Writes BED/BIM/FAM files.

def bed_writer(parser, keep, extract, args):
    """Writes BED/BIM/FAM files."""
    # The output bed and bim file
    bim_fn = args.output + ".bim"
    with open(bim_fn, "w") as bim, PyPlink(args.output, "w") as bed:
        # Getting the samples
        samples = np.array(parser.get_samples(), dtype=str)
        k = _get_sample_select(samples=samples, keep=keep)

        # Writing the FAM file
        with open(args.output + ".fam", "w") as fam:
            for sample in samples[k]:
                print(sample, sample, "0", "0", "0", "-1", sep=" ", file=fam)

        # Getting the data generator
        generator = _get_generator(parser=parser, extract=extract, keep=k,
                                   check_maf=args.maf)

        # The number of markers extracted
        nb_extracted = 0

        for data in generator:
            # Keeping only the required genotypes, changing NaN to -1 and
            # rounding to get a hard call
            genotypes = data.genotypes
            genotypes[np.isnan(genotypes)] = -1
            genotypes = np.round(genotypes, 0)

            # Writing the genotypes and the BIM file
            bed.write_genotypes(genotypes)
            print(
                _PLINK_CHROM_ENCODE.get(str(data.variant.chrom),
                                        data.variant.chrom),
                data.variant.name, "0", data.variant.pos, data.coded,
                data.reference, sep="\t", file=bim,
            )
            nb_extracted += 1

        if nb_extracted == 0:
            logger.warning("No markers matched the extract list")