def _initialize(self): """Initialize the resources needed for this work in the current env.""" if self.initialized: raise ValueError('Cannot initialize this object twice') self.ref_reader = genomics_io.make_ref_reader( self.options.reference_filename) self.sam_reader = self._make_sam_reader() self.in_memory_sam_reader = utils.InMemorySamReader([]) if self.options.realigner_enabled: self.realigner = realigner.Realigner( self.options.realigner_options, self.ref_reader) self.pic = pileup_image.PileupImageCreator( ref_reader=self.ref_reader, sam_reader=self.in_memory_sam_reader, options=self.options.pic_options) if in_training_mode(self.options): self.labeler = variant_labeler.VariantLabeler( genomics_io.make_vcf_reader( self.options.truth_variants_filename), read_confident_regions(self.options)) self.variant_caller = variant_caller.VariantCaller( self.options.variant_caller_options) self.random = np.random.RandomState(self.options.random_seed) self.initialized = True
def _initialize(self): """Initialize the resources needed for this work in the current env.""" if self.initialized: raise ValueError('Cannot initialize this object twice') self.ref_reader = fasta.IndexedFastaReader( self.options.reference_filename) self.sam_reader = self._make_sam_reader() self.in_memory_sam_reader = sam.InMemorySamReader([]) if self.options.realigner_enabled: self.realigner = realigner.Realigner( self.options.realigner_options, self.ref_reader) self.pic = pileup_image.PileupImageCreator( ref_reader=self.ref_reader, sam_reader=self.in_memory_sam_reader, options=self.options.pic_options) if in_training_mode(self.options): self.labeler = self._make_labeler_from_options() self.variant_caller = variant_caller.VariantCaller( self.options.variant_caller_options) self.random = np.random.RandomState(self.options.random_seed) self.initialized = True
def test_alt_combinations_no_het_alt(self, ref, alts, expected): options = pileup_image.default_options() options.multi_allelic_mode = ( deepvariant_pb2.PileupImageOptions.NO_HET_ALT_IMAGES) pic = pileup_image.PileupImageCreator(options, self.mock_ref_reader, self.mock_sam_reader) variant = variants_pb2.Variant(reference_bases=ref, alternate_bases=alts) self.assertEqual(expected, list(pic._alt_allele_combinations(variant)))
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_pic(self, **kwargs): return pileup_image.PileupImageCreator(self.options, self.mock_ref_reader, self.mock_sam_reader, **kwargs)