Commit 2ea82b2b authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: always use .toOutput(), even with non segmented sequences

Following a discussion with @mikael-s.
We want to have meaningfull names when the sequence is not segmented.
See !320 (comment 126622)
parent de88a137
......@@ -1382,11 +1382,6 @@ int main (int argc, char **argv)
out_clone << seg << endl ;
out_clones << seg << endl ;
// From FineSegmenter
if (seg.code.length() > 0)
clone->set("name", seg.code);
seg.toOutput(clone);
if (seg.isSegmented())
......@@ -1601,8 +1596,6 @@ int main (int argc, char **argv)
if (detect_CDR3)
s.findCDR3();
clone->set("name", s.code);
s.toOutput(clone);
g = germline ;
}
else
......@@ -1610,6 +1603,7 @@ int main (int argc, char **argv)
g = not_segmented ;
}
s.toOutput(clone);
clone->set("germline", g->code);
nb_segmented_by_germline[g->code]++ ;
......
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