448 lines
23 KiB
C
448 lines
23 KiB
C
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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 <stdio.h>
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#include <immintrin.h>
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#include <emmintrin.h>
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#include "thread_mem.h"
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#ifdef __GNUC__
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#define LIKELY(x) __builtin_expect((x), 1)
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#define UNLIKELY(x) __builtin_expect((x), 0)
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#else
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#define LIKELY(x) (x)
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#define UNLIKELY(x) (x)
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#endif
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#undef MAX
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#undef MIN
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#define MAX(x, y) ((x) > (y) ? (x) : (y))
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#define MIN(x, y) ((x) < (y) ? (x) : (y))
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#define SIMD_WIDTH 16
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#define BASE_BYTES 2
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#define SCORE_BYTES 2
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#define BOUNDARY_SCORE_NUM 2
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#define TMP_SCORE_ARRAY_NUM 9
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#define MEM_ALIGN_BYTES 32
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#define ALIGN_SHIFT_BITS 5
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#define SIMD_BYTES 32
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#define AMBIGUOUS_BASE_CODE 4
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#define AMBIGUOUS_BASE_SCORE -1
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// 32字节对齐（256位）
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#define align_mem(x) (((x) + 31) >> 5 << 5)
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#define align_number(x) align_mem(x)
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/* 去掉多余计算的值 */
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static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
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{0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0},
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{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff}};
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// #define permute_mask _MM_SHUFFLE(0, 1, 2, 3)
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#define permute_mask 27
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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, last_max_vec = _mm256_set1_epi16(init_score); \
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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_epi16(-oe_del); \
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oe_ins_vec = _mm256_set1_epi16(-oe_ins); \
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e_del_vec = _mm256_set1_epi16(-e_del); \
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e_ins_vec = _mm256_set1_epi16(-e_ins); \
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__m256i match_sc_vec = _mm256_set1_epi16(base_match_score); \
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__m256i mis_sc_vec = _mm256_set1_epi16(-base_mis_score); \
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__m256i amb_sc_vec = _mm256_set1_epi16(AMBIGUOUS_BASE_SCORE); \
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__m256i amb_vec = _mm256_set1_epi16(AMBIGUOUS_BASE_CODE); \
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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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/*
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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 *)(&cur_match_arr[j])); \
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__m256i e1 = _mm256_loadu_si256((__m256i *)(&cur_del_arr[j])); \
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__m256i m1j1 = _mm256_loadu_si256((__m256i *)(&cur_match_arr[j - 1])); \
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__m256i f1j1 = _mm256_loadu_si256((__m256i *)(&cur_ins_arr[j - 1])); \
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__m256i h0j1 = _mm256_loadu_si256((__m256i *)(&last_max_arr[j - 1])); \
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__m256i qs_vec = _mm256_loadu_si256((__m256i *)(&read_seq[j])); \
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__m256i ts_vec = _mm256_loadu_si256((__m256i *)(&ref_seq[i]));
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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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/* 将待比对的target序列逆序排列 */ \
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ts_vec = _mm256_permute4x64_epi64(ts_vec, permute_mask); \
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ts_vec = _mm256_shufflelo_epi16(ts_vec, permute_mask); \
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ts_vec = _mm256_shufflehi_epi16(ts_vec, permute_mask); \
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__m256i match_mask_vec = _mm256_cmpeq_epi16(qs_vec, ts_vec); /* 比对query和target字符序列 */ \
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__m256i mis_score_vec = _mm256_andnot_si256(match_mask_vec, mis_sc_vec); /* 未匹配上的位置赋值mismatch分数 */ \
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__m256i score_vec = _mm256_and_si256(match_sc_vec, match_mask_vec); /* 匹配上的位置赋值match分数 */ \
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score_vec = _mm256_or_si256(score_vec, mis_score_vec); \
