Commit e90c48b8 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: experimental -I option, ignore common k-mers between different germlines

This option is sponsored by UPMC.
parent a15f0a91
......@@ -154,6 +154,7 @@ void usage(char *progname)
<< " -G <prefix> prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa) (basename gives germline code)" << endl
<< " -g <path> multiple germlines (in the path <path>, takes TRA, TRB, TRG, TRD, IGH and IGL and sets window prediction parameters)" << endl
<< " -i multiple germlines, also incomplete rearrangements (experimental, must be used with -g)" << endl
<< " -I ignore k-mers common to different germline systems (experimental, must be used with -g, do not use)" << endl
<< endl
<< "Window prediction" << endl
......@@ -288,6 +289,7 @@ int main (int argc, char **argv)
bool output_unsegmented = false;
bool multi_germline = false;
bool multi_germline_incomplete = false;
bool multi_germline_mark = false;
string multi_germline_file = DEFAULT_MULTIGERMLINE;
string forced_edges = "" ;
......@@ -303,7 +305,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "Ahaig:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uU")) != EOF)
while ((c = getopt(argc, argv, "AhaiIg:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uU")) != EOF)
switch (c)
{
......@@ -354,6 +356,10 @@ int main (int argc, char **argv)
case 'i':
multi_germline_incomplete = true;
break;
case 'I':
multi_germline_mark = true;
break;
case 'G':
germline_system = string(optarg);
......@@ -720,6 +726,9 @@ int main (int argc, char **argv)
cout << endl ;
if (multi_germline_mark)
multigermline->mark_cross_germlines_as_ambiguous();
cout << "Germlines loaded" << endl ;
cout << *multigermline ;
cout << endl ;
......
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