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/*
* The MIT License
*
* Wavefront Alignment Algorithms
* Copyright (c) 2017 by Santiago Marco-Sola <santiagomsola@gmail.com>
*
* This file is part of Wavefront Alignment Algorithms.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* PROJECT: Wavefront Alignment Algorithms
* AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
* DESCRIPTION: WaveFront aligner data structure
*/
#pragma once
#include "utils/heatmap.h"
#include "system/profiler_counter.h"
#include "system/profiler_timer.h"
#include "system/mm_stack.h"
#include "alignment/cigar.h"
#include "wfa.h"
/*
* Initialize Aligner (to perform a new alignment)
*/
void wavefront_aligner_init(
wavefront_aligner_t* const wf_aligner,
const int align_level);
/*
* Utils
*/
uint64_t wavefront_aligner_get_size(
wavefront_aligner_t* const wf_aligner);
bool wavefront_aligner_maxtrim_cigar(
wavefront_aligner_t* const wf_aligner);
/*
* Display
*/
void wavefront_aligner_print_mode(
FILE* const stream,
wavefront_aligner_t* const wf_aligner);
void wavefront_aligner_print_scope(
FILE* const stream,
wavefront_aligner_t* const wf_aligner);
void wavefront_aligner_print_conf(
FILE* const stream,
wavefront_aligner_t* const wf_aligner);