547 lines
24 KiB
C
547 lines
24 KiB
C
/*********************************************************************************************
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Description: sw extend functions in bwa-mem (implemented in avx2, uint8_t stands for score scope)
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Copyright : All right reserved by NCIC.ICT
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Author : Zhang Zhonghai
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Date : 2024/04/08
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***********************************************************************************************/
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#include <stdlib.h>
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#include <stdint.h>
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#include <assert.h>
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#include <emmintrin.h>
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#include <stdio.h>
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#include <immintrin.h>
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#include <emmintrin.h>
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#include "byte_alloc.h"
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#include "utils.h"
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#define KSW_EQUAL
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#define ARR_FOR_EQUAL_CHECK 1
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#define PRUNING 0
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#define REVERSE_TARGET 0
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#define SIMD_WIDTH 32
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static const uint8_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
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{0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0},
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{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff}};
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// static const uint8_t reverse_mask[SIMD_WIDTH] = {1, 0, 3, 2, 5, 4, 7, 6, 9, 8, 11, 10, 13, 12, 15, 14, 1, 0, 3, 2, 5, 4, 7, 6, 9, 8, 11, 10, 13, 12, 15, 14};
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#if REVERSE_TARGET
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static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, 15, 14, 13, 12, 11, 10, 9, 8};
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#endif
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#define permute_mask _MM_SHUFFLE(0, 1, 2, 3)
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// const int permute_mask = _MM_SHUFFLE(0, 1, 2, 3);
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// 初始化变量
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#define SIMD_INIT \
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int oe_del = o_del + e_del, oe_ins = o_ins + e_ins; \
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__m256i zero_vec; \
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__m256i max_vec; \
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__m256i oe_del_vec; \
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__m256i oe_ins_vec; \
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__m256i e_del_vec; \
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__m256i e_ins_vec; \
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__m256i h_vec_mask[SIMD_WIDTH]; \
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zero_vec = _mm256_setzero_si256(); \
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oe_del_vec = _mm256_set1_epi8(oe_del); \
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oe_ins_vec = _mm256_set1_epi8(oe_ins); \
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e_del_vec = _mm256_set1_epi8(e_del); \
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e_ins_vec = _mm256_set1_epi8(e_ins); \
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__m256i match_sc_vec = _mm256_set1_epi8(a); \
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__m256i mis_sc_vec = _mm256_set1_epi8(b); \
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__m256i amb_sc_vec = _mm256_set1_epi8(1); \
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__m256i amb_vec = _mm256_set1_epi8(4); \
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for (i = 0; i < SIMD_WIDTH; ++i) \
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h_vec_mask[i] = _mm256_loadu_si256((__m256i *)(&h_vec_int_mask[i]));
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#if REVERSE_TARGET
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#define LOAD_TARGET \
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__m256i ts_vec = _mm256_loadu_si256((__m256i *)(&ref[i])); \
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ts_vec = _mm256_permute4x64_epi64(ts_vec, permute_mask); \
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ts_vec = _mm256_shuffle_epi8(ts_vec, reverse_mask_vec);
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#else
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#define LOAD_TARGET \
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__m256i ts_vec = _mm256_loadu_si256((__m256i *)(&ref[tlen - i]));
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#endif
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/*
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* e 表示当前ref的碱基被删除
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* f 表示当前seq的碱基插入
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* m 表示当前碱基匹配（可以相等，也可以不想等）
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* h 表示最大值
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*/
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// load向量化数据
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#define SIMD_LOAD \
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__m256i m1 = _mm256_loadu_si256((__m256i *)(&mA1[j])); \
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__m256i e1 = _mm256_loadu_si256((__m256i *)(&eA1[j])); \
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__m256i m1j1 = _mm256_loadu_si256((__m256i *)(&mA1[j - 1])); \
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__m256i f1j1 = _mm256_loadu_si256((__m256i *)(&fA1[j - 1])); \
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__m256i h0j1 = _mm256_loadu_si256((__m256i *)(&hA0[j - 1])); \
