#!/usr/bin/env python3

"""
 Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>

 This file is part of Bowtie 2.

 Bowtie 2 is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.

 Bowtie 2 is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.

 You should have received a copy of the GNU General Public License
 along with Bowtie 2.  If not, see <http://www.gnu.org/licenses/>.
"""

import os
import sys
import gzip
import struct
import inspect
import logging
import argparse
import subprocess

def get_gunzip_size(fn):
    size = 0
    with gzip.open(fn) as f:
        while True:
            data = f.read(8192)
            size += len(data)
            if not data:
                break
    return size

def main():
    parser = argparse.ArgumentParser(add_help = False)

    parser.add_argument('--large-index', action='store_true')
    parser.add_argument('--verbose', action='store_true')

    group = parser.add_mutually_exclusive_group()
    group.add_argument('--debug', action='store_true')
    group.add_argument('--sanitized', action='store_true')

    logging.basicConfig(level=logging.ERROR,
                        format='%(levelname)s: %(message)s'
                        )
    delta               = 200
    small_index_max_size= 4 * 1024**3 - delta
    build_bin_name      = 'bowtie2-build'
    build_bin_s         = 'bowtie2-build-s'
    build_bin_l         = 'bowtie2-build-l'
    curr_script         = os.path.realpath(inspect.getsourcefile(main))
    ex_path             = os.path.dirname(curr_script)
    build_bin_spec      = os.path.join(ex_path,build_bin_s)

    script_options, argv = parser.parse_known_args()

    if script_options.verbose:
        logging.getLogger().setLevel(logging.INFO)

    if script_options.debug:
        build_bin_spec += '-debug'
        build_bin_l += '-debug'

    if script_options.sanitized:
        build_bin_spec += '-sanitized'
        build_bin_l += '-sanitized'

    fastas = []
    if '-c' not in argv and len(argv) >= 2:
        for index in reversed(range(len(argv) - 1)):
            arg = argv[index]
            if arg.startswith('-') or arg.isdigit():
                break
            fastas.insert(0, arg)
            argv.remove(arg)
        if fastas:
            fastas = ','.join(fastas)
            argv.insert(len(argv) - 1, fastas)

    if script_options.large_index:
        build_bin_spec = os.path.join(ex_path,build_bin_l)
    elif fastas:
        tot_size = 0
        for fn in fastas.split(','):
            if os.path.exists(fn):
                if fn.endswith('.gz') or fn.endswith(".Z"):
                    tot_size += get_gunzip_size(fn)
                else:
                    statinfo = os.stat(fn)
                    tot_size += statinfo.st_size
        if tot_size > small_index_max_size:
            build_bin_spec = os.path.join(ex_path,build_bin_l)

    if not os.path.exists(build_bin_spec):
        sys.stderr.write('{0} does not exist, try running `[g]make {0}\'\n'.format(os.path.basename(build_bin_spec)))
        sys.exit(1)

    argv.insert(0, 'basic-0')
    argv.insert(0, '--wrapper')
    argv.insert(0, build_bin_spec)
    logging.info('Command: %s' % ' '.join(argv))
    sys.exit(subprocess.call(argv))

if __name__ == '__main__':
    main()