Commit cecaed9c authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: ad-hoc code for W61, D7-27/J1 non-recombined sequence

Closes #2232.
parent fda5f1a3
Pipeline #32571 passed with stages
in 41 minutes and 29 seconds
......@@ -1414,6 +1414,14 @@ int main (int argc, char **argv)
clones_map_windows[code] = it->first ;
}
// Non-recombined D7-27/J1 sequence
if ((code.find("IGHD7-27*01") != string::npos)
&& (code.find("IGHJ1*01") != string::npos)
&& (code.size() == 11 + 3 + 92 + 3 + 8))
{
json_add_warning(json_clone, "W61", "Non-recombined D7-27/J1 sequence", LEVEL_ERROR);
}
// Output best V, (D) and J germlines to CLONE_FILENAME-*
if ((segmented_germline->seg_method == SEG_METHOD_53) || (segmented_germline->seg_method == SEG_METHOD_543))
out_clone << ">" << seg.box_V->ref_label << endl << seg.box_V->ref << endl ;
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment