; distance estimator:

de
{
    linkage_distance_coeff    	0.0
    max_distance_coeff        	2.0
    max_distance_coeff_scaff  	2000.0
    clustered_filter_threshold	2.0
    raw_filter_threshold	2
    rounding_coeff              0.5 ; rounding : min(de_max_distance * rounding_coeff, rounding_thr)
    rounding_threshold          0
}

ade
{
    ;data dividing
        threshold          80 ;maximal distance between two points in cluster

    ;local maximum seeking
        range_coeff          0.2 ;data_length*range_coeff := width of the averaging window
        delta_coeff          0.4 ;data_length*delta_coeff := maximal difference between possible distance and real peak on the graph

    ;fft smoothing
        percentage          0.01 ;percent of data for baseline subraction
        cutoff              3 ;the number of the lowest freqs in fourier decomp being taken

    ;other
        min_peak_points       3 ;the minimal number of points in cluster to be considered
        inv_density         5.0 ;maximal inverse density of points in cluster to be considered

    ;hard_mode arguments
        derivative_threshold  0.2 ;threshold for derivative in hard mode

}

; ambiguous pair info checker parameters 
amb_de {
    enabled                         false
    haplom_threshold                500
    relative_length_threshold       0.8
    relative_seq_threshold          0.5
}