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__m256i qs_vec = _mm256_loadu_si256((__m256i *)(&seq[j - 1])); \
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LOAD_TARGET
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// 比对ref和seq的序列，计算罚分
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#define SIMD_CMP_SEQ \
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__m256i match_mask_vec = _mm256_cmpeq_epi8(qs_vec, ts_vec); \
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__m256i mis_score_vec = _mm256_andnot_si256(match_mask_vec, mis_sc_vec); \
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__m256i match_score_vec = _mm256_and_si256(match_sc_vec, match_mask_vec); \
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__m256i q_amb_mask_vec = _mm256_cmpeq_epi8(qs_vec, amb_vec); \
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__m256i t_amb_mask_vec = _mm256_cmpeq_epi8(ts_vec, amb_vec); \
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__m256i amb_mask_vec = _mm256_or_si256(q_amb_mask_vec, t_amb_mask_vec); \
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__m256i amb_score_vec = _mm256_and_si256(amb_mask_vec, amb_sc_vec); \
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mis_score_vec = _mm256_andnot_si256(amb_mask_vec, mis_score_vec); \
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mis_score_vec = _mm256_or_si256(amb_score_vec, mis_score_vec); \
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match_score_vec = _mm256_andnot_si256(amb_mask_vec, match_score_vec);
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// 向量化计算h, e, f, m
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#define SIMD_COMPUTE \
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__m256i en_vec0 = _mm256_max_epu8(m1, oe_del_vec); \
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en_vec0 = _mm256_subs_epu8(en_vec0, oe_del_vec); \
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__m256i en_vec1 = _mm256_max_epu8(e1, e_del_vec); \
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en_vec1 = _mm256_subs_epu8(en_vec1, e_del_vec); \
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__m256i en_vec = _mm256_max_epu8(en_vec0, en_vec1); \
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__m256i fn_vec0 = _mm256_max_epu8(m1j1, oe_ins_vec); \
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fn_vec0 = _mm256_subs_epu8(fn_vec0, oe_ins_vec); \
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__m256i fn_vec1 = _mm256_max_epu8(f1j1, e_ins_vec); \
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fn_vec1 = _mm256_subs_epu8(fn_vec1, e_ins_vec); \
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__m256i fn_vec = _mm256_max_epu8(fn_vec0, fn_vec1); \
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__m256i mn_vec0 = _mm256_adds_epu8(h0j1, match_score_vec); \
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mn_vec0 = _mm256_max_epu8(mn_vec0, mis_score_vec); \
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mn_vec0 = _mm256_subs_epu8(mn_vec0, mis_score_vec); \
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__m256i mn_mask = _mm256_cmpeq_epi8(h0j1, zero_vec); \
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__m256i mn_vec = _mm256_andnot_si256(mn_mask, mn_vec0); \
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__m256i hn_vec0 = _mm256_max_epu8(en_vec, fn_vec); \
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__m256i hn_vec = _mm256_max_epu8(hn_vec0, mn_vec);
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// 存储向量化结果
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#define SIMD_STORE \
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max_vec = _mm256_max_epu8(max_vec, hn_vec); \
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_mm256_storeu_si256((__m256i *)&eA2[j], en_vec); \
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_mm256_storeu_si256((__m256i *)&fA2[j], fn_vec); \
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_mm256_storeu_si256((__m256i *)&mA2[j], mn_vec); \
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_mm256_storeu_si256((__m256i *)&hA2[j], hn_vec);
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// 去除多余的部分
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#define SIMD_REMOVE_EXTRA \
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en_vec = _mm256_and_si256(en_vec, h_vec_mask[end - j]); \
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fn_vec = _mm256_and_si256(fn_vec, h_vec_mask[end - j]); \
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mn_vec = _mm256_and_si256(mn_vec, h_vec_mask[end - j]); \
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hn_vec = _mm256_and_si256(hn_vec, h_vec_mask[end - j]);
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// 找最大值和位置
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#define SIMD_FIND_MAX \
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uint8_t *maxVal = (uint8_t *)&max_vec; \
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max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 1)); \
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max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 2)); \
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max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 3)); \
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max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 4)); \
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max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 5)); \
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max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 6)); \
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max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 7)); \
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max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 8)); \
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max_vec = _mm256_max_epu8(max_vec, _mm256_permute2x128_si256(max_vec, max_vec, 0x01)); \
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m = MAX(m, maxVal[0]); \
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/*if (maxVal[0] > 0 && m >= max) \
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{ \
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for (j = beg, i = iend; j <= end; j += SIMD_WIDTH, i -= SIMD_WIDTH) \
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{ \
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__m256i h2_vec = _mm256_loadu_si256((__m256i *)(&hA2[j])); \
