vidjil.cpp: species in json output

Fixes #1987.

vidjil.cpp: species in json output
Fixes #1987.
c694636a · Mathieu Giraud · 101e2d3c · c694636a
Commit c694636a authored Jan 25, 2017 by Mathieu Giraud
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algo/vidjil.cpp algo/vidjil.cpp +3 -0

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--- a/algo/vidjil.cpp
+++ b/algo/vidjil.cpp
@@ -1577,6 +1577,9 @@ 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"] = {