In main_bwa_hmm.c lines 871 and 872 we have an uppercase 'N' as the first argument:
mat_vec_mul( 'N', nstates, nsymbols, b_d, nstates,
ones_s_d, 0, c_d, 0);
but mat_vec_mul ignores all arguments other than 'n' and 't' on line 339 of the same file.
I don't get consistent results between runs with "-v n -n 60" unless I change it to 'n'. I think the change yields the proper results