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/* 计算模棱两可的字符（N)的位置的分数 */ \
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__m256i q_amb_mask_vec = _mm256_cmpeq_epi16(qs_vec, amb_vec); \
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__m256i t_amb_mask_vec = _mm256_cmpeq_epi16(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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score_vec = _mm256_andnot_si256(amb_mask_vec, score_vec); \
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__m256i amb_score_vec = _mm256_and_si256(amb_mask_vec, amb_sc_vec); \
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score_vec = _mm256_or_si256(score_vec, amb_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_add_epi16(m1, oe_del_vec); \
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__m256i en_vec1 = _mm256_add_epi16(e1, e_del_vec); \
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__m256i en_vec = _mm256_max_epi16(en_vec0, en_vec1); \
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__m256i fn_vec0 = _mm256_add_epi16(m1j1, oe_ins_vec); \
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__m256i fn_vec1 = _mm256_add_epi16(f1j1, e_ins_vec); \
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__m256i fn_vec = _mm256_max_epi16(fn_vec0, fn_vec1); \
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__m256i mn_vec0 = _mm256_add_epi16(h0j1, score_vec); \
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__m256i mn_mask = _mm256_cmpgt_epi16(h0j1, zero_vec); \
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__m256i mn_vec = _mm256_and_si256(mn_vec0, mn_mask); \
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__m256i hn_vec0 = _mm256_max_epi16(en_vec, fn_vec); \
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__m256i hn_vec = _mm256_max_epi16(hn_vec0, mn_vec); \
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en_vec = _mm256_max_epi16(en_vec, zero_vec); \
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fn_vec = _mm256_max_epi16(fn_vec, zero_vec); \
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mn_vec = _mm256_max_epi16(mn_vec, zero_vec); \
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hn_vec = _mm256_max_epi16(hn_vec, zero_vec);
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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 *)&next_del_arr[j], en_vec); \
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_mm256_storeu_si256((__m256i *)&next_ins_arr[j], fn_vec); \
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_mm256_storeu_si256((__m256i *)&next_match_arr[j], mn_vec); \
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_mm256_storeu_si256((__m256i *)&next_max_arr[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[read_end_pos - j]); \
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fn_vec = _mm256_and_si256(fn_vec, h_vec_mask[read_end_pos - j]); \
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mn_vec = _mm256_and_si256(mn_vec, h_vec_mask[read_end_pos - j]); \
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hn_vec = _mm256_and_si256(hn_vec, h_vec_mask[read_end_pos - j]);
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// 找最大值和位置
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#define SIMD_FIND_MAX \
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__m256i cmp_max = _mm256_cmpgt_epi16(max_vec, last_max_vec); \
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uint32_t cmp_result = _mm256_movemask_epi8(cmp_max); \
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if (cmp_result > 0) \
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{ \
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max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 2)); \
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max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 4)); \
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max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 6)); \
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max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 8)); \
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max_vec = _mm256_max_epu16(max_vec, _mm256_permute2x128_si256(max_vec, max_vec, 0x01)); \
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int16_t *maxVal = (int16_t *)&max_vec; \
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m = maxVal[0]; \
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for (j = aligned_read_start_pos, i = aligned_ref_end_pos; j <= read_end_pos; j += SIMD_WIDTH, i -= SIMD_WIDTH) \
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{ \
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__m256i h2_vec = _mm256_loadu_si256((__m256i *)(&next_max_arr[j])); \
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__m256i vcmp = _mm256_cmpeq_epi16(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)) >> 1); \
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mj = j - 1 + pos; \
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mi = i - 1 - pos; \
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for (; mj + 1 < qlen && mi + 1 < tlen; mj++, mi++) \
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{ \
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if (read_seq[mj + 2] == ref_seq[mi + 1 + SIMD_WIDTH]) \
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{ \
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m += base_match_score; \
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} \
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else \
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{ \
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break; \
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} \
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} \
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} \
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} \
