BWA::BWA(const char* ann_filename,
const char* amb_filename,
const char* pac_filename,
const char* forward_bwt_filename,
const char* forward_sa_filename,
const char* reverse_bwt_filename,
const char* reverse_sa_filename)
{
// Load the bns (?) and reference
bns = bns_restore_core(ann_filename,amb_filename,pac_filename);
reference = new ubyte_t[bns->l_pac/4+1];
rewind(bns->fp_pac);
fread(reference, 1, bns->l_pac/4+1, bns->fp_pac);
fclose(bns->fp_pac);
bns->fp_pac = NULL;
// Load the BWTs (both directions) and suffix arrays (both directions)
bwts[0] = bwt_restore_bwt(forward_bwt_filename);
bwt_restore_sa(forward_sa_filename, bwts[0]);
bwts[1] = bwt_restore_bwt(reverse_bwt_filename);
bwt_restore_sa(reverse_sa_filename, bwts[1]);
load_default_options();
// Always reinitialize the random seed whenever a new set of files are loaded.
initialize_random_seed();
// initialize the bwase subsystem
bwase_initialize();
}
int main(int argc, char *argv[])
{
initialize_random_seed();
#if 1
make_castle();
#else
do_tests();
#endif
return 0;
}
