text: // ==========================================================================
  //                                 SeqCons
  // ==========================================================================
  // Copyright (c) 2006-2016, Knut Reinert, FU Berlin
  // 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 Knut Reinert or the FU Berlin 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 KNUT REINERT OR THE FU BERLIN 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.
  //
  // ==========================================================================
  // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
  // ==========================================================================
  
  #ifndef APPS_SEQCONS2_SEQCONS_OPTIONS_H_
  #define APPS_SEQCONS2_SEQCONS_OPTIONS_H_
  
  #include <iosfwd>
  #include <string>
  
  #include <seqan/arg_parse.h>
  
  // ============================================================================
  // Forwards
  // ============================================================================
  
  // ============================================================================
  // Tags, Classes, Enums
  // ============================================================================
  
  // ----------------------------------------------------------------------------
  // Class SeqConsOptions
  // ----------------------------------------------------------------------------
  
  struct SeqConsOptions
  {
      // Verbosity level, 0 -- quiet, 1 -- normal, 2 -- verbose, 3 -- very verbose
      int verbosity;
  
      // The operation to perform.
      enum Operation
      {
          NOP = 0,            // do nothing, just convert files
          REALIGN = 1,        // just realign, only works with SAM input
          POS_CONSENSUS = 2,  // consensus, interpreting positions
          CTG_CONSENSUS = 3,  // consensus, interpreting contig information
          OVL_CONSENSUS = 4,  // "de novo" consensus, just overlap MSA and consensus
          ALN_CONSENSUS = 5   // "de novo" consensus, just global MSA and consensus
      };
  
      // The operation to perform.
      Operation operation;
  
      // -----------------------------------------------------------------------
      // I/O Options
      // -----------------------------------------------------------------------
  
      // Path to the input file.
      std::string inputFile;
      // Path to the output files for read alignments and resulting consensus.
      std::string outputFileAlignment;
      std::string outputFileConsensus;
  
      // -----------------------------------------------------------------------
      // Alignment Quality Filter Options
      // -----------------------------------------------------------------------
  
      // Minimal overlap length.
      int overlapMinLength;
      // Maximal error rate in percent for a read.
      double overlapMaxErrorRate;
      // Minimal number of overlap for a read.
      int overlapMinCount;
      // Window size to look for overlaps when positions are considered.
      int overlapWindowSize;
  
      // -----------------------------------------------------------------------
      // K-mer Filter Options
      // -----------------------------------------------------------------------
  
      // K-mer length to use for identifying overlap candidates.
      int kMerSize;
      // K-mers with a higher number of occurences are ignored.
      int kMerMaxOcc;
  
      // -----------------------------------------------------------------------
      // Realignment Options
      // -----------------------------------------------------------------------
  
      // The bandwidth to use in the banded alignment when realigning.
      int reAlignmentBandwidth;
      // The environment for profile extraction.
      int reAlignmentEnvironment;
  
      // -----------------------------------------------------------------------
      // Member Functions
      // -----------------------------------------------------------------------
  
      SeqConsOptions() :
          verbosity(1),
          operation(NOP),
          overlapMinLength(20),
          overlapMaxErrorRate(5),
          overlapMinCount(3),
          overlapWindowSize(20),
          kMerSize(20),
          kMerMaxOcc(200),
          reAlignmentBandwidth(10),
          reAlignmentEnvironment(20)
      {}
  
      // Check whether the combination of operation and input file is valid.  Throws an exception in the case that it is
      // not.
      void checkConsistency();
  
      // Print options to a C++ stream.
      void print(std::ostream & out) const;
  };
  
  // ============================================================================
  // Metafunctions
  // ============================================================================
  
  // ============================================================================
  // Functions
  // ============================================================================
  
  // --------------------------------------------------------------------------
  // Function parseCommandLine()
  // --------------------------------------------------------------------------
  
  seqan::ArgumentParser::ParseResult
  parseCommandLine(SeqConsOptions & options, int argc, char const ** argv);
  
  #endif  // #ifndef APPS_SEQCONS2_SEQCONS_OPTIONS_H_
  