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last_max_vec = _mm256_set1_epi16(m); \
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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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int16_t *tmp = last_max_arr; \
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last_max_arr = cur_max_arr; \
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cur_max_arr = next_max_arr; \
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next_max_arr = tmp; \
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tmp = cur_del_arr; \
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cur_del_arr = next_del_arr; \
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next_del_arr = tmp; \
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tmp = cur_ins_arr; \
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cur_ins_arr = next_ins_arr; \
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next_ins_arr = tmp; \
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tmp = cur_match_arr; \
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cur_match_arr = next_match_arr; \
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next_match_arr = tmp;
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int ksw_extend_avx2_aligned(thread_mem_t *tmem,
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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 extend_left, // 是不是向左扩展
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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SIMD_BTYES
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int base_match_score, // 碱基match时的分数
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int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
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int window_size, // 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, // 如果query比对到了最后一个字符，额外奖励分值
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int init_score, // 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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int16_t *cur_match_arr, *next_match_arr,
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*last_max_arr, *cur_max_arr, *next_max_arr,
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*cur_del_arr, *next_del_arr,
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*cur_ins_arr, *next_ins_arr; // hA0保存上上个col的H，其他的保存上个H E F M
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int16_t *read_seq, *ref_seq;
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uint8_t *mem_addr;
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int read_size = align_number(qlen * BASE_BYTES + MEM_ALIGN_BYTES);
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int ref_size = align_number((tlen + SIMD_WIDTH) * BASE_BYTES);
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int back_diagnal_num = tlen + qlen; // 循环跳出条件 D从1开始遍历
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int score_array_size = align_number((qlen + BOUNDARY_SCORE_NUM) * SCORE_BYTES);
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int score_element_num = score_array_size / SCORE_BYTES;
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int score_mem_size = score_array_size * TMP_SCORE_ARRAY_NUM;
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int request_mem_size = read_size + ref_size + score_mem_size + MEM_ALIGN_BYTES * 3; // 左侧内存地址对齐 + 数据向左偏移一个元素 + 末尾SIMD补齐
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int i, ref_start_pos, di, j, read_start_pos, read_end_pos, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
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int span, beg1, end1; // 边界条件计算
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int aligned_read_start_pos, aligned_ref_end_pos;
|
|||
|
|
int ref_end_pos;
|
|||
|
|
|
|||
|
|
SIMD_INIT; // 初始化simd用的数据
|
|||
|
|
|
|||
|
|
assert(init_score > 0);
|
|||
|
|
|
|||
|
|
// allocate memory
|
|||
|
|
mem_addr = thread_mem_request(tmem, request_mem_size);
|
|||
|
|
mem_addr = (void *)align_mem((uint64_t)mem_addr);
|
|||
|
|
ref_seq = (int16_t *)&mem_addr[0];
|
|||
|
|
read_seq = (int16_t *)(mem_addr + ref_size + SIMD_BYTES - BASE_BYTES);
|
|||
|
|
if (extend_left)
|
|||
|
|
{
|
|||
|
|
for (i = 0; i < qlen; ++i)
|
|||
|
|
read_seq[i + 1] = query[qlen - 1 - i];
|
|||
|
|
for (i = 0; i < tlen; ++i)
|
|||
|
|
ref_seq[i + SIMD_WIDTH] = target[tlen - 1 - i];
|
|||
|
|
}
|
|||
|
|
else
|
|||
|
|
{
|
|||
|
|
for (i = 0; i < qlen; ++i)
|
|||
|
|
read_seq[i + 1] = query[i];
|
|||
|
|
for (i = 0; i < tlen; ++i)
|
|||
|
|
ref_seq[i + SIMD_WIDTH] = target[i];
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
mem_addr += read_size + ref_size + (SIMD_BYTES - SCORE_BYTES);
|
|||
|
|
for (i = 0; i < score_mem_size; i += SIMD_BYTES)
|
|||
|
|
{
|
|||
|
|
_mm256_storeu_si256((__m256i *)&mem_addr[i], zero_vec);
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
last_max_arr = (int16_t *)&mem_addr[0];
|
|||
|
|
cur_max_arr = &last_max_arr[score_element_num];
|
|||
|
|
next_max_arr = &cur_max_arr[score_element_num];
|
|||
|
|
cur_match_arr = &next_max_arr[score_element_num];
|
|||
|
|
next_match_arr = &cur_match_arr[score_element_num];
|
|||
|
|
cur_del_arr = &next_match_arr[score_element_num];
|
|||
|
|
next_del_arr = &cur_del_arr[score_element_num];
|
|||
|
|
cur_ins_arr = &next_del_arr[score_element_num];
|
|||
|
|
next_ins_arr = &cur_ins_arr[score_element_num];
|
|||
|
|
|
|||
|
|
// adjust $window_size if it is too large
|
|||
|
|
// get the max score
|
|||
|
|
max = base_match_score;
|
|||
|
|
max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
|
|||
|
|
max_ins = max_ins > 1 ? max_ins : 1;
|
|||
|
|
window_size = window_size < max_ins ? window_size : max_ins;
|
|||
|
|
max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
|
|||
|
|
max_del = max_del > 1 ? max_del : 1;
|
|||
|
|
window_size = window_size < max_del ? window_size : max_del; // TODO: is this necessary?
