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())))
