def __init__(
self,
file_name, # type: str
range_tracker, # type: range_trackers.OffsetRangeTracker
file_pattern, # type: str
compression_type, # type: str
allow_malformed_records, # type: bool
representative_header_lines=None, # type: List[str]
**kwargs # type: **str
):
# type: (...) -> None
# If `representative_header_lines` is given, header lines in `file_name`
# are ignored; refer to _process_header_lines() logic.
self._representative_header_lines = representative_header_lines
self._file_name = file_name
self._allow_malformed_records = allow_malformed_records
text_source = textio._TextSource(
file_pattern,
0, # min_bundle_size
compression_type,
True, # strip_trailing_newlines
coders.StrUtf8Coder(), # coder
validate=False,
header_processor_fns=(lambda x: not x.strip() or x.startswith('#'),
self._process_header_lines),
**kwargs)
self._text_lines = text_source.read_records(self._file_name,
range_tracker)
def _create_source(self, path, schema):
if not self.use_json_exports:
return _create_avro_source(path, use_fastavro=True)
else:
return _TextSource(path,
min_bundle_size=0,
compression_type=CompressionTypes.UNCOMPRESSED,
strip_trailing_newlines=True,
coder=_JsonToDictCoder(schema))
def __init__(
self,
file_name, # type: str
range_tracker, # type: range_trackers.OffsetRangeTracker
file_pattern, # type: str
compression_type, # type: str
allow_malformed_records, # type: bool
representative_header_lines=None, # type: List[str]
**kwargs # type: **str
):
# type: (...) -> None
# If `representative_header_lines` is given, header lines in `file_name`
# are ignored.
self._header_lines = []
self._representative_header_lines = representative_header_lines
self._last_record = None
self._file_name = file_name
self._allow_malformed_records = allow_malformed_records
text_source = textio._TextSource(
file_pattern,
0, # min_bundle_size
compression_type,
True, # strip_trailing_newlines
coders.StrUtf8Coder(), # coder
validate=False,
header_processor_fns=(lambda x: x.startswith('#'),
self._store_header_lines),
**kwargs)
self._text_lines = text_source.read_records(
self._file_name, range_tracker)
try:
self._vcf_reader = vcf.Reader(fsock=self._create_generator())
except SyntaxError as e:
raise ValueError('Invalid VCF header in %s: %s' %
(self._file_name, str(e)))
def __init__(
self,
file_name, # type: str
range_tracker, # type: range_trackers.OffsetRangeTracker
file_pattern, # type: str
compression_type, # type: str
allow_malformed_records, # type: bool
representative_header_lines=None, # type: List[str]
splittable_bgzf=False, # type: bool
pre_infer_headers=False, # type: bool
sample_name_encoding=SampleNameEncoding.
WITHOUT_FILE_PATH, # type: int
use_1_based_coordinate=False, # type: bool
**kwargs # type: **str
):
# type: (...) -> None
# If `representative_header_lines` is given, header lines in `file_name`
# are ignored; refer to _process_header_lines() logic.
self._representative_header_lines = representative_header_lines
self._file_name = file_name
self._allow_malformed_records = allow_malformed_records
self._pre_infer_headers = pre_infer_headers
self._sample_name_encoding = sample_name_encoding
self._use_1_based_coordinate = use_1_based_coordinate
if splittable_bgzf:
text_source = bgzf.BGZFBlockSource(
file_name,
range_tracker,
representative_header_lines,
compression_type,
header_processor_fns=(
lambda x: not x.strip() or x.startswith('#'),
self._process_header_lines),
**kwargs)
elif compression_type == filesystems.CompressionTypes.GZIP:
text_source = bgzf.BGZFSource(
file_pattern,
0, # min_bundle_size
compression_type,
True, # strip_trailing_newlines
coders.StrUtf8Coder(), # coder
validate=False,
header_processor_fns=(
lambda x: not x.strip() or x.startswith('#'),
self._process_header_lines),
**kwargs)
else:
text_source = textio._TextSource(
file_pattern,
0, # min_bundle_size
compression_type,
True, # strip_trailing_newlines
coders.StrUtf8Coder(), # coder
validate=False,
header_processor_fns=(
lambda x: not x.strip() or x.startswith('#'),
self._process_header_lines),
**kwargs)
self._text_lines = text_source.read_records(self._file_name,
range_tracker)
