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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 attributes
*/
#include "utils/commons.h"
#include "wavefront_attributes.h"
/*
* Default parameters
*/
wavefront_aligner_attr_t wavefront_aligner_attr_default = {
// Distance model & Penalties
.distance_metric = gap_affine,
.alignment_scope = compute_alignment,
.alignment_form = {
.span = alignment_end2end,
.pattern_begin_free = 0,
.pattern_end_free = 0,
.text_begin_free = 0,
.text_end_free = 0,
},
// Custom matching functions
.match_funct = NULL, // Use default match-compare function
.match_funct_arguments = NULL, // No arguments
// Penalties
.linear_penalties = {
.match = 0,
.mismatch = 4,
.indel = 2,
},
.affine_penalties = {
.match = 0,
.mismatch = 4,
.gap_opening = 6,
.gap_extension = 2,
},
.affine2p_penalties = {
.match = 0,
.mismatch = 4,
.gap_opening1 = 6,
.gap_extension1 = 2,
.gap_opening2 = 24,
.gap_extension2 = 1,
},
// Heuristic
.heuristic = {
.strategy = wf_heuristic_wfadaptive,
.min_wavefront_length = 10,
.max_distance_threshold = 50,
.steps_between_cutoffs = 1,
},
// Memory model
.memory_mode = wavefront_memory_high,
// MM
.mm_allocator = NULL, // Use private MM
// Display
.plot = {
.enabled = false,
.resolution_points = 2000,
.align_level = 0,
},
// System
.system = {
.max_alignment_score = INT_MAX, // Unlimited
.probe_interval_global = 3000,
.probe_interval_compact = 6000,
.max_memory_compact = -1, // Automatically set based on memory-mode
.max_memory_resident = -1, // Automatically set based on memory-mode
.max_memory_abort = UINT64_MAX, // Unlimited
.verbose = 0, // Quiet
.check_alignment_correct = false,
.max_num_threads = 1, // Single thread by default
.min_offsets_per_thread = 500 // Minimum WF-length to spawn a thread
},
};
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