Commit c7a85b67 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: load incomplete germlines '-i' at the end, ignoring '-1'/'-2'

Loading incomplete germlines in the same index may give some problems,
as the same sequences will be loaded several times with different roles,
leading to AFFECT_AMBIGUOUS affectations. We thus ignore the '-1' setting
for incomplete germlines, and do not consider these germline for MAX12 ('-2').

Now '-i' should work with '-1' and/or '-2', and the previous test passes.
parent d83cbae3
......@@ -83,9 +83,9 @@ ostream &operator<<(ostream &out, const Germline &germline);
class MultiGermline {
private:
bool one_index_per_germline;
public:
bool one_index_per_germline;
list <Germline*> germlines;
// A unique index can be used
......
......@@ -768,8 +768,6 @@ int main (int argc, char **argv)
if (multi_germline)
{
multigermline->build_default_set(multi_germline_file);
if (multi_germline_incomplete)
multigermline->build_incomplete_set(multi_germline_file);
}
else
{
......@@ -801,6 +799,12 @@ int main (int argc, char **argv)
multigermline->germlines.push_back(pseudo);
}
// 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
multigermline->build_incomplete_set(multi_germline_file);
}
if (multi_germline_mark)
multigermline->mark_cross_germlines_as_ambiguous();
......
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