Commit 943d7552 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: -c germlines, read a list a germline files

TODO: the list should not be hard-coded.
parent 3251bf81
......@@ -579,6 +579,25 @@ int main (int argc, char **argv)
/////////////////////////////////////////
if (command == CMD_GERMLINES)
{
list< char* > f_germlines ;
f_germlines.push_back("germline/TRGV.fa");
f_germlines.push_back("germline/TRGJ.fa");
f_germlines.push_back("germline/IGHV.fa");
f_germlines.push_back("germline/IGHD.fa");
f_germlines.push_back("germline/IGHJ.fa");
// Read germline and build one unique index
bool rc = true ;
IKmerStore<KmerStringAffect> *index = KmerStoreFactory::createIndex<KmerStringAffect>(seed, rc);
map <string, int> stats_kmer;
for (list< char* >::const_iterator it = f_germlines.begin(); it != f_germlines.end(); ++it)
{
Fasta rep(*it, 2, "|", cout);
index->insert(rep, *it);
stats_kmer[string(*it)] = 0 ;
}
exit(0);
}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment