Commit 929c41f6 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: display all germlines, each with its own deltas and seed/s/k settings

The -s/-k/-m/-M command line settings are not used with -g or -i.
parent 5f63c833
......@@ -688,7 +688,7 @@ int main (int argc, char **argv)
MultiGermline *multigermline = new MultiGermline();
{
cout << "Build Kmer indexes" << endl ;
cout << "Load germlines and build Kmer indexes" << endl ;
if (multi_germline)
{
......@@ -717,7 +717,12 @@ int main (int argc, char **argv)
}
}
cout << endl ;
cout << "Germlines loaded" << endl ;
cout << *multigermline ;
cout << endl ;
//////////////////////////////////
//$$ Read sequence files
......@@ -822,15 +827,6 @@ int main (int argc, char **argv)
////////////////////////////////////////
if (command == CMD_CLONES || command == CMD_WINDOWS) {
//////////////////////////////////
cout << "# seed = " << seed << "," ;
cout << " weight = " << seed_weight(seed) << "," ;
cout << " span = " << seed.size() << endl ;
cout << "# k = " << k << "," ;
cout << " w = " << w << "," ;
cout << " delta = [" << delta_min << "," << delta_max << "]" << endl ;
//////////////////////////////////
//$$ Kmer Segmentation
......
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