Commit e3b9f5b5 authored by Marc Duez's avatar Marc Duez

c++ : segment.cpp : segmenter store germline used

update json output for 2014.10.10 format
parent c853dbf6
......@@ -230,7 +230,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, MultiGermline *multigermline)
// removeChevauchement is called once info was already computed: it is only to output info_extra
info_extra += removeChevauchement();
finishSegmentation();
system = germline->code;
return ;
}
} // end for (Germlines)
......@@ -725,31 +725,30 @@ JsonList FineSegmenter::toJsonList(Germline *germline){
result.add("sequence", revcomp(sequence, reversed) );
if (isSegmented()) {
result.add("name", code_short);
result.add("Jstart", Jstart);
result.add("Nlength", (del_V+del_J+seg_N.size()) );
result.add("Vend", Vend);
JsonArray jsonV;
JsonArray jsonJ;
// TODO: what is going on if some list is smaller than JSON_REMEMBER_BEST ?
for (int i=0; i<JSON_REMEMBER_BEST; i++) jsonV.add( germline->rep_5.label(score_V[i].second) ) ;
result.add("V", jsonV);
JsonList seg;
// TODO: what is going on if some list is smaller than JSON_REMEMBER_BEST ?
JsonArray jsonV;
for (int i=0; i<JSON_REMEMBER_BEST; i++) jsonV.add( germline->rep_5.label(score_V[i].second) ) ;
seg.add("5", jsonV);
seg.add("5start", 0);
seg.add("5end", Vend);
if (score_D.size()>0){
result.add("Dstart", Dstart);
result.add("Dend", Dend);
JsonArray jsonD;
for (int i=0; i<JSON_REMEMBER_BEST; i++) jsonD.add( germline->rep_4.label(score_D[i].second) ) ;
result.add("D", jsonD);
result.add("4", jsonD);
result.add("4start", Dstart);
result.add("4end", Dend);
}
JsonArray jsonJ;
for (int i=0; i<JSON_REMEMBER_BEST; i++) jsonJ.add( germline->rep_3.label(score_J[i].second) ) ;
result.add("J", jsonJ);
seg.add("3", jsonJ);
seg.add("3start", Jstart);
result.add("seg", seg);
}
return result;
}
......
......@@ -54,7 +54,7 @@ protected:
string info_extra; // .vdj.fa header, other information, at the end of the header
int best_V, best_J ;
int del_V, del_D_left, del_D_right, del_J ;
string seg_V, seg_N, seg_J;
string seg_V, seg_N, seg_J, system;
int best_D;
string seg_N1, seg_D, seg_N2;
......
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