Commit 8bee7be3 authored by Marc Duez's avatar Marc Duez
Browse files

vidjil.cpp : output custom germlines

parent c533315b
......@@ -1276,6 +1276,30 @@ int main (int argc, char **argv)
JsonList *json_reads_germlineList;
json_reads_germlineList = new JsonList();
//germlines field
JsonList *json_germlines;
json_germlines=new JsonList();
JsonList *json_custom_germline;
json_custom_germline = new JsonList();
json_custom_germline->add("shortcut", "X");
JsonArray json_3;
JsonArray json_4;
JsonArray json_5;
for (list<string>::iterator it = f_reps_V.begin(); it != f_reps_V.end(); it++){
for (list<string>::iterator it = f_reps_D.begin(); it != f_reps_D.end(); it++){
for (list<string>::iterator it = f_reps_J.begin(); it != f_reps_J.end(); it++){
json_custom_germline->add("3", json_3);
json_custom_germline->add("4", json_4);
json_custom_germline->add("5", json_5);
json_germlines->add("custom", *json_custom_germline);
if (multi_germline)
for (list<Germline*>::const_iterator it = multigermline->germlines.begin(); it != multigermline->germlines.end(); ++it)
......@@ -1296,6 +1320,8 @@ int main (int argc, char **argv)
json->add("samples", *json_samples);
json->add("reads", *json_reads);
json->add("clones", jsonSortedWindows);
json->add("germlines", *json_germlines);
if (epsilon || forced_edges.size()){
JsonArray json_clusters = comp.toJson(clones_windows);
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