mode rna

simp
{
    ; enable advanced ec removal algo
    topology_simplif_enabled false
    tc
    {
        ; rctc: tip_cov < rctc * not_tip_cov
        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
        condition  "{ mmm 3 tc_lb 3.5, cb 100000, rctc 0.1 } { tc_lb 3.5, cb 4, rctc 10000 } { tc_lb 0.1, cb 20, rctc 10000 }"
    }
    ; bulge remover:
    br
    {
        max_additive_length_coefficient 100
        max_coverage            1000000.0
        max_relative_coverage       100000.0 ; bulge_cov < this * not_bulge_cov
    }
    ; erroneous connections remover:
    ec
    { 
       ; ec_lb: max_ec_length = k + ec_lb
       ; icb: iterative coverage bound
       ; to_ec_lb: max_ec_length = 2*tip_length(to_ec_lb) - 1
       ; condition               "{ ec_lb 9, icb 40.0 }"
       condition               "{ ec_lb 30, icb auto }"
    }
    rcc
    {
        enabled true
        coverage_gap    20.
        max_length_coeff    2.0
        max_length_with_tips_coeff   3.0
        max_vertex_cnt      30
        max_ec_length_coefficient   30
        max_coverage_coeff  5.0
    }
    ;all topology based erroneous connection removers are off
    ier
    {
        enabled                     true
        max_length                  200
        max_coverage                4
        max_length_any_cov          0 ; will be taken max with read_length
    }
    ; hidden ec remover
    her
    {
        enabled                     true
        uniqueness_length           1500
        unreliability_threshold     0.2
        relative_threshold          5
    }

    init_clean
    {
        activation_cov  -1.
        ier
        {
            enabled false
        }

        tip_condition   ""
        ec_condition    ""
    }

}

pe {
params {
    multi_path_extend   true
    remove_overlaps     false
}
}
