rep_D(f_rep_D, 2, "|", cout);
Fasta rep_J(f_rep_J, 2, "|", cout);
Germline *germline;
germline = new Germline(rep_V, rep_D, rep_J, seed,
delta_min, delta_max);
......@@ -1283,6 +1284,11 @@ int main (int argc, char **argv)
<< "* They should be checked with other softwares such as IgBlast, iHHMune-align or IMGT/V-QUEST." << endl
;
Fasta rep_V(f_rep_V, 2, "|", cout);
Fasta rep_D(f_rep_D, 2, "|", cout);
Fasta rep_J(f_rep_J, 2, "|", cout);
Germline *germline;
// Here, it could be run without building the index
......
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