Commit dfd8ef75 authored by Mathieu Giraud's avatar Mathieu Giraud

core/germline.{h,cpp}: mark Cys104 and Phe118/Trp118 from gapped V/J sequences

parent 985b62fa
......@@ -44,6 +44,7 @@ Germline::Germline(string _code, char _shortcut,
f_reps_4.push_back(f_rep_4);
f_reps_3.push_back(f_rep_3);
/// no CYS104_IN_GAPPED_V / PHE118_TRP118_IN_GAPPED_J here ?
rep_5 = Fasta(f_rep_5, 2, "|");
rep_4 = Fasta(f_rep_4, 2, "|");
rep_3 = Fasta(f_rep_3, 2, "|");
......@@ -64,9 +65,9 @@ Germline::Germline(string _code, char _shortcut,
f_reps_4 = _f_reps_4 ;
f_reps_3 = _f_reps_3 ;
rep_5 = Fasta(2, "|") ;
rep_5 = Fasta(2, "|", CYS104_IN_GAPPED_V);
rep_4 = Fasta(2, "|") ;
rep_3 = Fasta(2, "|") ;
rep_3 = Fasta(2, "|", PHE118_TRP118_IN_GAPPED_J);
for (list<string>::const_iterator it = f_reps_5.begin(); it != f_reps_5.end(); ++it)
rep_5.add(*it);
......@@ -108,9 +109,9 @@ Germline::Germline(string code, char shortcut, string path, json json_recom, int
init(code, shortcut, delta_min, max_indexing);
rep_5 = Fasta(2, "|") ;
rep_5 = Fasta(2, "|", CYS104_IN_GAPPED_V) ;
rep_4 = Fasta(2, "|") ;
rep_3 = Fasta(2, "|") ;
rep_3 = Fasta(2, "|", PHE118_TRP118_IN_GAPPED_J) ;
for (json::iterator it = json_recom["5"].begin();
it != json_recom["5"].end(); ++it)
......
......@@ -17,6 +17,12 @@ enum SEGMENTATION_METHODS {
SEG_METHOD_MAX1U // Pseudo-germline, most frequent kmer affection and unknwon affectation (-4)
} ;
// JUNCTION/CDR3 extraction from gapped V/J sequences
#define CYS104_IN_GAPPED_V 310 // First nucleotide of Cys104
#define PHE118_TRP118_IN_GAPPED_J 38 // Last nucleotide of Phe118/Trp118
using namespace std;
using json = nlohmann::json;
......
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