Commit c77b2496 authored by Mathieu Giraud's avatar Mathieu Giraud

core/germline.{h,cpp}: also index rep_4 if affect_4 is set

parent 677948d3
......@@ -10,6 +10,7 @@ Germline::Germline(string _code, char _shortcut,
index = 0 ;
affect_5 = "V" ;
affect_4 = "";
affect_3 = "J" ;
rep_5 = Fasta(f_rep_5, 2, "|", cout);
......@@ -34,6 +35,7 @@ Germline::Germline(string _code, char _shortcut,
// affect_5 = KmerAffect("", "V", 0) ;
// affect_3 = KmerAffect("", "J", 0) ;
affect_5 = "V" ;
affect_4 = "" ;
affect_3 = "J" ;
rep_5 = _rep_5 ;
......@@ -65,8 +67,13 @@ void Germline::use_index(IKmerStore<KmerAffect> *_index)
void Germline::update_index()
{
index->insert(rep_5, affect_5);
if (affect_4.size())
index->insert(rep_4, affect_4);
index->insert(rep_3, affect_3);
cout << " index " << index << " updated " << affect_5 << "/" << affect_3 << endl;
cout << " --- index " << index << " updated " << affect_5 << "/" << affect_4 << "/" << affect_3 << endl;
}
Germline::~Germline()
......
......@@ -43,6 +43,7 @@ class Germline {
// KmerAffect affect_5 ;
// KmerAffect affect_3 ;
string affect_5 ;
string affect_4 ;
string affect_3 ;
Fasta rep_5 ;
......
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