mode rna

preserve_raw_paired_index true

contig_output {
    scaffolds_name  transcripts
    ; none  --- do not output broken scaffolds | break_gaps --- break only by N steches | break_all --- break all with overlap < k
    output_broken_scaffolds     none
}

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 }"
    }

    dead_end
    {
        condition  "{ tc_lb 3.5, cb 2 }"
        enabled true
    }

    ; 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
       ; nbr: use not bulge erroneous connections remover 
       ; condition               "{ ec_lb 9, icb 40.0, nbr }"
       condition               "{ ec_lb 30, icb 50 }"
    }

    ; relative coverage erroneous connections remover:
    rcec
    {
            enabled true
            rcec_lb 30
            rcec_cb 0.5
    }

    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                     false
        max_length                  100
        max_coverage                2
        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    ""
    }

}

; disable filtering in rna mode
de
{
    raw_filter_threshold	0
}

pe {
params {
    multi_path_extend   true
    remove_overlaps     false

    scaffolding_mode old

    extension_options
    {
        use_default_single_threshold true
        single_threshold           0.05
    }

    scaffolder {
        cutoff        1
        hard_cutoff   10

	cluster_info false

	min_overlap_for_rna_scaffolding 10
    }

    path_cleaning
    {
        enabled true
        min_length  30
        isolated_min_length 50
        min_length_for_low_covered 150
        min_coverage 2
    }

}
}