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__m256i vcmp = _mm256_cmpeq_epi8(h2_vec, max_vec); \
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uint32_t mask = _mm256_movemask_epi8(vcmp); \
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if (mask > 0) \
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{ \
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int pos = SIMD_WIDTH - 1 - __builtin_clz(mask); \
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mj = j - 1 + pos; \
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mi = i - 1 - pos; \
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} \
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} \
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}*/
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// 每轮迭代后，交换数组
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#define SWAP_DATA_POINTER \
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uint8_t *tmp = hA0; \
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hA0 = hA1; \
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hA1 = hA2; \
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hA2 = tmp; \
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tmp = eA1; \
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eA1 = eA2; \
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eA2 = tmp; \
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tmp = fA1; \
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fA1 = fA2; \
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fA2 = tmp; \
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tmp = mA1; \
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mA1 = mA2; \
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mA2 = tmp;
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int extend_avx2_u8(byte_mem_t *bmem,
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int qlen, // query length 待匹配段碱基的query长度
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const uint8_t *query, // read碱基序列
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int tlen, // target length reference的长度
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const uint8_t *target, // reference序列
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int m, // 碱基种类 (5)
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const int8_t *mat, // 每个位置的query和target的匹配得分 m*m
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int o_del, // deletion 错配开始的惩罚系数
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int e_del, // deletion extension的惩罚系数
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int o_ins, // insertion 错配开始的惩罚系数
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int e_ins, // insertion extension的惩罚系数
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int w, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
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int end_bonus,
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int zdrop,
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int h0, // 该seed的初始得分（完全匹配query的碱基数）
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int *_qle, // 匹配得到全局最大得分的碱基在query的位置
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int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
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int *_gtle, // query全部匹配上的target的长度
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int *_gscore, // query的端到端匹配得分
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int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值)
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{
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uint8_t *mA, *hA, *eA, *fA, *mA1, *mA2, *hA0, *hA1, *eA1, *fA1, *hA2, *eA2, *fA2; // hA0保存上上个col的H，其他的保存上个H E F M
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uint8_t *seq, *ref;
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uint8_t *mem, *qtmem, *vmem;
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int is_left = 0; // 是不是向左扩展
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int a = 1; // 碱基match时的分数
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int b = 4; // 碱基mismatch时的惩罚分数（正数）
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int seq_size = qlen + SIMD_WIDTH, ref_size = tlen + SIMD_WIDTH;
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int i, ibeg, D, j, k, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
|
||
int Dloop = tlen + qlen; // 循环跳出条件
|
||
int span, beg1, end1; // 边界条件计算
|
||
int col_size = qlen + 2 + SIMD_WIDTH;
|
||
int val_mem_size = (col_size * 9 + 31) >> 5 << 5; // 32字节的整数倍
|
||
int mem_size = seq_size + ref_size + val_mem_size;
|
||
|
||
SIMD_INIT; // 初始化simd用的数据
|
||
#if REVERSE_TARGET
|
||
__m256i reverse_mask_vec;
|
||
reverse_mask_vec = _mm256_loadu_si256((__m256i *)(reverse_mask));
|
||
#endif
|
||
|
||
assert(h0 > 0);
|
||
|
||
// allocate memory
|
||
// mem = malloc(mem_size);
|
||
mem = byte_mem_request(bmem, mem_size);
|
||
|
||
qtmem = &mem[0];
|
||
seq = (uint8_t *)&qtmem[0];
|
||
ref = (uint8_t *)&qtmem[seq_size];
|
||
if (is_left)
|
||
{
|
||
for (i = 0; i < qlen; ++i) seq[i] = query[qlen - 1 - i];
|
||
#if REVERSE_TARGET
|
||
for (i = 0; i < tlen; ++i) ref[i + SIMD_WIDTH] = target[tlen - 1 - i];
|
||
#else
|
||
for (i=0; i<tlen; ++i) ref[i] = target[i];
|
||
#endif
|
||
} else {
|
||
for (i = 0; i < qlen; ++i) seq[i] = query[i];
|
||
#if REVERSE_TARGET
|
||
for (i = 0; i < tlen; ++i) ref[i + SIMD_WIDTH] = target[i];
|
||
#else
|
||
for (i=0; i<tlen; ++i) ref[i] = target[tlen - 1 - i];
|
||
#endif
|
||
}
|
||
|
||
vmem = &ref[ref_size];
|
||
for (i = 0; i < val_mem_size; i += SIMD_WIDTH)
|
||
{
|
||
_mm256_storeu_si256((__m256i *)&vmem[i], zero_vec);
|
||
}
|
||
|
||
hA = &vmem[0];
|
||
mA = &vmem[col_size * 3];
|
||
eA = &vmem[col_size * 5];
|
||
fA = &vmem[col_size * 7];
|
||
|
||
hA0 = &hA[0];
|
||
hA1 = &hA[col_size];
|
||
hA2 = &hA1[col_size];
|
||
mA1 = &mA[0];
|
||
mA2 = &mA[col_size];
|
||
eA1 = &eA[0];
|
||
eA2 = &eA[col_size];
|
||
fA1 = &fA[0];
|
||
fA2 = &fA[col_size];
|
||
|
||
// adjust $w if it is too large
|
||
k = m * m;
|
||
// get the max score
|
||
for (i = 0, max = 0; i < k; ++i)
|
||
max = max > mat[i] ? max : mat[i];
|
||
max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
|
||
max_ins = max_ins > 1 ? max_ins : 1;
|
||
w = w < max_ins ? w : max_ins;
|
||
max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
|
||
max_del = max_del > 1 ? max_del : 1;
|
||
w = w < max_del ? w : max_del; // TODO: is this necessary?
