Compute LD using Plink.

    :param options: the options.

    :type options: argparse.Namespace

    :returns: the name of the output file (from Plink).

def selectSNPsAccordingToLD(options):
    """Compute LD using Plink.

    :param options: the options.

    :type options: argparse.Namespace

    :returns: the name of the output file (from Plink).

    """
    # The plink command
    outPrefix = options.out + ".pruning_" + options.indep_pairwise[2]
    plinkCommand = [
        "plink",
        "--noweb",
        "--bfile", options.bfile,
        "--maf", options.maf,
        "--indep-pairwise",
    ] + options.indep_pairwise + ["--out", outPrefix]

    runCommand(plinkCommand)

    # Finding the autosomal markers
    autosomes = {str(i) for i in range(1, 23)}
    autosomal_snps = set()
    with open(options.bfile + ".bim", "r") as i_file:
        for line in i_file:
            chrom, snp = line.rstrip("\r\n").split("\t")[:2]
            if chrom in autosomes:
                autosomal_snps.add(snp)

    # Reading the pruned markers
    pruned_snps = None
    with open(outPrefix + ".prune.in", "r") as i_file:
        pruned_snps = set(i_file.read().splitlines())

    # Writing the pruned markers located on an autosome
    with open(outPrefix + ".prune.in.autosomal", "w") as o_file:
        for snp in autosomal_snps & pruned_snps:
            print >>o_file, snp

    return outPrefix + ".prune.in.autosomal"