docstr: Confirms that adding extra flags can overwrite the default from mode.
docstr_tok: ["Confirms","that","adding","extra","flags","can","overwrite","the","default","from","mode","."]
code: def test_pacbio_args_overwrite(
      self, make_examples_extra_args, expected_args, expected_stdout
  ):
      """Confirms that adding extra flags can overwrite the default from mode."""
      FLAGS.model_type = "PACBIO"
      FLAGS.ref = "your_ref"
      FLAGS.sample_name_child = "your_sample_child"
      FLAGS.sample_name_parent1 = "your_sample_parent1"
      FLAGS.sample_name_parent2 = "your_sample_parent2"
      FLAGS.reads_child = "your_bam_child"
      FLAGS.reads_parent1 = "your_bam_parent1"
      FLAGS.reads_parent2 = "your_bam_parent2"
      FLAGS.output_vcf_child = "your_vcf_child"
      FLAGS.output_vcf_parent1 = "your_vcf_parent1"
      FLAGS.output_vcf_parent2 = "your_vcf_parent2"
      FLAGS.output_gvcf_child = "your_gvcf_child"
      FLAGS.output_gvcf_parent1 = "your_gvcf_parent1"
      FLAGS.output_gvcf_parent2 = "your_gvcf_parent2"
      FLAGS.num_shards = 64
      FLAGS.regions = None
      FLAGS.make_examples_extra_args = make_examples_extra_args
      commands, _, _ = self._create_all_commands_and_check_stdout(
          expected_stdout
      )
      self.assertEqual(
          commands[0],
          "time seq 0 63 | parallel -q --halt 2 --line-buffer "
          "/opt/deepvariant/bin/deeptrio/make_examples --mode candidate_sweep "
          '--ref "your_ref" --reads_parent1 "your_bam_parent1" '
          '--reads_parent2 "your_bam_parent2" '
          '--reads "your_bam_child" '
          '--examples "/tmp/deeptrio_tmp_output/make_examples.tfrecord@64.gz" '
          '--sample_name "your_sample_child" '
          '--sample_name_parent1 "your_sample_parent1" '
          '--sample_name_parent2 "your_sample_parent2" '
          "%s"
          "--task {}" % expected_args,
      )
  
imports: import io
  from unittest import mock
  from absl import flags
  from absl.testing import absltest
  from absl.testing import flagsaver
  from absl.testing import parameterized
  from deepvariant.opensource_only.scripts import run_deeptrio
label_desc: Use image node_id 9 for calling the RunDeeptrioTest obj's underlying member method code with example usage: obj.test_pacbio_args_overwrite(make_examples_extra_args, expected_args, expected_stdout) without return types