def test_validate_args_ok(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
args = Namespace(input=input_dir.path,
output=output_dir.path,
allow_inconsistent_sample_sets=0,
varscan_hc_filter_filename=None)
input_dir.write("claimed.vcf", b"foo")
translate.variant_caller_factory = MockVariantCallerFactory()
translate.validate_args(args)
self.ok()
def test_validate_args_ok(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
args = Namespace(input=input_dir.path,
output=output_dir.path,
allow_inconsistent_sample_sets=0,
varscan_hc_filter_filename=None)
input_dir.write("claimed.vcf", b"foo")
translate.variant_caller_factory = MockVariantCallerFactory()
translate.validate_args(args)
self.ok()
def test_validate_args_snpIndelPairingAllowInconsistentSampleSetsOK(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
args = Namespace(input=input_dir.path,
output=output_dir.path,
force=False,
allow_inconsistent_sample_sets=1,
varscan_hc_filter_filename=None)
input_dir.write("claimed.foo.vcf", b"foo")
input_dir.write("claimed2.foo.vcf", b"foo")
input_dir.write("claimed2.bar.vcf", b"foo")
translate.variant_caller_factory = MockVariantCallerFactory()
translate.validate_args(args)
self.ok()
def test_validate_args_snpIndelPairingAllowInconsistentSampleSetsOK(self):
with TempDirectory() as input_dir, TempDirectory() as output_dir:
args = Namespace(input=input_dir.path,
output=output_dir.path,
force=False,
allow_inconsistent_sample_sets=1,
varscan_hc_filter_filename=None)
input_dir.write("claimed.foo.vcf", b"foo")
input_dir.write("claimed2.foo.vcf", b"foo")
input_dir.write("claimed2.bar.vcf", b"foo")
translate.variant_caller_factory = MockVariantCallerFactory()
translate.validate_args(args)
self.ok()
