def default_options(read_requirements=None):
"""Creates a PileupImageOptions populated with good default values."""
if not read_requirements:
read_requirements = core_pb2.ReadRequirements(
min_base_quality=DEFAULT_MIN_BASE_QUALITY,
min_mapping_quality=DEFAULT_MIN_MAPPING_QUALITY,
min_base_quality_mode=core_pb2.ReadRequirements.ENFORCED_BY_CLIENT)
return deepvariant_pb2.PileupImageOptions(
reference_band_height=5,
base_color_offset_a_and_g=40,
base_color_offset_t_and_c=30,
base_color_stride=70,
allele_supporting_read_alpha=1.0,
allele_unsupporting_read_alpha=0.6,
reference_matching_read_alpha=0.2,
reference_mismatching_read_alpha=1.0,
indel_anchoring_base_char='*',
reference_alpha=0.4,
reference_base_quality=60,
positive_strand_color=70,
negative_strand_color=240,
base_quality_cap=40,
mapping_quality_cap=60,
height=100,
width=221,
read_overlap_buffer_bp=5,
read_requirements=read_requirements,
multi_allelic_mode=deepvariant_pb2.PileupImageOptions.
ADD_HET_ALT_IMAGES,
# Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'.
random_seed=2101079370)
def default_options(read_requirements=None):
"""Creates a PileupImageOptions populated with good default values."""
if not read_requirements:
read_requirements = reads_pb2.ReadRequirements(
min_base_quality=10,
min_mapping_quality=10,
min_base_quality_mode=reads_pb2.ReadRequirements.ENFORCED_BY_CLIENT)
return deepvariant_pb2.PileupImageOptions(
reference_band_height=5,
base_color_offset_a_and_g=40,
base_color_offset_t_and_c=30,
base_color_stride=70,
allele_supporting_read_alpha=1.0,
allele_unsupporting_read_alpha=0.6,
other_allele_supporting_read_alpha=0.6,
reference_matching_read_alpha=0.2,
reference_mismatching_read_alpha=1.0,
indel_anchoring_base_char='*',
reference_alpha=0.4,
reference_base_quality=60,
positive_strand_color=70,
negative_strand_color=240,
base_quality_cap=40,
mapping_quality_cap=60,
height=dv_constants.PILEUP_DEFAULT_HEIGHT,
width=dv_constants.PILEUP_DEFAULT_WIDTH,
num_channels=6,
read_overlap_buffer_bp=5,
read_requirements=read_requirements,
multi_allelic_mode=deepvariant_pb2.PileupImageOptions.ADD_HET_ALT_IMAGES,
# Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'.
random_seed=2101079370,
sequencing_type=deepvariant_pb2.PileupImageOptions.UNSPECIFIED_SEQ_TYPE,
alt_aligned_pileup='none',
types_to_alt_align='indels',
min_non_zero_allele_frequency=0.00001,
use_allele_frequency=False)
def _make_image_creator(ref_reader, sam_reader_obj, **kwargs):
options = pileup_image.default_options()
options.MergeFrom(deepvariant_pb2.PileupImageOptions(**kwargs))
return pileup_image.PileupImageCreator(options, ref_reader, sam_reader_obj)
def _make_encoder(**kwargs):
"""Make a PileupImageEncoderNative with overrideable default options."""
options = pileup_image.default_options()
options.MergeFrom(deepvariant_pb2.PileupImageOptions(**kwargs))
return pileup_image_native.PileupImageEncoderNative(options)
