Commit 09f51300 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: remove -i option, this behavior is set by default

See #2153.
parent 06ada6e9
......@@ -172,7 +172,6 @@ void usage(char *progname, bool advanced)
<< "Locus/recombinations" << endl
<< " -d try to detect several D (experimental)" << endl
<< " -i try to detect incomplete/unusual recombinations (locus with '+', must be used with -g)" << endl
<< " -2 try to detect unexpected recombinations (must be used with -g)" << endl
<< endl ;
......@@ -375,7 +374,6 @@ int main (int argc, char **argv)
bool several_D = false;
bool multi_germline = false;
bool multi_germline_incomplete = false;
bool multi_germline_mark = false;
bool multi_germline_one_index_per_germline = true;
bool multi_germline_unexpected_recombinations_12 = false;
......@@ -401,7 +399,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "A!x:X:hHadiI124g:V:D:J:k:r:vw:e:E:C:f:W:l:Fc:m:N:s:b:Sn:o:L%:y:z:uUK3E:t:#:q")) != EOF)
while ((c = getopt(argc, argv, "A!x:X:hHadI124g:V:D:J:k:r:vw:e:E:C:f:W:l:Fc:m:N:s:b:Sn:o:L%:y:z:uUK3E:t:#:q")) != EOF)
switch (c)
{
......@@ -477,10 +475,6 @@ int main (int argc, char **argv)
several_D = true;
break;
case 'i':
multi_germline_incomplete = true;
break;
case 'I':
multi_germline_mark = true;
break;
......@@ -907,7 +901,7 @@ int main (int argc, char **argv)
}
// Should come after the initialization of regular (and possibly pseudo) germlines
if (multi_germline_incomplete) {
{
for (pair <string, string> path_file: multi_germline_paths_and_files)
multigermline->build_from_json(path_file.first, path_file.second, GERMLINES_INCOMPLETE, trim_sequences);
if (! multigermline->one_index_per_germline) {
......
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