old_contents: import argparse
  import logging
  
  from pyim.align.pipelines import get_pipelines
  from pyim.model import Insertion
  
  logging.basicConfig(
      format='[%(asctime)-15s]  %(message)s',
      level=logging.INFO,
      datefmt='%Y-%m-%d %H:%M:%S')
  
  
  def main():
      """Main function for pyim-align."""
  
      args = parse_args()
  
      # Run pipeline.
      pipeline = args.pipeline.from_args(args)
      pipeline.run(read_path=args.reads,
                   output_dir=args.output_dir,
                   read2_path=args.reads2)
  
  
  def parse_args():
      """Parses arguments for pyim-align."""
  
      # Setup main parser.
      parser = argparse.ArgumentParser(prog='pyim-align')
      subparsers = parser.add_subparsers(dest='pipeline')
      subparsers.required = True
  
      # Register pipelines.
      pipelines = get_pipelines()
  
      for pipeline_name in sorted(pipelines.keys()):
          pipeline_class = pipelines[pipeline_name]
  
          pipeline_parser = subparsers.add_parser(pipeline_name)
          pipeline_class.configure_args(pipeline_parser)
          pipeline_parser.set_defaults(pipeline=pipeline_class)
  
      return parser.parse_args()
  
  
  if __name__ == '__main__':
      main()
  
new_contents: import argparse
  import logging
  
  from pyim.align.pipelines import get_pipelines
  
  logging.basicConfig(
      format='[%(asctime)-15s]  %(message)s',
      level=logging.INFO,
      datefmt='%Y-%m-%d %H:%M:%S')
  
  
  def main():
      """Main function for pyim-align."""
  
      args = parse_args()
  
      # Run pipeline.
      pipeline = args.pipeline.from_args(args)
      pipeline.run(read_path=args.reads,
                   output_dir=args.output_dir,
                   read2_path=args.reads2)
  
  
  def parse_args():
      """Parses arguments for pyim-align."""
  
      # Setup main parser.
      parser = argparse.ArgumentParser(prog='pyim-align')
      subparsers = parser.add_subparsers(dest='pipeline')
      subparsers.required = True
  
      # Register pipelines.
      pipelines = get_pipelines()
  
      for pipeline_name in sorted(pipelines.keys()):
          pipeline_class = pipelines[pipeline_name]
  
          pipeline_parser = subparsers.add_parser(pipeline_name)
          pipeline_class.configure_args(pipeline_parser)
          pipeline_parser.set_defaults(pipeline=pipeline_class)
  
      return parser.parse_args()
  
  
  if __name__ == '__main__':
      main()
  
subject: Remove unused import.