SW# - CUDA parallelized Smith Waterman with applying Hirschberg's algorithm
Copyright (C) 2011 Matija Korpar

This program 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.

This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.

Contact the author by mkorpar@gmail.com.

1) DEPENDENCIES
2) INSTALLATION
3) USAGE

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1) DEPENDENCIES
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Application uses following software:
    1) Linux shell
    2) gcc 4.*+
    3) nvcc 2.*+
    4) make

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2) INSTALLATION
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For installation run the install script in the application root directory from
the command line. Application root directory must be writable.

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3) USAGE
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./sw# -i <first_sequnce> -j <second_sequnce> [OPTIONS] [FLAGS]

OPTIONS:
    --query, -i <first_sequnce>                                      
        fasta query file path
    --target, -j <second_sequnce>
        fasta database file path
        fasta database are appended fasta files in a single text file
    --matrix-file <file_path> 
        (optional)
        similarity matrix file path 
        if given the similarity matrix is loaded from the file
    --matrix-table <BLOSUM50|BLOSUM55|BLOSUM62|BLOSUM70|DNA|BLAST|CHIAR>
        embedded similarity matrix
        (optional) 
        (default: CHIAR) 
        if given --matrix-file option won't be used
    --match <float> 
        (optional)
        match value  
        if --match and --mismatch are given, --matrix-table and --matrix-file 
        options are not used
    --mismatch <float> 
        (optional)
        mismacth value  
        if --match and --mismatch are given, --matrix-table and --matrix-file 
        options are not used
    --gap-open, -g <float> 
        (optional)
        (default: 5.0)
        gap open value
    --gap-extend, -e <float> 
        (optional)
        (default: 2.0)
        gap extend value  
    --threshold <float>
        (optional)
        (default: NO_THRESHOLD)
        score threshold
        program will output not just the max score and its reconstruction, but
        all the scores which are above the given threshold
    --min-hits <int>
        (optional)
        (default: 0)
        the option is used with --window option, it means there must be at 
        least min_hits of matchings in every window length segment
    --window <int>
        (optional)
        (default: 0)
        the option is used with --min-hits option, it means there must be at 
        least min_hits of matchings in every window length segment
FLAGS:
    --complement 
        (optional)
        if input is a nucleotide, search also the other strand 
    --solve 
        (optional)
        solve only 
    --cpu 
        (optional)
        force CPU solving
    --param-search 
        (optional)
        CUDA block and thread number optimization search
    --verbose
        (optional)
        verbose
    --global 
        (optional)
        global aligment 
        if given --threshold this option won't be used