rv, err = self.execute(params)
self.assertEqual(0, rv)
self.assertFilesEqual(expected_file, output_file, filter_regex="##fileDate=")
def test_sample2_none_second(self):
both_samples = self.inputFiles("vcf-merge/consensus/merge-S1-S2.vcf")[0]
sample2_none = self.inputFiles("vcf-merge/consensus/merge-S2-none.vcf")[0]
sample2_empty = self.inputFiles("vcf-merge/consensus/merge-S2-empty.vcf")[0]
expected_file = self.inputFiles("vcf-merge/consensus/expected-S1-S2_S2-none.vcf")[0]
output_file = self.tempFile("output.vcf")
base_params = [ "vcf-merge", "-s", "-R 1.0,FILT,FILT", "-o", output_file ]
equivalent_inputs = [
[both_samples, sample2_none],
[both_samples, sample2_empty]
]
base_params = [ "vcf-merge", "-s", "-R 1.0,FILT,FILT", "-o", output_file ]
for inputs in equivalent_inputs:
params = base_params + inputs
rv, err = self.execute(params)
self.assertEqual(0, rv)
self.assertFilesEqual(expected_file, output_file, filter_regex="##fileDate=")
if __name__ == "__main__":
main()
]
rv, err = self.execute(params)
self.assertEqual(0, rv)
self.assertFilesEqual(expected_file,
output_file,
filter_regex="##fileDate=")
def test_vcf_merge_per_alt_list(self):
merge_strategy_file = self.tempFile("strategy.ms")
open(merge_strategy_file,
"w").write("info.CALLER=per-alt-delimited-list")
input_files = sorted(
self.inputFiles("vcf-merge/merge-per-alt-list-[12].vcf"))
self.assertEqual(2, len(input_files))
expected_file = self.inputFiles(
"vcf-merge/expected-merge-per-alt-list.vcf")[0]
output_file = self.tempFile("output.vcf")
params = ["vcf-merge", "-M", merge_strategy_file, "-o", output_file
] + input_files
rv, err = self.execute(params)
self.assertEqual(0, rv)
self.assertFilesEqual(expected_file,
output_file,
filter_regex="##fileDate=")
if __name__ == "__main__":
main()
import mdl
import xmltest
_parser = argparse.ArgumentParser()
_subparsers = _parser.add_subparsers(dest='cmd')
if __name__ == '__main__':
buildsystem_parser = buildsystem.init_parser(_subparsers)
integrationtest_parser = integrationtest.init_parser(_subparsers)
installer_parser = installer.init_parser(_subparsers)
odbhelper_parser = odb.init_parser(_subparsers)
mdl_parser = mdl.init_parser(_subparsers)
xmltest_parser = xmltest.init_parser(_subparsers)
args = _parser.parse_args()
if args.cmd is None:
_parser.print_help()
elif args.cmd == 'buildsystem':
buildsystem.main(args)
elif args.cmd == 'integrationtest':
integrationtest.main(args)
elif args.cmd == 'installer':
installer.main(args)
elif args.cmd == 'odb':
odb.main(args)
elif args.cmd == 'mdl':
mdl.main(args)
elif args.cmd == 'xmltest':
xmltest.main(args)
