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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
*/
#ifndef WAVEFRONT_ATTRIBUTES_H_
#define WAVEFRONT_ATTRIBUTES_H_
#include "alignment/cigar.h"
#include "alignment/affine_penalties.h"
#include "alignment/affine2p_penalties.h"
#include "alignment/linear_penalties.h"
#include "system/profiler_timer.h"
#include "system/mm_allocator.h"
#include "wavefront_penalties.h"
#include "wavefront_plot.h"
#include "wavefront_display.h"
#include "wavefront_heuristic.h"
/*
* Alignment scope
*/
typedef enum {
compute_score, // Only distance/score
compute_alignment, // Full alignment CIGAR
} alignment_scope_t;
typedef enum {
alignment_end2end, // End-to-end alignment (aka global)
alignment_endsfree, // Ends-free alignment (semiglobal, glocal, etc)
} alignment_span_t;
typedef struct {
// Mode
alignment_span_t span; // Alignment form (End-to-end/Ends-free)
// Ends-free
int pattern_begin_free; // Allow free-gap at the beginning of the pattern
int pattern_end_free; // Allow free-gap at the end of the pattern
int text_begin_free; // Allow free-gap at the beginning of the text
int text_end_free; // Allow free-gap at the end of the text
} alignment_form_t;
/*
* Custom extend-match function, e.g.:
*
* typedef struct {
* char* pattern;
* int pattern_length;
* char* text;
* int text_length;
* } match_function_params_t;
*
* int match_function(int v,int h,void* arguments) {
* // Extract parameters
* match_function_params_t* match_arguments = (match_function_params_t*)arguments;
* // Check match
* if (v > match_arguments->pattern_length || h > match_arguments->text_length) return 0;
* return (match_arguments->pattern[v] == match_arguments->text[h]);
* }
*/
typedef int (*alignment_match_funct_t)(int,int,void*);
/*
* Alignment system configuration
*/
typedef struct {
// Limits
int max_alignment_score; // Maximum score allowed before quit
// Probing intervals
int probe_interval_global; // Score-ticks interval to check any limits
int probe_interval_compact; // Score-ticks interval to check BT-buffer compacting
// Memory
uint64_t max_partial_compacts; // Maximum partial-compacts before attempting full-compact
uint64_t max_memory_compact; // Maximum BT-buffer memory allowed before trigger compact
uint64_t max_memory_resident; // Maximum memory allowed to be buffered before reap
uint64_t max_memory_abort; // Maximum memory allowed to be used before aborting alignment
// Verbose
// 0 - Quiet
// 1 - Report each sequence aligned (brief)
// 2 - Report each sequence/subsequence aligned (brief)
// 3 - Report WFA progress (heavy tasks) (verbose)
// 4 - Full report of each sequence/subsequence aligned (very verbose)
int verbose; // Verbose (regulates messages during alignment)
// Debug
bool check_alignment_correct; // Verify that the alignment CIGAR output is correct
// Profile
profiler_timer_t timer; // Time alignment
// OS
int max_num_threads; // Maximum number of threads to use to compute/extend WFs
int min_offsets_per_thread; // Minimum amount of offsets to spawn a thread
} alignment_system_t;
/*
* Low-memory modes
*/
typedef enum {
wavefront_memory_high = 0, // High-memore mode (fastest, stores all WFs explicitly)
wavefront_memory_med = 1, // Succing-memory mode piggyback-based (medium, offloads half-full BT-blocks)
wavefront_memory_low = 2, // Succing-memory mode piggyback-based (slow, offloads only full BT-blocks)
wavefront_memory_ultralow = 3, // Bidirectional WFA
} wavefront_memory_t;
/*
* Wavefront Aligner Attributes
*/
typedef struct {
// Distance model
distance_metric_t distance_metric; // Alignment metric/distance used
alignment_scope_t alignment_scope; // Alignment scope (score only or full-CIGAR)
alignment_form_t alignment_form; // Alignment mode (end-to-end/ends-free)
// Penalties
linear_penalties_t linear_penalties; // Gap-linear penalties (placeholder)
affine_penalties_t affine_penalties; // Gap-affine penalties (placeholder)
affine2p_penalties_t affine2p_penalties; // Gap-affine-2p penalties (placeholder)
// Heuristic strategy
wavefront_heuristic_t heuristic; // Wavefront heuristic
// Memory model
wavefront_memory_t memory_mode; // Wavefront memory strategy (modular wavefronts and piggyback)
// Custom function to compare sequences
alignment_match_funct_t match_funct; // Custom matching function (match(v,h,args))
void* match_funct_arguments; // Generic arguments passed to matching function (args)
// External MM (instead of allocating one inside)
mm_allocator_t* mm_allocator; // MM-Allocator
// Display
wavefront_plot_attr_t plot; // Plot wavefront
// System
alignment_system_t system; // System related parameters
} wavefront_aligner_attr_t;
/*
* Default parameters
*/
extern wavefront_aligner_attr_t wavefront_aligner_attr_default;
#endif /* WAVEFRONT_ATTRIBUTES_H_ */
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