def setUp(self):
self.bam = test_utils.genomics_core_testdata('test.bam')
self.options = reads_pb2.SamReaderOptions()
self.indexed_options = reads_pb2.SamReaderOptions(
index_mode=index_pb2.INDEX_BASED_ON_FILENAME)
def setUp(self):
self.bam = test_utils.genomics_core_testdata('test.bam')
self.options = reads_pb2.SamReaderOptions()
def __init__(self,
input_path,
read_requirements=None,
parse_aux_fields=False,
hts_block_size=None,
downsample_fraction=None,
random_seed=None):
"""Initializes a NativeSamReader.
Args:
input_path: str. A path to a resource containing SAM/BAM records.
Currently supports SAM text format and BAM binary format.
read_requirements: optional ReadRequirement proto. If not None, this proto
is used to control which reads are filtered out by the reader before
they are passed to the client.
parse_aux_fields: optional bool, defaulting to False. If False, we do not
parse the auxiliary fields of the SAM/BAM records (see SAM spec for
details). Parsing the aux fields is unnecessary for many applications,
and adds a significant parsing cost to access. If you need these aux
fields, set parse_aux_fields to True and these fields will be parsed and
populate the appropriate Read proto fields (e.g., read.info).
hts_block_size: int or None. If specified, this configures the block size
of the underlying htslib file object. Larger values (e.g. 1M) may be
beneficial for reading remote files. If None, the reader uses the
default htslib block size.
downsample_fraction: float in the interval [0.0, 1.0] or None. If
specified as a positive float, the reader will only keep each read with
probability downsample_fraction, randomly. If None or zero, all reads
are kept.
random_seed: None or int. The random seed to use with this sam reader, if
needed. If None, a fixed random value will be assigned.
Raises:
ValueError: If downsample_fraction is not None and not in the interval
(0.0, 1.0].
ImportError: If someone tries to load a tfbam file.
"""
if input_path.endswith('.tfbam'):
# Delayed loading of tfbam_lib.
try:
from tfbam_lib import tfbam_reader # pylint: disable=g-import-not-at-top
self._reader = tfbam_reader.make_sam_reader(
input_path,
read_requirements=read_requirements,
unused_block_size=hts_block_size,
downsample_fraction=downsample_fraction,
random_seed=random_seed)
except ImportError:
raise ImportError(
'tfbam_lib module not found, cannot read .tfbam files.')
else:
aux_field_handling = reads_pb2.SamReaderOptions.SKIP_AUX_FIELDS
if parse_aux_fields:
aux_field_handling = reads_pb2.SamReaderOptions.PARSE_ALL_AUX_FIELDS
# We make 0 be a valid value that means "keep all reads" so that proto
# defaults (=0) do not omit all reads.
if downsample_fraction is not None and downsample_fraction != 0:
if not 0.0 < downsample_fraction <= 1.0:
raise ValueError(
'downsample_fraction must be in the interval (0.0, 1.0]',
downsample_fraction)
if random_seed is None:
# Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'.
random_seed = 2928130004
self._reader = sam_reader.SamReader.from_file(
input_path.encode('utf8'),
reads_pb2.SamReaderOptions(
read_requirements=read_requirements,
aux_field_handling=aux_field_handling,
hts_block_size=(hts_block_size or 0),
downsample_fraction=downsample_fraction,
random_seed=random_seed))
self.header = self._reader.header
super(NativeSamReader, self).__init__()