Commit c5fc8186 authored by Mathieu Giraud's avatar Mathieu Giraud

core/germline.cpp: do not detect CDR3 in incomplete/unusual '+' germlines

This is a temporary fix. A more generic solution could be to encode
the CYS104_IN_GAPPED_V and PHE118_TRP118_IN_GAPPED_J constants
into the germlines.data file and to use these values through germline.cpp.
parent 1a92e21b
......@@ -65,9 +65,11 @@ Germline::Germline(string _code, char _shortcut,
f_reps_4 = _f_reps_4 ;
f_reps_3 = _f_reps_3 ;
rep_5 = Fasta(2, "|", CYS104_IN_GAPPED_V);
bool regular = (code.find("+") == string::npos);
rep_5 = Fasta(2, "|", regular ? CYS104_IN_GAPPED_V : 0);
rep_4 = Fasta(2, "|") ;
rep_3 = Fasta(2, "|", PHE118_TRP118_IN_GAPPED_J);
rep_3 = Fasta(2, "|", regular ? PHE118_TRP118_IN_GAPPED_J : 0);
for (list<string>::const_iterator it = f_reps_5.begin(); it != f_reps_5.end(); ++it)
rep_5.add(*it);
......@@ -108,10 +110,12 @@ Germline::Germline(string code, char shortcut, string path, json json_recom, int
}
init(code, shortcut, delta_min, max_indexing);
bool regular = (code.find("+") == string::npos);
rep_5 = Fasta(2, "|", CYS104_IN_GAPPED_V) ;
rep_5 = Fasta(2, "|", regular ? CYS104_IN_GAPPED_V : 0) ;
rep_4 = Fasta(2, "|") ;
rep_3 = Fasta(2, "|", PHE118_TRP118_IN_GAPPED_J) ;
rep_3 = Fasta(2, "|", regular ? PHE118_TRP118_IN_GAPPED_J : 0) ;
for (json::iterator it = json_recom["5"].begin();
it != json_recom["5"].end(); ++it)
......
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