How to use the pysam.asVCF function in pysam

    def __init__(self, inFile, ploidy=1, parser=pysam.asVCF()):
        # using old-style class superclass calling here
        # since TabixReader is derived from pysam.TabixFile
        # which is itself an old-style class (due to Cython version?)
        TabixReader.__init__(self, inFile, parser=parser)
        # when pysam uses new-style classes, we can replace with:
        #super(VcfReader, self).__init__(inFile, parser=parser)
        assert ploidy in (1, 2)
        self.ploidy = ploidy
        self.clens = []
        self.sample_names = None
        for line in self.header: # pylint: disable=E1101
            line = bytes_to_string(line)
            if line.startswith('##contig='):
                line = line[13:-1]
                c = line.split(',')[0]
                clen = int(line.split('=')[1])

    def __init__(self, inFile, ploidy=1, parser=pysam.asVCF()):
        super(VcfReader, self).__init__(inFile, parser=parser)
        assert ploidy in (1,2)
        self.ploidy = ploidy
        self.clens = []
        self.sample_names = None
        for line in self.header:
            line = bytes_to_string(line)
            if line.startswith('##contig='):
                line = line[13:-1]
                c = line.split(',')[0]
                clen = int(line.split('=')[1])
                self.clens.append((c,clen))
            elif line.startswith('#CHROM'):
                row = line.split('\t')
                self.sample_names = row[9:]
        self.clens = dict(self.clens)

    def __init__(self, inFile, ploidy=1, parser=pysam.asVCF()):
        super(VcfReader, self).__init__(inFile, parser=parser)
        assert ploidy in (1,2)
        self.ploidy = ploidy
        self.clens = []
        self.sample_names = None
        for line in self.header:
            if line.startswith('##contig='):
                line = line[13:-1]
                c = line.split(',')[0]
                clen = int(line.split('=')[1])
                self.clens.append((c,clen))
            elif line.startswith('#CHROM'):
                row = line.split('\t')
                self.sample_names = row[9:]
        self.clens = dict(self.clens)
        assert self.sample_names

def select_vcf_records(bed_records, vcf_records):
    """Returns an iterable of VCF records, corresponding to the contents of each
    region specified by the BED records. Records are returned at most once, even
    if covered by multiple BED records."""
    contigs = frozenset(vcf_records.contigs)
    vcf_parser = pysam.asVCF()

    # Timer class used processing progress; meant primarily for BAM files
    progress = timer.BAMTimer(None)

    # Cache of positions observed for this contig, to prevent returning
    # positions in overlapping regions multiple times
    contig_cache = None
    contig_cache_name = None

    for bed in sorted(bed_records):
        if bed.contig not in contigs:
            # Skip contigs for which no calls have been made (e.g. due to
            # low coverage. Otherwise Pysam raises an exception.
            continue
        elif contig_cache_name != bed.contig:
            # Reset cache per contig, to save memory

def read_tabix_VCF(lines):
    return read_tabix(lines, pysam.asVCF())

def process_piece(filename_vcf, chrom, chrom_length, sample_index, chain_info, diploid, passed, quality, vcf_keep, vcf_discard_file):
    ret = {'chrom': chrom, 'stats': {}, 'chain_info': chain_info}

    stats = OrderedDict()
    stats['ACCEPTED'] = 0

    if vcf_keep:
        vcf_discard = open(vcf_discard_file, "w")

    line_no = 0

    try:
        LOG.info("Processing Chromosome {0}...".format(chrom))
        tb = pysam.TabixFile(filename_vcf)

        for vcf_rec in tb.fetch(chrom, parser=pysam.asVCF()):
            line_no += 1

            try:
                gt = parse_gt_new(vcf_rec, sample_index)
            except:
                LOG.info("Unable to parse record, improper VCF file?")
                continue

            LOG.debug('\n')
            LOG.debug(vcf_rec)
            LOG.debug(gt)
            LOG.debug(vcf_rec[sample_index])

            if passed and 'PASS' not in vcf_rec.FILTER:

                LOG.debug("TOSSED: FILTERED ON PASS")

def _read_files(args):
    in_header = True
    has_filters = False
    vcf_parser = pysam.asVCF()
    for filename in args.filenames:
        with open_ro(filename, "rb") as handle:
            for line in handle:
                if not line.startswith(b"#"):
                    in_header = False
                    line = line.rstrip(b"\n\r")
                    vcf = vcf_parser(line, len(line))
                    if args.reset_filter:
                        vcf.filter = "."

                    yield vcf
                elif in_header:
                    if not (line.startswith(b"##") or has_filters):
                        has_filters = True
                        for item in sorted(vcffilter.describe_filters(args).items()):
                            print('##FILTER=' % item)

def filter_vcfs(genotype, contig, start, end):
    if contig in genotype.contigs:
        parser = pysam.asVCF()
        # This raises a ValueError if the VCF does not
        # contain any entries for the specified contig.
        for vcf in genotype.fetch(contig, start, end, parser=parser):
            if vcf.filter in ("PASS", "."):
                yield vcf