def main(argv=()):
with errors.clean_commandline_error_exit():
if len(argv) > 1:
errors.log_and_raise(
'Command line parsing failure: make_examples does not accept '
'positional arguments but some are present on the command line: '
'"{}".'.format(str(argv)), errors.CommandLineError)
del argv # Unused.
proto_utils.uses_fast_cpp_protos_or_die()
logging_level.set_from_flag()
hts_verbose.set(hts_verbose.htsLogLevel[FLAGS.hts_logging_level])
# Set up options; may do I/O.
options = default_options(add_flags=True, flags_obj=FLAGS)
# Check arguments that apply to any mode.
if not options.reference_filename:
errors.log_and_raise('ref argument is required.',
errors.CommandLineError)
if not options.reads_filename:
errors.log_and_raise('reads argument is required.',
errors.CommandLineError)
if not options.examples_filename:
errors.log_and_raise('examples argument is required.',
errors.CommandLineError)
if options.n_cores != 1:
errors.log_and_raise(
'Currently only supports n_cores == 1 but got {}.'.format(
options.n_cores), errors.CommandLineError)
# Check for argument issues specific to train mode.
if in_training_mode(options):
if not options.truth_variants_filename:
errors.log_and_raise(
'truth_variants is required when in training mode.',
errors.CommandLineError)
if not options.confident_regions_filename:
errors.log_and_raise(
'confident_regions is required when in training mode.',
errors.CommandLineError)
if options.gvcf_filename:
errors.log_and_raise('gvcf is not allowed in training mode.',
errors.CommandLineError)
else:
# Check for argument issues specific to calling mode.
if options.variant_caller_options.sample_name == _UNKNOWN_SAMPLE:
errors.log_and_raise(
'sample_name must be specified in calling mode.',
errors.CommandLineError)
if options.variant_caller_options.gq_resolution < 1:
errors.log_and_raise(
'gq_resolution must be a non-negative integer.',
errors.CommandLineError)
# Run!
make_examples_runner(options)
def main(argv=()):
with errors.clean_commandline_error_exit():
if len(argv) > 1:
errors.log_and_raise(
'Command line parsing failure: make_examples does not accept '
'positional arguments but some are present on the command line: '
'"{}".'.format(str(argv)), errors.CommandLineError)
del argv # Unused.
proto_utils.uses_fast_cpp_protos_or_die()
logging_level.set_from_flag()
hts_verbose.set(hts_verbose.htsLogLevel[FLAGS.hts_logging_level])
# Set up options; may do I/O.
options = default_options(add_flags=True, flags_obj=FLAGS)
# Check arguments that apply to any mode.
if not options.reference_filename:
errors.log_and_raise('ref argument is required.', errors.CommandLineError)
if not options.reads_filename:
errors.log_and_raise('reads argument is required.',
errors.CommandLineError)
if not options.examples_filename:
errors.log_and_raise('examples argument is required.',
errors.CommandLineError)
if options.n_cores != 1:
errors.log_and_raise(
'Currently only supports n_cores == 1 but got {}.'.format(
options.n_cores), errors.CommandLineError)
# Check for argument issues specific to train mode.
if in_training_mode(options):
if not options.truth_variants_filename:
errors.log_and_raise(
'truth_variants is required when in training mode.',
errors.CommandLineError)
if not options.confident_regions_filename:
errors.log_and_raise(
'confident_regions is required when in training mode.',
errors.CommandLineError)
if options.gvcf_filename:
errors.log_and_raise('gvcf is not allowed in training mode.',
errors.CommandLineError)
else:
# Check for argument issues specific to calling mode.
if options.variant_caller_options.sample_name == _UNKNOWN_SAMPLE:
errors.log_and_raise('sample_name must be specified in calling mode.',
errors.CommandLineError)
if options.variant_caller_options.gq_resolution < 1:
errors.log_and_raise('gq_resolution must be a non-negative integer.',
errors.CommandLineError)
# Run!
make_examples_runner(options)
def main(argv=()):
with errors.clean_commandline_error_exit():
if len(argv) > 1:
errors.log_and_raise(
'Command line parsing failure: make_examples does not accept '
'positional arguments but some are present on the command line: '
'"{}".'.format(str(argv)), errors.CommandLineError)
del argv # Unused.
proto_utils.uses_fast_cpp_protos_or_die()
logging_level.set_from_flag()
hts_verbose.set(hts_verbose.htsLogLevel[FLAGS.hts_logging_level])
# Set up options; may do I/O.
options = default_options(add_flags=True, flags_obj=FLAGS)
check_options_are_valid(options)
# Run!
make_examples_core.make_examples_runner(options)
def test_set(self):
hts_verbose.set(hts_verbose.htsLogLevel.HTS_LOG_TRACE)
level = hts_verbose.get()
self.assertEqual(level, hts_verbose.htsLogLevel.HTS_LOG_TRACE)
hts_verbose.set(hts_verbose.htsLogLevel.HTS_LOG_INFO)
level = hts_verbose.get()
self.assertEqual(level, hts_verbose.htsLogLevel.HTS_LOG_INFO)
hts_verbose.set(hts_verbose.htsLogLevel['HTS_LOG_DEBUG'])
level = hts_verbose.get()
self.assertEqual(level, hts_verbose.htsLogLevel.HTS_LOG_DEBUG)
def test_set(self):
hts_verbose.set(hts_verbose.htsLogLevel.HTS_LOG_TRACE)
level = hts_verbose.get()
self.assertEqual(level, hts_verbose.htsLogLevel.HTS_LOG_TRACE)
hts_verbose.set(hts_verbose.htsLogLevel.HTS_LOG_INFO)
level = hts_verbose.get()
self.assertEqual(level, hts_verbose.htsLogLevel.HTS_LOG_INFO)
hts_verbose.set(hts_verbose.htsLogLevel['HTS_LOG_DEBUG'])
level = hts_verbose.get()
self.assertEqual(level, hts_verbose.htsLogLevel.HTS_LOG_DEBUG)