def test_call_from_allele_counter(self):
ref = fasta.IndexedFastaReader(testdata.CHR20_FASTA)
sam_reader = sam.SamReader(testdata.CHR20_BAM)
size = 1000
region = ranges.make_range('chr20', 10000000, 10000000 + size)
allele_counter = _allelecounter.AlleleCounter(
ref.c_reader, region,
deepvariant_pb2.AlleleCounterOptions(partition_size=size))
caller = variant_calling.VariantCaller(
deepvariant_pb2.VariantCallerOptions(min_count_snps=2,
min_count_indels=2,
min_fraction_snps=0.12,
min_fraction_indels=0.12,
sample_name='sample_name',
p_error=0.001,
max_gq=50,
gq_resolution=1,
ploidy=2))
# Grab all of the reads in our region and add them to the allele_counter.
reads = list(sam_reader.query(region))
self.assertNotEmpty(reads)
for read in reads:
allele_counter.add(read)
# Get the candidates records for this whole region.
candidates = caller.calls_from_allele_counter(allele_counter)
# We should have at least some candidates and some gvcf records.
self.assertNotEmpty(candidates)
# Each candidate should be a DeepVariantCall.
for candidate in candidates:
self.assertIsInstance(candidate, deepvariant_pb2.DeepVariantCall)
def __init__(self, options, use_cache_table=True, max_cache_coverage=100):
self.options = options
self.cpp_variant_caller = variant_calling.VariantCaller(self.options)
self.max_cache_coverage = max_cache_coverage
if use_cache_table:
self.table = [[
self._calc_reference_confidence(n_ref, n_total)
for n_ref in range(n_total + 1)
] for n_total in range(self.max_cache_coverage + 1)]
else:
self.table = None
def __init__(self, options, use_cache_table, max_cache_coverage):
self.options = options
self.cpp_variant_caller = variant_calling.VariantCaller(self.options)
self.max_cache_coverage = max_cache_coverage
# pylint: disable=g-complex-comprehension
if use_cache_table:
self.table = [[
self._calc_reference_confidence(n_ref, n_total)
for n_ref in range(n_total + 1)
] for n_total in range(self.max_cache_coverage + 1)]
else:
self.table = None