def test_gvcf_basic_raises_with_bad_ref_base(self, ref): options = _reference_model_options(0.01, 100) caller = variant_caller.VariantCaller(options, use_cache_table=False) allele_counter = self.fake_allele_counter(100, [(0, 0, ref)]) with self.assertRaisesRegexp(ValueError, 'Invalid reference base={}'.format(ref)): list(caller.make_gvcfs(allele_counter.summary_counts()))
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_gvcf_basic(self, ref): options = _reference_model_options(0.01, 100) caller = variant_caller.VariantCaller(options, use_cache_table=False) allele_counter = self.fake_allele_counter(100, [(0, 0, ref)]) gvcfs = list(caller.make_gvcfs(allele_counter.summary_counts())) self.assertLen(gvcfs, 1) self.assertGVCF(gvcfs[0], ref=ref, gq=1.0, start=100, end=101, chrom='chr1', gls=[-0.47712125472] * 3, sample_name=options.sample_name)
def make_test_caller(self, p_error, max_gq, gq_resolution=1): options = _reference_model_options(p_error, max_gq, gq_resolution) return variant_caller.VariantCaller(options, use_cache_table=False)
def setUpClass(cls): options = _reference_model_options(0.1, 50) cls.raw_caller = variant_caller.VariantCaller( options, use_cache_table=False) cls.cache_caller = variant_caller.VariantCaller( options, use_cache_table=True, max_cache_coverage=_CACHE_COVERAGE)
def test_gvcf_basic_skips_iupac_ref_base(self, ref): options = _reference_model_options(0.01, 100) caller = variant_caller.VariantCaller(options, use_cache_table=False) allele_counter = self.fake_allele_counter(100, [(0, 0, ref)]) self.assertEmpty(list(caller.make_gvcfs(allele_counter.summary_counts())))