reader.py 文件源码

def __init__(self, stream, path=None, tabix_path=None,
                 record_checks=None, parsed_samples=None):
        #: stream (``file``-like object) to read from
        self.stream = stream
        #: optional ``str`` with the path to the stream
        self.path = path
        #: optional ``str`` with path to tabix file
        self.tabix_path = tabix_path
        #: checks to perform on records, can contain 'FORMAT' and 'INFO'
        self.record_checks = tuple(record_checks or [])
        #: if set, list of samples to parse for
        self.parsed_samples = parsed_samples
        #: the ``pysam.TabixFile`` used for reading from index bgzip-ed VCF;
        #: constructed on the fly
        self.tabix_file = None
        # the iterator through the Tabix file to use
        self.tabix_iter = None
        #: the parser to use
        self.parser = parser.Parser(stream, self.path, self.record_checks)
        #: the Header
        self.header = self.parser.parse_header(parsed_samples)