mode rnaviral
two_step_rr false

simp
{

    ; suspecies bulge remover:
    subspecies_br
    {
        enabled true
        main_iteration_only true
        max_bulge_length_coefficient    30.     ; max_bulge_length = max_bulge_length_coefficient * k
        max_coverage            1000000.0
        max_relative_coverage       15     ; bulge_cov < this * not_bulge_cov
        max_delta 45
        max_relative_delta 0.2
        min_identity 0.9
    }

     red
     {
         enabled true
         diff_mult  10.
         unconditional_diff_mult 50.
         edge_sum 0
     }

     final_br
     {
         enabled false
     }
}
