Project: s41467-025-60175-9 | Function: get_parameters (python)

system: You are an expert Python programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow Python best practices and maintain consistent code style.
Return **only** the complete Python function code.

user: Complete this Python function:

**DESCRIPTION:** Automatic parameter estimation function that calculates coverage estimates for primer design. Implements the coverage estimation formula from Equation 1 to optimize threshold and ambiguous base parameters.

**KEY TERMS:** {
  "coverage": "c (coverage fraction)",
  "distances": "Li (length stretches)",
  "args.n_ambig": "na (ambiguous nucleotides)",
  "config.PRIMER_SIZES[0]": "lmin (minimal primer length)"
}

**CONTEXT CODE:** """

# varVAMP
from varvamp.scripts import config


def calculate_frequencies(preprocessed_alignment):
    """
    calculate the max nucleotide freq at each pos
    """
    all_freqs = []

    for i in range(0, len(preprocessed_alignment[0][1])):
        nuc_dict = {
            "a": 0,
            "c": 0,
            "t": 0,
            "g": 0,
        }
        for seq in preprocessed_alignment:
            if seq[1][i] in nuc_dict:
                nuc_dict[seq[1][i]] += 1
        highest_freq = max(nuc_dict.values())
        all_freqs.append(highest_freq/len(preprocessed_alignment))

    return all_freqs


def calculate_distances(all_freqs, threshold):
    """
    calc the distance for each  nuc freq to the prior
    nuc freq that fell below the cutoff
    """

    current_dis = 0
    previous_dis = 0
    all_dis = []

    for idx, freq in enumerate(all_freqs):
        if freq < threshold:
            current_dis = 0
        current_dis += 1
        if current_dis <= previous_dis or idx == len(all_freqs)-1:
            all_dis.append(previous_dis)

        previous_dis = current_dis

    return all_dis


def get_parameters(preprocessed_alignment, args, log_file):
    # MASKED: Automatic parameter estimation function that calculates coverage estimates for primer design using coverage estimation formula implementation
    raise NotImplementedError("This function is masked for testing purposes.")


Complete the function implementation replacing "raise NotImplementedError".