Commit 088ac346 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: '-g' option loads the multigermline default set

parent 822316b5
...@@ -146,6 +146,7 @@ void usage(char *progname) ...@@ -146,6 +146,7 @@ void usage(char *progname)
<< " -D <file> D germline multi-fasta file (automatically implies -d)" << endl << " -D <file> D germline multi-fasta file (automatically implies -d)" << endl
<< " -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)" << endl << " -G <prefix> prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa)" << endl
<< " -g multiple germlines (experimental)" << endl
<< endl << endl
<< "Window prediction" << endl << "Window prediction" << endl
...@@ -276,6 +277,7 @@ int main (int argc, char **argv) ...@@ -276,6 +277,7 @@ int main (int argc, char **argv)
bool detailed_cluster_analysis = true ; bool detailed_cluster_analysis = true ;
bool output_segmented = false; bool output_segmented = false;
bool output_unsegmented = false; bool output_unsegmented = false;
bool multi_germline = false;
string forced_edges = "" ; string forced_edges = "" ;
...@@ -291,7 +293,7 @@ int main (int argc, char **argv) ...@@ -291,7 +293,7 @@ int main (int argc, char **argv)
//$$ options: getopt //$$ options: getopt
while ((c = getopt(argc, argv, "AhaG:V:D:J:k:r:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:Lx%:Z:z:uU")) != EOF) while ((c = getopt(argc, argv, "AhagG:V:D:J:k:r:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:Lx%:Z:z:uU")) != EOF)
switch (c) switch (c)
{ {
...@@ -353,6 +355,10 @@ int main (int argc, char **argv) ...@@ -353,6 +355,10 @@ int main (int argc, char **argv)
germline_system = "custom" ; germline_system = "custom" ;
break; break;
case 'g':
multi_germline = true ;
break;
case 'G': case 'G':
germline_system = string(optarg); germline_system = string(optarg);
f_rep_V = (germline_system + "V.fa").c_str() ; f_rep_V = (germline_system + "V.fa").c_str() ;
...@@ -772,12 +778,20 @@ int main (int argc, char **argv) ...@@ -772,12 +778,20 @@ int main (int argc, char **argv)
//$$ Build Kmer indexes //$$ Build Kmer indexes
cout << "Build Kmer indexes" << endl ; cout << "Build Kmer indexes" << endl ;
Germline *germline; MultiGermline *multigermline = new MultiGermline();
germline = new Germline(rep_V, rep_D, rep_J, seed,
delta_min, delta_max);
MultiGermline *multigermline; if (multi_germline)
multigermline = new MultiGermline(germline); {
multigermline->load_default_set();
}
else
{
Germline *germline;
germline = new Germline(rep_V, rep_D, rep_J, seed,
delta_min, delta_max);
multigermline->insert(germline);
}
////////////////////////////////// //////////////////////////////////
//$$ Kmer Segmentation //$$ Kmer Segmentation
......
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