Commit 014e9f91 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: -c germlines, all other germlines

This should not be hardcoded.
parent 62a02cf6
......@@ -583,20 +583,34 @@ int main (int argc, char **argv)
#define KMER_UNKNOWN "_"
list< char* > f_germlines ;
f_germlines.push_back("germline/TRGV.fa");
f_germlines.push_back("germline/TRGJ.fa");
// TR
f_germlines.push_back("germline/TRAV.fa");
f_germlines.push_back("germline/TRAJ.fa");
f_germlines.push_back("germline/TRBV.fa");
f_germlines.push_back("germline/TRDJ.fa");
f_germlines.push_back("germline/TRBJ.fa");
f_germlines.push_back("germline/TRDV.fa");
f_germlines.push_back("germline/TRDD.fa");
f_germlines.push_back("germline/TRDJ.fa");
f_germlines.push_back("germline/IGKV.fa");
f_germlines.push_back("germline/IGKJ.fa");
f_germlines.push_back("germline/TRGV.fa");
f_germlines.push_back("germline/TRGJ.fa");
// Ig
f_germlines.push_back("germline/IGHV.fa");
f_germlines.push_back("germline/IGHD.fa");
f_germlines.push_back("germline/IGHJ.fa");
f_germlines.push_back("germline/IGKV.fa");
f_germlines.push_back("germline/IGKJ.fa");
f_germlines.push_back("germline/IGLV.fa");
f_germlines.push_back("germline/IGLJ.fa");
// Read germline and build one unique index
bool rc = true ;
......
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