/* * The MIT License * * Wavefront Alignment Algorithms * Copyright (c) 2017 by Santiago Marco-Sola * * 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 * 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);