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Arna Óskarsdóttir
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seqan folder: SeqAnHTS fork of seqan
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‎seqan/LICENSE‎

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Copyright (c) 2006-2015, Knut Reinert, FU Berlin
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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* Neither the name of Knut Reinert or the FU Berlin nor the names of
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its contributors may be used to endorse or promote products derived
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from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
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OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
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DAMAGE.
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‎seqan/align.h‎

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// ==========================================================================
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// SeqAn - The Library for Sequence Analysis
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// ==========================================================================
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// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above copyright
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// notice, this list of conditions and the following disclaimer in the
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// documentation and/or other materials provided with the distribution.
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// * Neither the name of Knut Reinert or the FU Berlin nor the names of
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// its contributors may be used to endorse or promote products derived
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// from this software without specific prior written permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
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// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
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// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
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// DAMAGE.
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//
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// ==========================================================================
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// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
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// ==========================================================================
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#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_H_
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#define SEQAN_INCLUDE_SEQAN_ALIGN_H_
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// TODO(holtgrew): Usage of gapped value in align module is not consistent, need proxies in many places, reference not cleanly implemented everywhere yet.
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// TODO(holtgrew): The Author: tag at the top has to be corrected in the headers of this module.
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// TODO(holtgrew): Anchor Gaps must be integrated completely.
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// TODO(holtgrew): Local alignments & Fragments don't work nicely together at the moment, multiLocalAlignments() needs an equivalent in the new align module.
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// TODO(holtgrew): Align<>, AlignCol<> need some love and documentation.
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// TODO(holtgrew): Gaps need better documentation.
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// TODO(holtgrew): refinement should become graph_align and also host Graph<Alignment<>>
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// TODO(holtgrew): graph_msa should become align_msa, or so, see whitepaper.
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// TODO(holtgrew): The documentation and Tutorial need heavy updates, clipping alignments howto can go away.
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// ============================================================================
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// Prerequisites
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// ============================================================================
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#include <seqan/basic.h>
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#include <seqan/modifier.h> // ModifiedAlphabet<>.
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#include <seqan/align/align_metafunctions.h>
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#include <seqan/graph_align.h> // TODO(holtgrew): We should not have to depend on this.
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// TODO(holtgrew): Why not use priority queue from STL?
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#include <seqan/misc/priority_type_base.h>
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#include <seqan/misc/priority_type_heap.h>
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// ============================================================================
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// Support
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// ============================================================================
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#include <seqan/align/gapped_value_type.h>
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#include <seqan/align/align_config.h>
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#include <seqan/align/align_traceback.h>
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#include <seqan/align/matrix_base.h>
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// ============================================================================
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// Gaps & Gaps Iterator Data Structures
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// ============================================================================
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#include <seqan/align/fragment.h>
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#include <seqan/align/gaps_base.h>
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#include <seqan/align/gaps_iterator_base.h>
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#include <seqan/align/gaps_array.h>
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#include <seqan/align/gaps_iterator_array.h>
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#include <seqan/align/gap_anchor.h>
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#include <seqan/align/gaps_anchor.h>
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#include <seqan/align/gaps_iterator_anchor.h>
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// ============================================================================
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// Alignment Data Structures and Columns
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// ============================================================================
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#include <seqan/align/align_cols.h>
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#include <seqan/align/align_base.h>
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// ============================================================================
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// Alignment Algorithm Implementations.
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// ============================================================================
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//################################################################################
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// New module
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//################################################################################
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// The tags have to be available everywhere so we define them centrally.
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#include <seqan/align/alignment_algorithm_tags.h>
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// Defines all tags needed for the DP alignment.
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#include <seqan/align/dp_profile.h>
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// The DP Band
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#include <seqan/align/dp_band.h>