|
||
if (tlen < qlen)
|
||
w = MIN(tlen - 1, w);
|
||
|
||
// DP loop
|
||
max = h0, max_i = max_j = -1;
|
||
max_ie = -1, gscore = -1;
|
||
;
|
||
max_off = 0;
|
||
beg = 1;
|
||
end = qlen;
|
||
// init h0
|
||
hA0[0] = h0; // 左上角
|
||
|
||
if (qlen == 0 || tlen == 0)
|
||
Dloop = 0; // 防止意外情况
|
||
if (w >= qlen)
|
||
{
|
||
max_ie = 0;
|
||
gscore = 0;
|
||
}
|
||
int m_last = 0;
|
||
int iend;
|
||
#if PRUNING
|
||
#ifdef KSW_EQUAL
|
||
int midx = 1, icheck = 0, checkspecial = 1;
|
||
#if ARR_FOR_EQUAL_CHECK
|
||
int marr[10] = {0};
|
||
// int marr[b]; memset(marr, 0, 4 * b);
|
||
#else
|
||
int m3 = 0, m2 = 0, m1 = 0;
|
||
#endif
|
||
#endif
|
||
#endif
|
||
|
||
w = 1000;
|
||
for (D = 1; LIKELY(D < Dloop); ++D)
|
||
{
|
||
// 边界条件一定要注意！ tlen 大于，等于，小于 qlen时的情况
|
||
if (D > tlen)
|
||
{
|
||
span = MIN(Dloop - D, w);
|
||
beg1 = MAX(D - tlen + 1, ((D - w) / 2) + 1);
|
||
}
|
||
else
|
||
{
|
||
span = MIN(D - 1, w);
|
||
beg1 = MAX(1, ((D - w) / 2) + 1);
|
||
}
|
||
end1 = MIN(qlen, beg1 + span);
|
||
|
||
if (beg < beg1)
|
||
beg = beg1;
|
||
if (end > end1)
|
||
end = end1;
|
||
if (beg > end)
|
||
break; // 不用计算了，直接跳出，否则hA2没有被赋值，里边是上一轮hA0的值，会出bug
|
||
|
||
iend = D - (beg - 1); // ref开始计算的位置，倒序
|
||
span = end - beg;
|
||
ibeg = iend - span - 1; // 0开始的ref索引位置
|
||
|
||
// 每一轮需要记录的数据
|
||
int m = 0, mj = -1, mi = -1;
|
||
max_vec = zero_vec;
|
||
|
||
// 要处理边界
|
||
// 左边界 处理f (insert)
|
||
if (ibeg == 0)
|
||
{
|
||
hA1[end] = MAX(0, h0 - (o_ins + e_ins * end));
|
||
m = hA1[end];
|
||
}
|
||
// 上边界
|
||
if (beg == 1)
|
||
{
|
||
hA1[0] = MAX(0, h0 - (o_del + e_del * iend));
|
||
}
|
||
else if (D & 1)
|
||
{
|
||
hA1[beg - 1] = 0;
|
||
hA2[beg - 1] = 0;
|
||
}
|
||
|
||
for (j = beg, i = iend; j <= end + 1 - SIMD_WIDTH; j += SIMD_WIDTH, i -= SIMD_WIDTH)
|
||
{
|
||
// 取数据
|
||
SIMD_LOAD;
|
||
// 比对seq，计算罚分
|
||
SIMD_CMP_SEQ;
|
||
// 计算
|
||
SIMD_COMPUTE;
|
||
// 存储结果
|
||
SIMD_STORE;
|
||
}
|
||
// 剩下的计算单元
|
||
if (j <= end)
|
||
{
|
||
// 取数据
|
||
SIMD_LOAD;
|
||
// 比对seq，计算罚分
|
||
SIMD_CMP_SEQ;
|
||
// 计算
|
||
SIMD_COMPUTE;
|
||
// 去除多余计算的部分
|
||
SIMD_REMOVE_EXTRA;
|
||
// 存储结果
|
||
SIMD_STORE;
|
||
}
|
||
|
||
SIMD_FIND_MAX;
|
||
|
||
#if PRUNING
|
||
#ifdef KSW_EQUAL
|
||
#if ARR_FOR_EQUAL_CHECK
|
||
if (hA1[0] < b && checkspecial)
|
||
{
|
||
int mii;
|
||
if (hA1[0] == b - 1)
|
||
{
|
||
icheck = iend + 1;
|
||
}
|
||
for (mii = 0; mii < b - 1; ++mii)
|
||
{
|
||
