; output options

debug_output    false

output {
    write_overlaped_paths   true
    write_paths             true
}

visualize {
    print_overlaped_paths   true
    print_paths             true
}

; none | break_gaps | break_all
output_broken_scaffolds     break_gaps
cut_all_overlaps  false
singlecell {
    split_edge_length       99
    normalize_weight        true

    ; extension selection
    extension_options
    {
        recalculate_threshold      true
        single_threshold           0.001
        weight_threshold           0.6
        priority_coeff             1.5
    }

    mate_pair_options
    {
        recalculate_threshold      true
        single_threshold           0.0001
        weight_threshold           0.5
        priority_coeff             1.5
    }

    scaffolder {
        on              true
        cutoff          2
        rel_cutoff      0.1
        sum_threshold   3  

        cluster_info    true
        cl_threshold    0

        fix_gaps        true
        min_gap_score   0.7

        max_must_overlap  0.5
        max_can_overlap   0.5
        short_overlap     6
        artificial_gap    10
    }
    
    loop_removal
    {
        max_loops       10
        mp_max_loops    10
    }

    remove_overlaps     true
}



multicell {
    split_edge_length    99
    normalize_weight     false
    
    ; extension selection
    extension_options
    {
        recalculate_threshold      true
        single_threshold           1.75676
;    A.mirum threshold 0.076
;    E.coli RL36 threshold 0.717949
;    E.coli IS220 threshold 1.75676
        weight_threshold           0.5
        priority_coeff             1.5
    }    

    mate_pair_options
    {
        recalculate_threshold      true
        single_threshold           0.001
        weight_threshold           0.5
        priority_coeff             1.5
    }

    scaffolder {
        on            true
        cutoff        2
        rel_cutoff    0.1
        sum_threshold 3  

        cluster_info  true
        cl_threshold  0

        fix_gaps       true
        min_gap_score  0.7

        max_must_overlap  0.5
        max_can_overlap   0.5
        short_overlap     6
        artificial_gap    10
    }
    
    loop_removal
    {
        max_loops       10
        mp_max_loops    10
    }

    remove_overlaps     true
}


long_reads {

    pacbio_reads {
        filtering   2.5
        weight_priority    1.2
        unique_edge_priority 5.0
    }

    single_reads {
        filtering   2.5
        weight_priority    5.0
        unique_edge_priority 1000.0
    }

    coverage_base_rr {
        filtering   0.0
        weight_priority    1.5
        unique_edge_priority 2.0
    }
}
