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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: Packed CIGAR (Alignment operations in 2-bits)
*/
#ifndef WAVEFRONT_PACKED_CIGAR_H_
#define WAVEFRONT_PACKED_CIGAR_H_
#include "wavefront_attributes.h"
/*
* Configuration
*/
#define PCIGAR_32BITS
//#define PCIGAR_64BITS
/*
* Packed CIGAR
*/
#define PCIGAR_NULL 0ul
#define PCIGAR_DELETION 1ul
#define PCIGAR_MISMATCH 2ul
#define PCIGAR_INSERTION 3ul
#define PCIGAR_POP_FRONT(pcigar) pcigar = pcigar << 2
#define PCIGAR_PUSH_BACK(pcigar,operation) ((pcigar<<2) | operation)
#define PCIGAR_PUSH_BACK_INS(pcigar) ((pcigar<<2) | PCIGAR_INSERTION)
#define PCIGAR_PUSH_BACK_DEL(pcigar) ((pcigar<<2) | PCIGAR_DELETION)
#define PCIGAR_PUSH_BACK_MISMS(pcigar) ((pcigar<<2) | PCIGAR_MISMATCH)
#ifdef PCIGAR_32BITS
typedef uint32_t pcigar_t;
#define PCIGAR_MAX_LENGTH 16
#define PCIGAR_FULL_MASK 0x40000000u /* Completely full */
#define PCIGAR_ALMOST_FULL_MASK 0x10000000u /* 15-slots busy or more */
#define PCIGAR_HALF_FULL_MASK 0x00010000u /* 9-slots busy or more */
#define PCIGAR_IS_UTILISED(pcigar,mask) ((pcigar) >= mask)
#define PCIGAR_EXTRACT(pcigar) ((pcigar) >> 30)
#define PCIGAR_FREE_SLOTS(pcigar) ((pcigar)!=0) ? __builtin_clz(pcigar)/2 : PCIGAR_MAX_LENGTH;
#else
typedef uint64_t pcigar_t;
#define PCIGAR_MAX_LENGTH 32
#define PCIGAR_FULL_MASK 0x4000000000000000ul /* Completely full */
#define PCIGAR_ALMOST_FULL_MASK 0x1000000000000000ul /* 31-slots busy or more */
#define PCIGAR_HALF_FULL_MASK 0x0000000100000000ul /* 17-slots busy or more */
#define PCIGAR_IS_UTILISED(pcigar,mask) ((pcigar) >= mask)
#define PCIGAR_EXTRACT(pcigar) ((pcigar) >> 62)
#define PCIGAR_FREE_SLOTS(pcigar) ((pcigar)!=0) ? __builtin_clzl(pcigar)/2 : PCIGAR_MAX_LENGTH;
#endif
/*
* Accessors
*/
int pcigar_get_length(
const pcigar_t pcigar);
int pcigar_unpack(
pcigar_t pcigar,
char* cigar_buffer);
/*
* PCIGAR unpack
*/
void pcigar_unpack_linear(
pcigar_t pcigar,
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,
int* const v_pos,
int* const h_pos,
char* cigar_buffer,
int* const cigar_length);
void pcigar_unpack_affine(
pcigar_t pcigar,
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,
int* const v_pos,
int* const h_pos,
char* cigar_buffer,
int* const cigar_length,
affine_matrix_type* const current_matrix_type);
/*
* Display
*/
void pcigar_print(
FILE* const stream,
pcigar_t pcigar);
#endif /* WAVEFRONT_PACKED_CIGAR_H_ */
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