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)