Commit 30a7bb0c authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: remove old -G option

The recommended option is now '-g germline/homo-sapiens.g'.
parent 2e73c818
......@@ -398,7 +398,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "A!x:X:hHadiI124g:G: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: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)
switch (c)
{
......@@ -494,22 +494,6 @@ int main (int argc, char **argv)
multi_germline_unexpected_recombinations_1U = true ;
break;
case 'G':
germline_system = string(optarg);
f_reps_V.push_back((germline_system + "V.fa").c_str()) ;
// Takes D only if it exists
{
struct stat buffer;
string putative_f_rep_D = germline_system + "D.fa" ;
if (stat(putative_f_rep_D.c_str(), &buffer) == 0)
{
f_reps_D.push_back(putative_f_rep_D.c_str()) ;
delta_min = DEFAULT_DELTA_MIN_D ;
}
}
f_reps_J.push_back((germline_system + "J.fa").c_str()) ;
germline_system = extract_basename(germline_system);
break;
// Algorithm
......
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