Commit ff70521e authored by Mathieu Giraud's avatar Mathieu Giraud

vijdil.cpp: json output, 'ref', and move 'species' and 'species_taxon_id' to 'germlines'

These three values come from the germline/*.g file.
See #2155.
parent def2bb94
......@@ -1550,9 +1550,6 @@ int main (int argc, char **argv)
// Complete main json output
j["species"] = multigermline->species ;
j["species_taxon_id"] = multigermline->species_taxon_id ;
j["diversity"] = jsonDiversity ;
j["samples"]["log"] = { stream_segmentation_info.str() } ;
j["reads"] = {
......@@ -1562,7 +1559,11 @@ int main (int argc, char **argv)
} ;
j["clones"] = jsonSortedWindows ;
j["germlines"] = json_germlines ;
j["germlines"]["ref"] = multigermline->ref ;
j["germlines"]["species"] = multigermline->species ;
j["germlines"]["species_taxon_id"] = multigermline->species_taxon_id ;
if (epsilon || forced_edges.size()){
j["clusters"] = comp.toJson(clones_windows);
}
......
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