# set up directories for intermediate results

file_in = sys.argv[1]

file_out = sys.argv[2]

input = os.path.basename(file_in)

output_prefix, output_extension = os.path.splitext(input)

stamp = str(time.time())

split_dir = os.path.join(os.getcwd(), "temp-" + stamp + os.sep)

result_dir = os.path.join(os.getcwd(), "temp-processed-" + stamp + os.sep)

os.mkdir(split_dir)

os.mkdir(result_dir)

# split command

nr_of_threads_opt = elprep_io_wrapper.cmd_option('--nr-of-threads', sys.argv)

intermediate_files_opt = elprep_io_wrapper.cmd_option('--intermediate-files-output-type', sys.argv)

if intermediate_files_opt:

intermediate_files_output_type = intermediate_files_opt[1]

else:

intermediate_files_output_type = "sam"

elprep_io_wrapper.cmd_wrap_input(["elprep", "split"], file_in, split_dir, ["--output-prefix", output_prefix, "--output-type", intermediate_files_output_type] + nr_of_threads_opt)

spread_file = os.path.join(split_dir, output_prefix + "-spread." + intermediate_files_output_type)

splits_path = os.path.join(split_dir, "splits" + os.sep)

# gnu parallel command

nr_of_jobs_opt = elprep_io_wrapper.cmd_option('--nr-of-jobs', sys.argv)

read_group_string = elprep_io_wrapper.cmd_option('--replace-read-group', sys.argv)

given_cmd_opts = elprep_io_wrapper.remove_cmd_option(sys.argv[3:], '--nr-of-jobs')

given_cmd_opts = elprep_io_wrapper.remove_cmd_option(given_cmd_opts, '--intermediate-files-output-type')

cmd_opts = given_cmd_opts

if read_group_string:

cmd_opts = elprep_io_wrapper.remove_cmd_option(cmd_opts, '--replace-read-group')

cmd_opts = cmd_opts + ['--replace-read-group', '\"' + read_group_string[1] + '\"']

cmd_opts = cmd_opts + ['--split-file']

cmd_list = ["elprep"]

elprep_cmd = '\'' + reduce(append_cmd, cmd_list + ['{}', result_dir + '{/.}.' + intermediate_files_output_type ] + cmd_opts) + '\''

gnu_cmd = 'parallel --gnu -j ' + str(nr_of_jobs_opt[1]) + ' ' + elprep_cmd + ' ::: ' + splits_path + '*.' + intermediate_files_output_type

subprocess.check_call(gnu_cmd, shell=True)

# command for spread file

spread_out_file = os.path.join(result_dir, output_prefix + "-spread." + intermediate_files_output_type)

elprep_io_wrapper.cmd_wrap_io(["elprep"], spread_file, spread_out_file , given_cmd_opts)

# merge command

elprep_io_wrapper.cmd_wrap_output(["elprep", "merge"], result_dir, file_out, nr_of_threads_opt)

# remove directories for intermediate results

for root, dirs, files in os.walk(splits_path):

for file in files:

ffile = os.path.join(root, file)

os.remove(ffile)

os.rmdir(splits_path)

os.remove(spread_file)

os.rmdir(split_dir)

for root, dirs, files in os.walk(result_dir):

for file in files:

ffile = os.path.join(root, file)

os.remove(ffile)