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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 backtrace buffer to store bactrace-blocks
*/
#ifndef WAVEFRONT_BACKTRACE_BUFFER_H_
#define WAVEFRONT_BACKTRACE_BUFFER_H_
#include "alignment/cigar.h"
#include "utils/vector.h"
#include "utils/bitmap.h"
#include "system/mm_allocator.h"
#include "wavefront_pcigar.h"
#include "wavefront_offset.h"
#include "wavefront_attributes.h"
/*
* Separated Backtrace Block
*/
typedef uint32_t bt_block_idx_t; // Up to 2^31 references (~32GB of not-compactable pCIGARs)
#define BT_BLOCK_IDX_MAX UINT32_MAX
#define BT_BLOCK_IDX_NULL UINT32_MAX
typedef struct {
pcigar_t pcigar; // Packed CIGAR
bt_block_idx_t prev_idx; // Index of the previous BT-block
} __attribute__((packed)) bt_block_t;
/*
* Backtrace initial positions
*/
typedef struct {
int v;
int h;
} wf_backtrace_init_pos_t;
/*
* Backtrace Buffer
*/
typedef struct {
// Locator
int segment_idx; // Current segment idx
int segment_offset; // Current free position within segment
bt_block_t* block_next; // Next BT-block free
// Buffers
vector_t* segments; // Memory segments (bt_block_t*)
vector_t* alignment_init_pos; // Buffer to store alignment's initial coordinates (h,v) (wf_backtrace_init_pos_t)
bt_block_idx_t num_compacted_blocks; // Total compacted blocks in BT-buffer compacted (dense from 0..num_compacted_blocks-1)
int num_compactions; // Total compactions performed
// Internal buffers
vector_t* alignment_packed; // Temporal buffer to store final alignment (pcigar_t)
vector_t* prefetch_blocks_idxs; // Temporal buffer to store blocks_idxs (bt_block_idx_t)
// MM
mm_allocator_t* mm_allocator;
} wf_backtrace_buffer_t;
/*
* Setup
*/
wf_backtrace_buffer_t* wf_backtrace_buffer_new(
mm_allocator_t* const mm_allocator);
void wf_backtrace_buffer_clear(
wf_backtrace_buffer_t* const bt_buffer);
void wf_backtrace_buffer_reap(
wf_backtrace_buffer_t* const bt_buffer);
void wf_backtrace_buffer_delete(
wf_backtrace_buffer_t* const bt_buffer);
/*
* Accessors
*/
void wf_backtrace_buffer_add_used(
wf_backtrace_buffer_t* const bt_buffer,
const int used);
bt_block_idx_t wf_backtrace_buffer_get_mem(
wf_backtrace_buffer_t* const bt_buffer,
bt_block_t** const bt_block_mem,
int* const bt_blocks_available);
/*
* Store blocks
*/
bt_block_idx_t wf_backtrace_buffer_init_block(
wf_backtrace_buffer_t* const bt_buffer,
const int v,
const int h);
/*
* Unpack CIGAR
*/
bt_block_t* wf_backtrace_buffer_traceback_pcigar(
wf_backtrace_buffer_t* const bt_buffer,
bt_block_t* bt_block);
void wf_backtrace_buffer_unpack_cigar_linear(
wf_backtrace_buffer_t* const bt_buffer,
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length,
alignment_match_funct_t const match_funct,
void* const match_funct_arguments,
const int begin_v,
const int begin_h,
const int end_v,
const int end_h,
cigar_t* const cigar);
void wf_backtrace_buffer_unpack_cigar_affine(
wf_backtrace_buffer_t* const bt_buffer,
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length,
alignment_match_funct_t const match_funct,
void* const match_funct_arguments,
const int begin_v,
const int begin_h,
const int end_v,
const int end_h,
cigar_t* const cigar);
/*
* Compact
*/
void wf_backtrace_buffer_mark_backtrace(
wf_backtrace_buffer_t* const bt_buffer,
const bt_block_idx_t bt_block_idx,
bitmap_t* const bitmap);
void wf_backtrace_buffer_mark_backtrace_batch(
wf_backtrace_buffer_t* const bt_buffer,
wf_offset_t* const offsets,
bt_block_idx_t* const bt_block_idxs,
const int num_block_idxs,
bitmap_t* const bitmap);
bt_block_idx_t wf_backtrace_buffer_compact_marked(
wf_backtrace_buffer_t* const bt_buffer,
bitmap_t* const bitmap,
const int verbose);
/*
* Utils
*/
uint64_t wf_backtrace_buffer_get_used(
wf_backtrace_buffer_t* const bt_buffer);
bt_block_idx_t wf_backtrace_buffer_get_num_compacted_blocks(
wf_backtrace_buffer_t* const bt_buffer);
void wf_backtrace_buffer_set_num_compacted_blocks(
wf_backtrace_buffer_t* const bt_buffer,
const bt_block_idx_t num_compacted_blocks);
void wf_backtrace_buffer_reset_compaction(
wf_backtrace_buffer_t* const bt_buffer);
uint64_t wf_backtrace_buffer_get_size_allocated(
wf_backtrace_buffer_t* const bt_buffer);
uint64_t wf_backtrace_buffer_get_size_used(
wf_backtrace_buffer_t* const bt_buffer);
#endif /* WAVEFRONT_BACKTRACE_BUFFER_H_ */
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