def test_should_not_apply_bad_reads_to_insertion_if_all_supporting_reads_have_high_base_qualities(
self):
svc = SVCDriver(self) \
.with_var_filters("BR") \
.with_bad_reads_window_size(3) \
.with_min_bad_reads_score(15)
svc.with_ref_sequence(
# 1234567890123 456789
"AAAGCGTACAACCG*GGTTAGTCACAAACCCGTTACGTATGCATG").with_read(
"..............*..G...........................",
" 1 ",
n_rev=11,
n_fwd=10)
svc.with_read("..............T..............................",
n_rev=10,
n_fwd=10)
expect = svc.call()
vcf_expectation = expect.with_output_vcf()
vcf_expectation.record_count(1)
vcf_expectation \
.has_record_for_variant(Variant(DEFAULT_CHROM, 13, "G", "GT")) \
.with_no_filters()
class TestVariantCallerTimings(BaseTest):
def setUp(self):
BaseTest.setUp(self)
self.bed_filename = os.path.join(self.work_dir, "_.bed")
self.log_filename = os.path.join(self.work_dir, "_.log")
chrom = "1"
with BEDWriterContextManager(self.bed_filename) as bed_file:
bed_file.write_chrom_interval(ChromInterval(chrom, 0, 42))
self.output_vcf = os.path.join(self.work_dir, "output.vcf")
self.svc_driver = SVCDriver(self)
self.svc_driver.with_ref_sequence(
"AAAAAAAAAAACGCACCCCCCATAAAAAAAATTTTTTTTTTT", chrom=chrom)
self.svc_driver.with_read(" ..............C............. ",
chrom=chrom)
self.svc_driver.with_log_timings(True)
self.svc_driver.with_region_string(self.bed_filename)
self.svc_driver.with_log_filename(self.log_filename)
self.svc_driver.with_output_vcf_filename(self.output_vcf)
def __outputs_timings_for_files(self, expected_files):
observed_files = set()
with open(self.log_filename, "r") as log_file:
timing_data = log_timing_parser(log_file)
self.assertGreater(len(timing_data), 0)
for timing_data_item in timing_data:
self.assertEqual("IO", timing_data_item.timing_type)
self.assertEqual("us", timing_data_item.length_units)
self.assertIn("file", timing_data_item.metadata)
observed_files.add(timing_data_item.metadata["file"])
for expected in expected_files:
self.assertIn(expected, observed_files)
def test_should_contain_timings_output_for_bam(self):
self.svc_driver.with_bam_filenames(
[os.path.join(self.work_dir, "ba.bam")])
self.svc_driver.call()
self.__outputs_timings_for_files(
{os.path.join(self.work_dir, "ba.bam")})
def test_should_contain_timings_output_for_fasta_file(self):
ref = os.path.join(self.work_dir, "ref.fa")
self.svc_driver.with_ref_filename(ref)
self.svc_driver.call()
self.__outputs_timings_for_files({ref})
def test_should_contain_timings_output_for_fasta_index_file(self):
ref = os.path.join(self.work_dir, "ref.fa")
self.svc_driver.with_ref_filename(ref)
self.svc_driver.call()
self.__outputs_timings_for_files({ref + ".fai"})
def test_should_contain_timings_output_for_vcf(self):
self.svc_driver.call()
self.__outputs_timings_for_files({self.output_vcf})
def test_should_contain_timings_output_for_vcf_when_variant_caller_run_in_parallel(
self):
self.svc_driver.with_number_of_jobs(1)
self.svc_driver.with_work_dir(
os.path.join(self.work_dir, "vc_work_dir"))
self.svc_driver.call()
self.__outputs_timings_for_files({self.output_vcf})
def test_should_contain_timings_output_for_bed(self):
self.svc_driver.call()
self.__outputs_timings_for_files({self.bed_filename})