Commit cffcd742 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: new experimental option '-i', some incomplete rearrangements

parent 2d9c7ce4
...@@ -149,6 +149,7 @@ void usage(char *progname) ...@@ -149,6 +149,7 @@ void usage(char *progname)
<< " -J <file> J germline multi-fasta file" << endl << " -J <file> J germline multi-fasta file" << endl
<< " -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 <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 << " -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
<< endl << endl
<< "Window prediction" << endl << "Window prediction" << endl
...@@ -279,6 +280,7 @@ int main (int argc, char **argv) ...@@ -279,6 +280,7 @@ int main (int argc, char **argv)
bool output_segmented = false; bool output_segmented = false;
bool output_unsegmented = false; bool output_unsegmented = false;
bool multi_germline = false; bool multi_germline = false;
bool multi_germline_incomplete = false;
string multi_germline_file = DEFAULT_MULTIGERMLINE; string multi_germline_file = DEFAULT_MULTIGERMLINE;
string forced_edges = "" ; string forced_edges = "" ;
...@@ -294,7 +296,7 @@ int main (int argc, char **argv) ...@@ -294,7 +296,7 @@ int main (int argc, char **argv)
//$$ options: getopt //$$ options: getopt
while ((c = getopt(argc, argv, "Ahag: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, "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)
switch (c) switch (c)
{ {
...@@ -341,7 +343,11 @@ int main (int argc, char **argv) ...@@ -341,7 +343,11 @@ int main (int argc, char **argv)
multi_germline_file = string(optarg); multi_germline_file = string(optarg);
germline_system = "multi" ; germline_system = "multi" ;
break; break;
case 'i':
multi_germline_incomplete = true;
break;
case 'G': case 'G':
germline_system = string(optarg); germline_system = string(optarg);
f_reps_V.push_back((germline_system + "V.fa").c_str()) ; f_reps_V.push_back((germline_system + "V.fa").c_str()) ;
...@@ -676,6 +682,8 @@ int main (int argc, char **argv) ...@@ -676,6 +682,8 @@ int main (int argc, char **argv)
if (multi_germline) if (multi_germline)
{ {
multigermline->build_default_set(multi_germline_file); multigermline->build_default_set(multi_germline_file);
if (multi_germline_incomplete)
multigermline->build_incomplete_set(multi_germline_file);
} }
else if (command == CMD_GERMLINES) else if (command == CMD_GERMLINES)
{ {
......
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