Commit 4ae2df4b authored by Mikaël Salson's avatar Mikaël Salson

vidjil.cpp: Don't force building with one index

parent d4177b6c
......@@ -913,10 +913,11 @@ int main (int argc, char **argv)
// Should come after the initialization of regular (and possibly pseudo) germlines
if (multi_germline_incomplete) {
multigermline->one_index_per_germline = true; // Starting from now, creates new indexes
for (pair <string, string> path_file: multi_germline_paths_and_files)
multigermline->build_from_json(path_file.first, path_file.second, GERMLINES_INCOMPLETE, trim_sequences);
if (! multigermline->one_index_per_germline) {
multigermline->insert_in_one_index(multigermline->index, true);
if (multi_germline_mark)
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