Commit 873cd348 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: MAX1U, new '-4' option

parent c1ac9fac
......@@ -346,7 +346,8 @@ 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;
bool multi_germline_unexpected_recombinations_12 = false;
bool multi_germline_unexpected_recombinations_1U = false;
string multi_germline_file = DEFAULT_MULTIGERMLINE;
string forced_edges = "" ;
......@@ -367,7 +368,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "A!x:X:hHaiI12g:G:V:D:J:k:r:vw:e:C:f:W:l:Fc:m:N:s:b:Sn:o:L%:y:z:uUK3E:t:")) != EOF)
while ((c = getopt(argc, argv, "A!x:X:hHaiI124g:G:V:D:J:k:r:vw:e:C:f:W:l:Fc:m:N:s:b:Sn:o:L%:y:z:uUK3E:t:")) != EOF)
switch (c)
{
......@@ -429,7 +430,11 @@ int main (int argc, char **argv)
break;
case '2':
multi_germline_unexpected_recombinations = true ;
multi_germline_unexpected_recombinations_12 = true ;
break;
case '4':
multi_germline_unexpected_recombinations_1U = true ;
break;
case 'G':
......@@ -795,14 +800,23 @@ int main (int argc, char **argv)
multigermline->build_with_one_index(seed, true);
}
if (multi_germline_unexpected_recombinations) {
if (multi_germline_unexpected_recombinations_12 || multi_germline_unexpected_recombinations_1U) {
if (!multigermline->index) {
multigermline->build_with_one_index(seed, false);
}
}
if (multi_germline_unexpected_recombinations_12) {
Germline *pseudo = new Germline(PSEUDO_GERMLINE_MAX12, 'x', -10, trim_sequences);
pseudo->index = multigermline->index ;
multigermline->germlines.push_back(pseudo);
}
if (multi_germline_unexpected_recombinations_1U) {
Germline *pseudo_u = new Germline(PSEUDO_GERMLINE_MAX1U, 'y', -10, trim_sequences);
// TODO: there should be more up/downstream regions for the 'yyy' germline. And/or smaller seeds ?
pseudo_u->index = multigermline->index ;
multigermline->germlines.push_back(pseudo_u);
}
// Should come after the initialization of regular (and possibly pseudo) germlines
......
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