444 lines
21 KiB
C
444 lines
21 KiB
C
#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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#include "common.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 *)(&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])); \
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__m256i ts_vec = _mm256_loadu_si256((__m256i *)(&ref[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 *)&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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__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 <= 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_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 (seq[mj + 2] == ref[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 = 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 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 *mA1, *mA2,
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*hA0, *hA1, *hA2,
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*eA1, *eA2,
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*fA1, *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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int16_t *seq, *ref;
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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, ibeg, D, j, beg, end, 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;
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int iend;
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SIMD_INIT; // 初始化simd用的数据
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assert(init_score > 0);
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// allocate memory
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mem_addr = thread_mem_request(tmem, request_mem_size);
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mem_addr = (void *)align_mem((uint64_t)mem_addr);
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ref = (int16_t *)&mem_addr[0];
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seq = (int16_t *)(mem_addr + ref_size + SIMD_BYTES - BASE_BYTES);
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if (extend_left)
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{
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for (i = 0; i < qlen; ++i)
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seq[i + 1] = query[qlen - 1 - i];
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for (i = 0; i < tlen; ++i)
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ref[i + SIMD_WIDTH - 1] = target[tlen - 1 - i];
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}
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else
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{
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for (i = 0; i < qlen; ++i)
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seq[i + 1] = query[i];
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for (i = 0; i < tlen; ++i)
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ref[i + SIMD_WIDTH - 1] = target[i];
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}
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mem_addr += read_size + ref_size + (SIMD_BYTES - SCORE_BYTES);
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for (i = 0; i < score_mem_size; i += SIMD_BYTES)
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{
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_mm256_storeu_si256((__m256i *)&mem_addr[i], zero_vec);
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}
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hA0 = (int16_t *)&mem_addr[0];
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hA1 = &hA0[score_element_num];
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hA2 = &hA1[score_element_num];
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mA1 = &hA2[score_element_num];
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mA2 = &mA1[score_element_num];
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eA1 = &mA2[score_element_num];
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eA2 = &eA1[score_element_num];
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fA1 = &eA2[score_element_num];
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fA2 = &fA1[score_element_num];
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// adjust $window_size if it is too large
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// get the max score
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max = base_match_score;
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max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
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max_ins = max_ins > 1 ? max_ins : 1;
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window_size = window_size < max_ins ? window_size : max_ins;
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max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
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max_del = max_del > 1 ? max_del : 1;
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window_size = window_size < max_del ? window_size : max_del; // TODO: is this necessary?
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if (tlen < qlen)
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window_size = MIN(tlen - 1, window_size);
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// DP loop
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max = init_score, max_i = max_j = -1;
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max_ie = -1, gscore = -1;
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;
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max_off = 0;
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beg = 1;
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end = qlen;
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// init init_score
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hA0[0] = init_score; // 左上角
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fA1[1] = MAX(0, init_score - (o_ins + e_ins));
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eA2[0] = init_score;
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hA1[1] = fA1[1];
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if (qlen == 0 || tlen == 0)
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back_diagnal_num = 0; // 防止意外情况
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if (window_size >= qlen)
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{
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max_ie = 0;
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gscore = 0;
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}
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for (D = 1; LIKELY(D < back_diagnal_num); ++D)
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{
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if (D < tlen)
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beg1 = 1;
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else
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beg1 = D - tlen + 1;
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if (D < qlen)
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end1 = D; // 闭区间
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else
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end1 = qlen;
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beg1 = MAX(D - window_size, beg1);
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end1 = MIN(D + window_size, end1);
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beg = MAX(beg1, beg);
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end = MIN(end1, end);
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if (beg > end)
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break;
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// beg = beg1;
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// end = end1;
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iend = D - beg; // ref开始计算的位置，倒序
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span = end - beg;
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ibeg = iend - span; // 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;
|
||
// 处理左边界
|
||
if (beg == 1)
|
||
{
|
||
hA0[0] = eA2[0];
|
||
mA1[0] = 0;
|
||
eA1[0] = MAX(0, init_score - (o_del + e_del * (iend + 1)));
|
||
}
|
||
|
||
// aligned_read_start_pos = (beg >> ALIGN_SHIFT_BITS << ALIGN_SHIFT_BITS) + 1;
|
||
// aligned_ref_end_pos = iend + (beg - aligned_read_start_pos);
|
||
|
||
aligned_read_start_pos = beg;
|
||
aligned_ref_end_pos = iend;
|
||
|
||
// fprintf(stderr, "%d\t%d\n", beg, aligned_read_start_pos);
|
||
|
||
for (j = aligned_read_start_pos, i = aligned_ref_end_pos; 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;
|
||
}
|
||
// 处理上边界
|
||
if (ibeg == 0)
|
||
{
|
||
fA2[end + 1] = MAX(0, init_score - (o_ins + e_ins * (end + 1)));
|
||
hA2[end + 1] = fA2[end + 1];
|
||
mA2[end + 1] = 0;
|
||
}
|
||
SIMD_FIND_MAX;
|
||
|
||
// 注意最后跳出循环j的值
|
||
j = end + 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 > hA2[qlen] ? max_ie : ibeg;
|
||
gscore = gscore > hA2[qlen] ? gscore : hA2[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 = 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;
|
||
}
|
||
}
|
||
end = 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;
|
||
} |