def _get_sample_calls(vcf_file, name):
    """Get a set of positions called in the input VCF file for the sample.
    """
    gindex = None
    calls = set([])
    with open(vcf_file) as in_handle:
        for line in in_handle:
            if line.startswith("#CHROM"):
                gindex = line.strip().split("\t").index(name)
            elif not line.startswith("#"):
                assert gindex
                cur_parts = line.split("\t")
                cur_gt = cur_parts[gindex].split(":")[0]
                if len(set(cur_gt.split("|/")) - set(["0", "."])) > 0:
                    chrom, start = cur_parts[:2]
                    calls.add((chrom, int(start) - 1))
    return calls