def _extract_header_alignment(header, alignments, nt):
    """
    With a provided complete header, extract the alignment and process to correct format for fill in zeros
    :param header: reference sequence header string 
    :param alignments: alignments dictionary
    :return: sorted_fwd_alignment, sorted_rvs_alignment, aln_count list
    """
    sorted_fwd_alignment = []
    sorted_rvs_alignment = []
    aln_count = 0.0
    ref_len = 0

    if header in alignments:
        extracted_alignments = alignments[header]
        for alignment in extracted_alignments:
            ref_len = alignment[0]
            if alignment[3] =="+":
                sorted_fwd_alignment.append((alignment[2], alignment[4], alignment[5]))
            elif alignment[3] =="-":
                sorted_rvs_alignment.append((alignment[2], -alignment[4], alignment[5]))
            aln_count += alignment[4]
    return [sorted_fwd_alignment, sorted_rvs_alignment, aln_count], ref_len