parameters: (bubbles_in, subs_matrix, hopo_matrix,
                      consensus_out, num_threads, output_progress, use_hopo)
docstring: Invokes polishing binary
docstring_summary: Invokes polishing binary
docstring_tokens: Invokes polishing binary
function: def _run_polish_bin(bubbles_in, subs_matrix, hopo_matrix,
                      consensus_out, num_threads, output_progress, use_hopo):
      """
      Invokes polishing binary
      """
      cmdline = [POLISH_BIN, "polisher", "--bubbles", bubbles_in, "--subs-mat", subs_matrix,
                 "--hopo-mat", hopo_matrix, "--out", consensus_out,
                 "--threads", str(num_threads)]
      if not output_progress:
          cmdline.append("--quiet")
  
      if use_hopo:
          cmdline.append("--enable-hopo")
  
      try:
          subprocess.check_call(cmdline)
      except subprocess.CalledProcessError as e:
          if e.returncode == -9:
              logger.error("Looks like the system ran out of memory")
          raise PolishException(str(e))
      except OSError as e:
          raise PolishException(str(e))
function_tokens: def _run_polish_bin ( bubbles_in , subs_matrix , hopo_matrix , consensus_out , num_threads , output_progress , use_hopo ) : cmdline = [ POLISH_BIN , "polisher" , "--bubbles" , bubbles_in , "--subs-mat" , subs_matrix , "--hopo-mat" , hopo_matrix , "--out" , consensus_out , "--threads" , str ( num_threads ) ] if not output_progress : cmdline . append ( "--quiet" ) if use_hopo : cmdline . append ( "--enable-hopo" ) try : subprocess . check_call ( cmdline ) except subprocess . CalledProcessError as e : if e . returncode == - 9 : logger . error ( "Looks like the system ran out of memory" ) raise PolishException ( str ( e ) ) except OSError as e : raise PolishException ( str ( e ) )