#!/usr/bin/env python

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

 This file is part of Bowtie.

 Bowtie 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 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.  If not, see <http://www.gnu.org/licenses/>.
"""


import os
import imp
import inspect
import logging



def main():
    logging.basicConfig(level=logging.ERROR,
                        format='%(levelname)s: %(message)s'
                        )
    bin_name            = "bowtie"
    bin_s               = "bowtie-align-s"
    bin_l               = "bowtie-align-l"
    idx_ext_l           = '.1.ebwtl' 
    idx_ext_s           = '.1.ebwt' 
    curr_script         = os.path.realpath(inspect.getsourcefile(main))
    ex_path             = os.path.dirname(curr_script)
    bin_spec            = os.path.join(ex_path,bin_s)
    bld                 = imp.load_source('bowtie-build', os.path.join(ex_path, 'bowtie-build'))
    options,arguments   = bld.build_args()

    if '--verbose' in options:
        logging.getLogger().setLevel(logging.INFO)
        
    if '--debug' in options:
        bin_spec += '-debug'
        bin_l += '-debug'
        
    if '--large-index' in options:
        bin_spec = os.path.join(ex_path, bin_l)
    elif len(arguments) >= 2:
        idx_basename = arguments[-2]
        large_idx_exists = os.path.exists(idx_basename + idx_ext_l)
        small_idx_exists = os.path.exists(idx_basename + idx_ext_s)
        if large_idx_exists and not small_idx_exists:
            logging.info("No small index but a large one is present. Using large index.")
            bin_spec = os.path.join(ex_path,bin_l)
    
    arguments[0] = bin_name
    arguments.insert(1, 'basic-0')
    arguments.insert(1, '--wrapper')
    logging.info('Command: %s %s' %  (bin_spec,' '.join(arguments[1:])))
    os.execv(bin_spec, arguments)        
        
        
if __name__ == "__main__":
    main()





