; distance estimator:

sc_de
{
    linkage_distance_coeff      0.0
    max_distance_coeff  	    2.0
    max_distance_coeff_scaff    2000.0 
    filter_threshold            2.0 
}

usual_de
{
    linkage_distance_coeff    0.0
    max_distance_coeff        2.0
    max_distance_coeff_scaff  2000.0
    filter_threshold          2.0
}

old_sc_de
{
    linkage_distance_coeff      0.3
    max_distance_coeff      	2.0
    max_distance_coeff_scaff    2000.0
    filter_threshold            10.0 ;bigger than in non-single cell because normalization is disabled
}

old_usual_de
{
    linkage_distance_coeff      0.3
    max_distance_coeff          2.0
    max_distance_coeff_scaff    2000.0
    filter_threshold            0.2
}

; advanced distance estimator:

sc_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

}

usual_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; true
        haplom_threshold                500
        relative_length_threshold       0.8
        relative_seq_threshold          0.5
}

sensitive_mapper {
    k   19
}
