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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, 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 INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNMENT_OPTIONS_H_
#define INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNMENT_OPTIONS_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Class ConsensusAlignmentOptions
// ----------------------------------------------------------------------------
/*!
* @class ConsensusAlignmentOptions
* @headerfile <seqan/consensus.h>
* @brief Configuration for @link consensusAlignment @endlink
*
* @signature struct ConsensusAlignmentOptions;
*/
struct ConsensusAlignmentOptions
{
/*!
* @var unsigned ConsensusAlignmentOptions::INVALID;
* @brief Static member variable with a marker for invalid contig ids.
*/
static const unsigned INVALID = (unsigned)-1;
ConsensusAlignmentOptions() :
contigID(INVALID), useContigID(true), usePositions(true), useGlobalAlignment(false),
posDelta(30), runRealignment(true), verbosity(0), overlapMaxErrorRate(5), overlapMinLength(20),
overlapMinCount(3), kMerSize(20), kMerMaxOcc(200),
scoreMatch(5), scoreMismatch(-5), scoreGapOpen(-5), scoreGapExtend(-1)
{}
/*!
* @var unsigned ConsensusAlignmentOptions::contigID;
* @brief The id of the contig to compute the consensus for, defaults to <tt>INVALID</tt>.
*
* Set to <tt>INVALID</tt> for all.
*/
unsigned contigID;
/*!
* @var bool ConsensusAlignmentOptions::useContigID;
* @brief Whether or not to use the value of <tt>contigID</tt> (default is <tt>true</tt>).
*
* When this variable is set to <tt>false</tt> then the value of <tt>contigID</tt> is ignored and treated
* as if it was <tt>INVALID</tt>.
*/
bool useContigID;
/*!
* @var bool ConsensusAlignmentOptions::usePositions;
* @brief Whether or not to use positions of the in the @link FragmentStore::alignedReadStore @endlink (default is <tt>true</tt>).
*
* When set to <tt>false</tt>, then the @link FragmentStore::alignedReadStore @endlink will be cleared and filled
* with new entries, one for each read.
*/
bool usePositions;
bool useGlobalAlignment;
/*!
* @var unsigned ConsensusAlignmentOptions::posDelta;
* @brief Positions are considered with an environment of <tt>posDelta</tt> (default is <tt>30</tt>).
*
* When positions are not used then this value is ignored.
*
* See @link consensusAlignment @endlink for more details.
*/
unsigned posDelta; // TODO(holtgrew): Rename to overlapWindowSize
/*!
* @var bool ConsensusAlignmentOptions::runRealignment;
* @brief Perform a realignment using standard parameters, depending on the sequence length (default is <tt>true</tt>).
*
* Defaults to <tt>true</tt>.
*/
bool runRealignment;
int verbosity;
int overlapMaxErrorRate;
int overlapMinLength;
int overlapMinCount;
int kMerSize;
int kMerMaxOcc;
int scoreMatch;
int scoreMismatch;
int scoreGapOpen;
int scoreGapExtend;
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
} // namespace seqan
#endif // #ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNMENT_OPTIONS_H_
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