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)
