def fill_in_zeros(fwd_rvs_align_list, ref_len, nt):
    """
    Generate alignment counts for every nucleotide in the reference
    :param fwd_rvs_align_list:  list of sorted forwards and reverse alignments
    :param ref_len: number of nucleotides in the reference sequence (int)
    :param nt: length of the aligned reads (int)
    :return: reference_x_axis ([0,0,...] (list(int)) - length of refseq seq,
             fwd_alignment_y_axis [2,4,5.2,6,....] (list(float)) - sense strand alignment count (positive),
             fwd_rvs_align_list [-3,-4,-5.6,...] (list(float)) - antisense strand alignment count (negative)
    """
    sorted_fwd_alignment = fwd_rvs_align_list[0]
    sorted_rvs_alignment = fwd_rvs_align_list[1]
    fwd_alignment_y_axis = [0] * ref_len
    revs_alignment_y_axis = [0] * ref_len
    reference_x_axis = list(range(0, ref_len))
    for i in sorted_fwd_alignment:
        fwd_alignment_y_axis[i[0] + int(nt / 2)] = i[1]
    for i in sorted_rvs_alignment:
        revs_alignment_y_axis[i[0] - int(nt / 2)] = i[1]
    return reference_x_axis, fwd_alignment_y_axis, revs_alignment_y_axis
