Commit c752bd3c authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: MAX12, '-2' without '-1'

n+1 indexes: the n regular ones, and the common one for MAX12.
parent b14ff728
......@@ -162,7 +162,7 @@ void usage(char *progname, bool advanced)
cerr << "Experimental options (do not use)" << endl
<< " -I ignore k-mers common to different germline systems (experimental, must be used with -g, do not use)" << endl
<< " -1 use a unique index for all germline systems (experimental, must be used with -g, do not use)" << endl
<< " -2 try to detect unexpected recombinations (experimental, must be used with -g1, do not use)" << endl
<< " -2 try to detect unexpected recombinations (experimental, must be used with -g, do not use)" << endl
<< " -! keep unsegmented reads as clones, taking for junction the complete sequence, to be used on very small datasets (for example -!AX 20)" << endl
<< endl
......@@ -789,12 +789,16 @@ int main (int argc, char **argv)
if (!multi_germline_one_index_per_germline) {
multigermline->build_with_one_index(seed, true);
}
if (multi_germline_unexpected_recombinations) {
if (!multigermline->index) {
multigermline->build_with_one_index(seed, false);
}
Germline *pseudo = new Germline(PSEUDO_GERMLINE_MAX12, 'x', -10, 80);
pseudo->index = multigermline->index ;
multigermline->germlines.push_back(pseudo);
}
}
if (multi_germline_mark)
......
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