|
|||
|
|
if (tlen < qlen)
|
|||
|
|
window_size = MIN(tlen - 1, window_size);
|
|||
|
|
|
|||
|
|
// DP loop
|
|||
|
|
max = init_score, max_i = max_j = -1;
|
|||
|
|
max_ie = -1, gscore = -1;
|
|||
|
|
;
|
|||
|
|
max_off = 0;
|
|||
|
|
read_start_pos = 1;
|
|||
|
|
read_end_pos = qlen;
|
|||
|
|
// init init_score
|
|||
|
|
last_max_arr[0] = init_score; // 左上角
|
|||
|
|
|
|||
|
|
if (qlen == 0 || tlen == 0)
|
|||
|
|
back_diagnal_num = 0; // 防止意外情况
|
|||
|
|
if (window_size >= qlen)
|
|||
|
|
{
|
|||
|
|
max_ie = 0;
|
|||
|
|
gscore = 0;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
for (di = 1; LIKELY(di < back_diagnal_num); ++di)
|
|||
|
|
{
|
|||
|
|
// 边界条件一定要注意！ tlen 大于，等于，小于 qlen时的情况
|
|||
|
|
if (di > tlen)
|
|||
|
|
{
|
|||
|
|
span = MIN(back_diagnal_num - di, window_size); // 计算的窗口，或者说范围
|
|||
|
|
beg1 = MAX(di - tlen + 1, ((di - window_size) / 2) + 1);
|
|||
|
|
}
|
|||
|
|
else
|
|||
|
|
{
|
|||
|
|
span = MIN(di - 1, window_size);
|
|||
|
|
beg1 = MAX(1, ((di - window_size) / 2) + 1);
|
|||
|
|
}
|
|||
|
|
end1 = MIN(qlen, beg1 + span);
|
|||
|
|
|
|||
|
|
if (read_start_pos < beg1)
|
|||
|
|
read_start_pos = beg1;
|
|||
|
|
if (read_end_pos > end1)
|
|||
|
|
read_end_pos = end1;
|
|||
|
|
if (read_start_pos > read_end_pos)
|
|||
|
|
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
|
|||
|
|
|
|||
|
|
read_start_pos = 1;
|
|||
|
|
read_end_pos = qlen;
|
|||
|
|
ref_end_pos = di - (read_start_pos - 1); // ref开始计算的位置，倒序
|
|||
|
|
span = read_end_pos - read_start_pos;
|
|||
|
|
ref_start_pos = ref_end_pos - 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 (ref_start_pos == 0)
|
|||
|
|
{
|
|||
|
|
cur_max_arr[read_end_pos] = MAX(0, init_score - (o_ins + e_ins * read_end_pos));
|
|||
|
|
}
|
|||
|
|
// 上边界 delete
|
|||
|
|
if (read_start_pos == 1)
|
|||
|
|
{
|
|||
|
|
cur_max_arr[0] = MAX(0, init_score - (o_del + e_del * ref_end_pos));
|
|||
|
|
}
|
|||
|
|
else
|
|||
|
|
{
|
|||
|
|
cur_max_arr[read_start_pos - 1] = 0;
|
|||
|
|
cur_del_arr[read_start_pos - 1] = 0;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
// aligned_read_start_pos = (read_start_pos >> ALIGN_SHIFT_BITS << ALIGN_SHIFT_BITS) + 1;
|
|||
|
|
// aligned_ref_end_pos = ref_end_pos + (read_start_pos - aligned_read_start_pos);
|
|||
|
|
|
|||
|
|
aligned_read_start_pos = read_start_pos;
|
|||
|
|
aligned_ref_end_pos = ref_end_pos;
|
|||
|
|
|
|||
|
|
// fprintf(stderr, "%d\t%d\n", read_start_pos, aligned_read_start_pos);
|
|||
|
|
|
|||
|
|
for (j = aligned_read_start_pos, i = aligned_ref_end_pos; j <= read_end_pos + 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 <= read_end_pos)
|
|||
|
|
{
|
|||
|
|
// 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;
|
|||
|
|
|
|||
|
|
// 注意最后跳出循环j的值
|
|||
|
|
j = read_end_pos + 1;
|
|||
|
|
|
|||
|
|
if (j == qlen + 1) // 遍历到了query最后一个碱基，此时next_max_arr[qlen]为全局匹配的最大分值
|
|||
|
|
{
|
|||
|
|
max_ie = gscore > next_max_arr[qlen] ? max_ie : ref_start_pos;
|
|||
|
|
gscore = gscore > next_max_arr[qlen] ? gscore : next_max_arr[qlen];
|
|||
|
|
}
|
|||
|
|
if (m > max)
|
|||
|
|
{
|
|||
|
|
max = m, max_i = mi, max_j = mj;
|
|||
|
|
max_off = max_off > abs(mj - mi) ? max_off : abs(mj - mi);
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
// 调整计算的边界
|
|||
|
|
// for (j = read_start_pos; LIKELY(j <= read_end_pos); ++j)
|
|||
|
|
//{
|
|||
|
|
// int has_val = cur_max_arr[j - 1] | next_max_arr[j];
|
|||
|
|
// if (has_val)
|
|||
|
|
// {
|
|||
|
|
// break;
|
|||
|
|
// }
|
|||
|
|
//}
|
|||
|
|
// read_start_pos = j;
|
|||
|
|
//
|
|||
|
|
// next_max_arr[read_end_pos + 1] = 0;
|
|||
|
|
// for (j = read_end_pos + 1; LIKELY(j >= read_start_pos); --j)
|
|||
|
|
//{
|
|||
|
|
// int has_val = cur_max_arr[j - 1] | next_max_arr[j];
|
|||
|
|
// if (has_val)
|
|||
|
|
// {
|
|||
|
|
// break;
|
|||
|
|
// }
|
|||
|
|
//}
|
|||
|
|
// read_end_pos = j + 1 <= qlen ? j + 1 : qlen;
|
|||
|
|
// swap m, h, e, f
|
|||
|
|
SWAP_DATA_POINTER;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
thread_mem_release(tmem, request_mem_size);
|
|||
|
|
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;
|
|||
|
|
}
|