Fix problem alleles and reference/variant bases in VCF line.

def fix_line_problems(parts):
    """Fix problem alleles and reference/variant bases in VCF line.
    """
    varinfo = parts[:9]
    genotypes = []
    # replace haploid calls
    for x in parts[9:]:
        if len(x) == 1:
            x = "./."
        genotypes.append(x)
    if varinfo[3] == "0": varinfo[3] = "N"
    if varinfo[4] == "0": varinfo[4] = "N"
    return varinfo, genotypes