Commit f5ba19b2 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: experimental option '-2', MAX12 germline

parent 888d0c69
......@@ -162,6 +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
<< " -! keep unsegmented reads as clones, taking for junction the complete sequence, to be used on very small datasets (for example -!AX 20)" << endl
<< endl
......@@ -326,6 +327,7 @@ int main (int argc, char **argv)
bool multi_germline_incomplete = false;
bool multi_germline_mark = false;
bool multi_germline_one_index_per_germline = true;
bool multi_germline_unexpected_recombinations = false;
string multi_germline_file = DEFAULT_MULTIGERMLINE;
string forced_edges = "" ;
......@@ -344,7 +346,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "A!x:X:hHaiI1g:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uUK3E:")) != EOF)
while ((c = getopt(argc, argv, "A!x:X:hHaiI12g:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uUK3E:")) != EOF)
switch (c)
{
......@@ -406,7 +408,11 @@ int main (int argc, char **argv)
case '1':
multi_germline_one_index_per_germline = false ;
break;
case '2':
multi_germline_unexpected_recombinations = true ;
break;
case 'G':
germline_system = string(optarg);
f_reps_V.push_back((germline_system + "V.fa").c_str()) ;
......@@ -781,9 +787,16 @@ int main (int argc, char **argv)
cout << endl ;
if (!multi_germline_one_index_per_germline)
if (!multi_germline_one_index_per_germline) {
multigermline->build_with_one_index(seed);
if (multi_germline_unexpected_recombinations) {
Germline *pseudo = new Germline(PSEUDO_GERMLINE_MAX12, 'x', -10, 80);
pseudo->index = multigermline->index ;
multigermline->germlines.push_back(pseudo);
}
}
if (multi_germline_mark)
multigermline->mark_cross_germlines_as_ambiguous();
......
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