scripts/run_deepvariant.py
def create_all_commands(intermediate_results_dir):
  """Creates 3 commands to be executed later."""
  commands = []
  # make_examples
  nonvariant_site_tfrecord_path = None
  if FLAGS.output_gvcf is not None:
    nonvariant_site_tfrecord_path = os.path.join(
        intermediate_results_dir,
        'gvcf.tfrecord@{}.gz'.format(FLAGS.num_shards))

  examples = os.path.join(
      intermediate_results_dir,
      'make_examples.tfrecord@{}.gz'.format(FLAGS.num_shards))

  commands.append(
      make_examples_command(
          FLAGS.ref,
          FLAGS.reads,
          examples,
          FLAGS.make_examples_extra_args,
          gvcf=nonvariant_site_tfrecord_path,
          regions=FLAGS.regions,
          sample_name=FLAGS.sample_name))

  # call_variants
  call_variants_output = os.path.join(intermediate_results_dir,
                                      'call_variants_output.tfrecord.gz')
  model_ckpt = get_model_ckpt(FLAGS.model_type, FLAGS.customized_model)
  commands.append(
      call_variants_command(call_variants_output, examples, model_ckpt,
                            FLAGS.call_variants_extra_args))

  # postprocess_variants
  commands.append(
      postprocess_variants_command(
          FLAGS.ref,
          call_variants_output,
          FLAGS.output_vcf,
          FLAGS.postprocess_variants_extra_args,
          nonvariant_site_tfrecord_path=nonvariant_site_tfrecord_path,
          gvcf_outfile=FLAGS.output_gvcf,
          vcf_stats_report=FLAGS.vcf_stats_report,
          sample_name=FLAGS.sample_name))

  return commands
Creates 3 commands to be executed later.
Creates 3 commands to be executed later.
Creates 3 commands to be executed later .
def create_all_commands(intermediate_results_dir):
  commands = []
  nonvariant_site_tfrecord_path = None
  if FLAGS.output_gvcf is not None:
    nonvariant_site_tfrecord_path = os.path.join(
        intermediate_results_dir,
        'gvcf.tfrecord@{}.gz'.format(FLAGS.num_shards))
  examples = os.path.join(
      intermediate_results_dir,
      'make_examples.tfrecord@{}.gz'.format(FLAGS.num_shards))
  commands.append(
      make_examples_command(
          FLAGS.ref,
          FLAGS.reads,
          examples,
          FLAGS.make_examples_extra_args,
          gvcf=nonvariant_site_tfrecord_path,
          regions=FLAGS.regions,
          sample_name=FLAGS.sample_name))
  call_variants_output = os.path.join(intermediate_results_dir,
                                      'call_variants_output.tfrecord.gz')
  model_ckpt = get_model_ckpt(FLAGS.model_type, FLAGS.customized_model)
  commands.append(
      call_variants_command(call_variants_output, examples, model_ckpt,
                            FLAGS.call_variants_extra_args))
  commands.append(
      postprocess_variants_command(
          FLAGS.ref,
          call_variants_output,
          FLAGS.output_vcf,
          FLAGS.postprocess_variants_extra_args,
          nonvariant_site_tfrecord_path=nonvariant_site_tfrecord_path,
          gvcf_outfile=FLAGS.output_gvcf,
          vcf_stats_report=FLAGS.vcf_stats_report,
          sample_name=FLAGS.sample_name))
  return commands
def create_all_commands ( intermediate_results_dir ) : commands = [ ] nonvariant_site_tfrecord_path = None if FLAGS . output_gvcf is not None : nonvariant_site_tfrecord_path = os . path . join ( intermediate_results_dir , 'gvcf.tfrecord@{}.gz' . format ( FLAGS . num_shards ) ) examples = os . path . join ( intermediate_results_dir , 'make_examples.tfrecord@{}.gz' . format ( FLAGS . num_shards ) ) commands . append ( make_examples_command ( FLAGS . ref , FLAGS . reads , examples , FLAGS . make_examples_extra_args , gvcf = nonvariant_site_tfrecord_path , regions = FLAGS . regions , sample_name = FLAGS . sample_name ) ) call_variants_output = os . path . join ( intermediate_results_dir , 'call_variants_output.tfrecord.gz' ) model_ckpt = get_model_ckpt ( FLAGS . model_type , FLAGS . customized_model ) commands . append ( call_variants_command ( call_variants_output , examples , model_ckpt , FLAGS . call_variants_extra_args ) ) commands . append ( postprocess_variants_command ( FLAGS . ref , call_variants_output , FLAGS . output_vcf , FLAGS . postprocess_variants_extra_args , nonvariant_site_tfrecord_path = nonvariant_site_tfrecord_path , gvcf_outfile = FLAGS . output_gvcf , vcf_stats_report = FLAGS . vcf_stats_report , sample_name = FLAGS . sample_name ) ) return commands
Creates 3 commands to be executed later.
Creates 3 commands to be executed later .
"""Creates 3 commands to be executed later.""" # make_examples # call_variants # postprocess_variants
intermediate_results_dir