/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

///\page nvbwt_page nvBWT
///\htmlonly
/// <img src="nvidia_cubes.png" style="position:relative; bottom:-10px; border:0px;"/>
///\endhtmlonly
///\par
///\n
/// <b>nvBWT</b> is an application built on top of \ref nvbio_page to perform BWT-based
/// reference indexing for nvBowtie and potentially other FM-index based applications.
///\par
/// Given one or multiple fasta files, it will create both the forward and reverse
/// BWT as well as 2-bit packed representation of the files and a few other auxiliary indices:
///
///\verbatim
/// ./nvBWT my-reference.fasta my-index
///\endverbatim
///\par
/// will generate the following files:
///
///\verbatim
/// my-index.pac
/// my-index.rpac
/// my-index.bwt
/// my-index.rbwt
/// my-index.sa
/// my-index.rsa
/// my-index.ann
/// my-index.amb
///\endverbatim
///
/// \section PerformanceSection Performance
///\par
/// nvBWT runs the BWT construction on the GPU, using newly developed parallel algorithms.
/// Here's a graph showing its superior performance compared to two other popular CPU based
/// BWT builders:
///
/// <img src="benchmark-bwt.png" style="position:relative; bottom:-10px; border:0px;" width="80%" height="80%"/>
///
///\section OptionsSection Options
///\par
/// nvBWT supports the following command options:
///
///\verbatim
///   nvBWT [options] input_file output-prefix
///   options:
///    -v       | --verbosity     int (0-6) [5]		// select the verbosity level
///    -m       | --max-length    int       [inf]   // clamp input length
///    -b       | --byte-packing                    // output a byte-encoded .pac file
///    -w       | --word-packing                    // output a word-encoded .wpac file (more efficient)
///    -c       | --crc                             // compute CRCs
///    -d		| --device							// select a cuda device
///\endverbatim
///
