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// ==========================================================================
// SeqCons
// ==========================================================================
// Copyright (c) 2006-2026, 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 occurrences 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()
// --------------------------------------------------------------------------
seqan2::ArgumentParser::ParseResult
parseCommandLine(SeqConsOptions & options, int argc, char const ** argv);
#endif // #ifndef APPS_SEQCONS2_SEQCONS_OPTIONS_H_
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