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// The DP Scout
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#include <seqan/align/dp_scout.h>
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// Stores the score value of a particular cell in the dp matrix.
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// If affine gap costs are selected one cell stores the three values
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// for all three dp matrices.
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#include <seqan/align/dp_cell.h>
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#include <seqan/align/dp_cell_linear.h>
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#include <seqan/align/dp_cell_affine.h>
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#include <seqan/align/dp_cell_dynamic.h>
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// Stores the actual trace segment that was detected during traceback.
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// The trace segments can be adapted into any alignment representation
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// form.
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#include <seqan/align/dp_trace_segment.h>
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#include <seqan/align/dp_traceback_adaptor.h>
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// Implements the different recursion formula of the alignment algorithms.
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#include <seqan/align/dp_formula.h>
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#include <seqan/align/dp_formula_linear.h>
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#include <seqan/align/dp_formula_affine.h>
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#include <seqan/align/dp_formula_dynamic.h>
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// Defines meta informations which determine how to compute a column and a
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// certain cell for different profiles.
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#include <seqan/align/dp_meta_info.h>
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// Actual matrix to store the values. Uses the matrix_base.h definitions
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// as a host.
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#include <seqan/align/dp_matrix.h>
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#include <seqan/align/dp_matrix_sparse.h>
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// The navigator that based on the selected profile and band chooses the
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// correct way to navigate through the matrix.
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#include <seqan/align/dp_matrix_navigator.h>
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#include <seqan/align/dp_matrix_navigator_score_matrix.h>
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#include <seqan/align/dp_matrix_navigator_score_matrix_sparse.h>
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#include <seqan/align/dp_matrix_navigator_trace_matrix.h>
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// Ensures the backwards compatibility for the global interfaces of the
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// alignment algorithms. Based on the called function this selects the
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// correct parameters for the new alignment module.
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#include <seqan/align/dp_context.h>
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#include <seqan/align/dp_setup.h>
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// The actual implementations of the traceback and the dynamic programming that
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// is used by all different alignment algorithms.
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#include <seqan/align/dp_traceback_impl.h>
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#include <seqan/align/dp_algorithm_impl.h>
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//################################################################################
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// Old module
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//################################################################################
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// Also, we have an implementation of Hirschberg's algorithm to compute
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// alignments.
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#include <seqan/align/global_alignment_hirschberg_impl.h>
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// The implementations of Myers' bitvector algorithm for alignments can only
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// compute alignment scores. The combination of Hirschberg's and Myers'
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// algorithm is limited in the same way.
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#include <seqan/align/global_alignment_myers_impl.h>
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#include <seqan/align/global_alignment_myers_hirschberg_impl.h>
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// Implementations of the local alignment algorithms with declumping. We also
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// use them for the localAlignment() calls and return the best local alignment
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// only.
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// TODO(rmaerker): Replace this with a new implementation based on the new alignment module.
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#include <seqan/align/local_alignment_waterman_eggert_impl.h>
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#include <seqan/align/local_alignment_banded_waterman_eggert_impl.h>
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// We carry around this implementation of Smith-Waterman because it supports
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// aligning into fragment strings and alignment graphs. Eventually, it could
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// go away if Waterman-Eggert supports them.
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//#include <seqan/align/local_alignment_smith_waterman_impl.h>
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// ============================================================================
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// Alignment Algorithm Interfaces
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// ============================================================================
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// The front-end functions for global alignments.
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#include <seqan/align/global_alignment_unbanded.h>
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#include <seqan/align/global_alignment_banded.h>
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// The front-end functions for local alignments.
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#include <seqan/align/local_alignment_unbanded.h>
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#include <seqan/align/local_alignment_banded.h>
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// The front-end for enumeration of local alignments.
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#include <seqan/align/local_alignment_enumeration.h> // documentation
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#include <seqan/align/local_alignment_enumeration_unbanded.h>
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#include <seqan/align/local_alignment_enumeration_banded.h>
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// The front-end functions for the more specialized alignment algorithms such as
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// Hirschberg, Myers and Myers-Hirschberg.
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#include <seqan/align/global_alignment_specialized.h>
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// ============================================================================
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// Operations On Alignments
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// ============================================================================
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#include <seqan/align/alignment_operations.h>
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#include <seqan/align/evaluate_alignment.h>
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#endif // SEQAN_INCLUDE_SEQAN_ALIGN_H_

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