if (midx - mii > 0)
|
||
marr[mii] = MAX(marr[mii], hA2[midx - mii]);
|
||
}
|
||
midx += 1;
|
||
if (ibeg > icheck)
|
||
{
|
||
int stopCalc = 0;
|
||
for (mii = 0; mii < b - 1; ++mii)
|
||
{
|
||
stopCalc |= !marr[mii];
|
||
}
|
||
if (stopCalc)
|
||
break;
|
||
else
|
||
checkspecial = 0;
|
||
}
|
||
}
|
||
#else
|
||
if (hA1[0] < 4 && checkspecial)
|
||
{ // b == 4
|
||
if (hA1[0] == 3)
|
||
{
|
||
icheck = iend + 1;
|
||
}
|
||
else if (midx == 2)
|
||
{
|
||
m2 = MAX(m2, hA2[midx - 1]);
|
||
}
|
||
else
|
||
{
|
||
m2 = MAX(m2, hA2[midx - 1]);
|
||
m1 = MAX(m1, hA2[midx - 2]);
|
||
}
|
||
m3 = MAX(m3, hA2[midx]);
|
||
midx += 1;
|
||
if (ibeg > icheck)
|
||
{
|
||
if (!m1 || !m2 || !m3)
|
||
break;
|
||
else
|
||
checkspecial = 0;
|
||
}
|
||
}
|
||
#endif
|
||
#endif
|
||
#endif
|
||
// 注意最后跳出循环j的值
|
||
j = end + 1;
|
||
|
||
if (j == qlen + 1)
|
||
{
|
||
max_ie = gscore > hA2[qlen] ? max_ie : ibeg;
|
||
gscore = gscore > hA2[qlen] ? gscore : hA2[qlen];
|
||
}
|
||
#if PRUNING
|
||
if (m == 0 && m_last == 0) break; // 一定要注意，斜对角遍历和按列遍历的不同点
|
||
#endif
|
||
if (m > max)
|
||
{
|
||
max = m, max_i = mi, max_j = mj;
|
||
max_off = max_off > abs(mj - mi) ? max_off : abs(mj - mi);
|
||
}
|
||
else if (m == max && max_i >= mi && mj > max_j)
|
||
{
|
||
max_i = mi, max_j = mj;
|
||
max_off = max_off > abs(mj - mi) ? max_off : abs(mj - mi);
|
||
}
|
||
else if (zdrop > 0 && mi > -1)
|
||
{
|
||
#if PRUNING
|
||
if (mi - max_i > mj - max_j)
|
||
{
|
||
if (max - m - ((mi - max_i) - (mj - max_j)) * e_del > zdrop)
|
||
break;
|
||
}
|
||
else
|
||
{
|
||
if (max - m - ((mj - max_j) - (mi - max_i)) * e_ins > zdrop)
|
||
break;
|
||
}
|
||
#endif
|
||
}
|
||
|
||
// 调整计算的边界
|
||
#if PRUNING
|
||
for (j = beg; LIKELY(j <= end); ++j)
|
||
{
|
||
int has_val = hA1[j - 1] | hA2[j];
|
||
if (has_val) break;
|
||
}
|
||
beg = j;
|
||
for (j = end + 1; LIKELY(j >= beg); --j)
|
||
{
|
||
int has_val = hA1[j - 1] | hA2[j];
|
||
if (has_val) break;
|
||
else hA0[j - 1] = 0;
|
||
}
|
||
end = j + 1 <= qlen ? j + 1 : qlen;
|
||
#else
|
||
beg = 1; end = qlen;
|
||
#endif
|
||
m_last = m;
|
||
// swap m, h, e, f
|
||
SWAP_DATA_POINTER;
|
||
}
|
||
|
||
// free(mem);
|
||
byte_mem_clear(bmem);
|
||
if (_qle) *_qle = max_j + 1;
|
||
if (_tle) *_tle = max_i + 1;
|
||
if (_gtle) *_gtle = max_ie + 1;
|
||
if (_gscore) *_gscore = gscore;
|
||
if (_max_off) *_max_off = max_off;
|
||
return max;
|
||
}
|