replace with newer versions
This commit is contained in:
Heng Li
parent
fbfd4a3eff
commit
c6d5dea314
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#ifndef KSW2_H_
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#define KSW2_H_
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#include <stdint.h>
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#define KSW_NEG_INF -0x40000000
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#define KSW_EZ_SCORE_ONLY 0x01 // don't record alignment path/cigar
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#define KSW_EZ_RIGHT 0x02 // right-align gaps
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#define KSW_EZ_GENERIC_SC 0x04 // without this flag: match/mismatch only; last symbol is a wildcard
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#define KSW_EZ_GLOBAL_ONLY 0x08 // don't record best score and ignore z-drop; significantly faster
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#define KSW_EZ_DYN_BAND 0x10 // once used, ksw_extz_t::{mqe,mte} may be wrong
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typedef struct {
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int max, max_q, max_t; // max extension score and coordinate
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int mqe, mqe_t; // max score when reaching the end of query
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int mte, mte_q; // max score when reaching the end of target
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int score; // max score reaching both ends; may be KSW_NEG_INF
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int m_cigar, n_cigar;
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uint32_t *cigar;
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} ksw_extz_t;
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#ifdef __cplusplus
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extern "C" {
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#endif
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/**
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* NW-like extension
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*
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* @param km memory pool, when used with kalloc
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* @param qlen query length
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* @param query query sequence with 0 <= query[i] < m
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* @param tlen target length
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* @param target target sequence with 0 <= target[i] < m
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* @param m number of residue types
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* @param mat m*m scoring mattrix in one-dimension array
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* @param gapo gap open penalty; a gap of length l cost "-(gapo+l*gape)"
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* @param gape gap extension penalty
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* @param w band width
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* @param zdrop off-diagonal drop-off to stop extension (positive)
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* @param flag flag (see KSW_EZ_* macros)
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* @param ez (out) scores and cigar
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*/
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void ksw_extz(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez);
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void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez);
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/**
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* Global alignment
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*
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* (first 10 parameters identical to ksw_extz_sse())
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* @param m_cigar (modified) max CIGAR length; feed 0 if cigar==0
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* @param n_cigar (out) number of CIGAR elements
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* @param cigar (out) BAM-encoded CIGAR; caller need to deallocate with kfree(km, )
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*
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* @return score of the alignment
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*/
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int ksw_gg(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *m_cigar_, int *n_cigar_, uint32_t **cigar_);
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int ksw_gg2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *m_cigar_, int *n_cigar_, uint32_t **cigar_);
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int ksw_gg2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *m_cigar_, int *n_cigar_, uint32_t **cigar_);
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#ifdef __cplusplus
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}
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#endif
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/************************************
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*** Private macros and functions ***
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************************************/
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#ifdef HAVE_KALLOC
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#include "kalloc.h"
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#else
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#include <stdlib.h>
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#define kmalloc(km, size) malloc((size))
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#define kcalloc(km, count, size) calloc((count), (size))
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#define krealloc(km, ptr, size) realloc((ptr), (size))
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#define kfree(km, ptr) free((ptr))
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#endif
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static inline uint32_t *ksw_push_cigar(void *km, int *n_cigar, int *m_cigar, uint32_t *cigar, uint32_t op, int len)
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{
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if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
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if (*n_cigar == *m_cigar) {
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*m_cigar = *m_cigar? (*m_cigar)<<1 : 4;
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cigar = (uint32_t*)krealloc(km, cigar, (*m_cigar) << 2);
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}
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cigar[(*n_cigar)++] = len<<4 | op;
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} else cigar[(*n_cigar)-1] += len<<4;
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return cigar;
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}
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static inline void ksw_backtrack(void *km, int is_rot, const uint8_t *p, const int *off, int n_col, int i0, int j0, int *m_cigar_, int *n_cigar_, uint32_t **cigar_)
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{
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int n_cigar = 0, m_cigar = *m_cigar_, which = 0, i = i0, j = j0, r;
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uint32_t *cigar = *cigar_, tmp;
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while (i >= 0 && j >= 0) {
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if (is_rot) r = i + j, tmp = p[r * n_col + i - off[r]];
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else tmp = p[i * n_col + j - off[i]];
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which = tmp >> (which << 1) & 3;
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if (which == 0 && tmp>>6) break;
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if (which == 0) which = tmp & 3;
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if (which == 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 0, 1), --i, --j; // match
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else if (which == 1) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 2, 1), --i; // deletion
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else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --j; // insertion
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}
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if (i >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 2, i + 1); // first deletion
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if (j >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, j + 1); // first insertion
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for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
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tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
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*m_cigar_ = m_cigar, *n_cigar_ = n_cigar, *cigar_ = cigar;
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}
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static inline int ksw_cigar2score(int8_t m, const int8_t *mat, int8_t q, int8_t e, const uint8_t *query, const uint8_t *target, int n_cigar, const uint32_t *cigar)
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{
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int i, j, k, l, score;
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for (k = 0, score = 0, i = j = 0; k < n_cigar; ++k) {
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int op = cigar[k] & 0xf, len = cigar[k] >> 4;
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if (op == 0) {
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for (l = 0; l < len; ++l)
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score += mat[target[i + l] * m + query[j + l]];
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i += len, j += len;
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} else if (op == 1) {
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score -= q + len * e;
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j += len;
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} else if (op == 2) {
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score -= q + len * e;
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i += len;
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}
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}
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return score;
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}
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#endif
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@ -0,0 +1,280 @@
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#include <string.h>
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#include "ksw2.h"
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#ifdef __SSE2__
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#include <emmintrin.h>
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#ifdef __SSE4_1__
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#include <smmintrin.h>
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#endif
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void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez)
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{
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#define __dp_code_block1 \
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z = _mm_add_epi8(_mm_load_si128(&s[t]), qe2_); \
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xt1 = _mm_load_si128(&x[t]); /* xt1 <- x[r-1][t..t+15] */ \
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tmp = _mm_srli_si128(xt1, 15); /* tmp <- x[r-1][t+15] */ \
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xt1 = _mm_or_si128(_mm_slli_si128(xt1, 1), x1_); /* xt1 <- x[r-1][t-1..t+14] */ \
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x1_ = tmp; \
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vt1 = _mm_load_si128(&v[t]); /* vt1 <- v[r-1][t..t+15] */ \
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tmp = _mm_srli_si128(vt1, 15); /* tmp <- v[r-1][t+15] */ \
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vt1 = _mm_or_si128(_mm_slli_si128(vt1, 1), v1_); /* vt1 <- v[r-1][t-1..t+14] */ \
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v1_ = tmp; \
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a = _mm_add_epi8(xt1, vt1); /* a <- x[r-1][t-1..t+14] + v[r-1][t-1..t+14] */ \
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ut = _mm_load_si128(&u[t]); /* ut <- u[t..t+15] */ \
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b = _mm_add_epi8(_mm_load_si128(&y[t]), ut); /* b <- y[r-1][t..t+15] + u[r-1][t..t+15] */
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#define __dp_code_block2 \
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z = _mm_max_epu8(z, b); /* z = max(z, b); this works because both are non-negative */ \
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_mm_store_si128(&u[t], _mm_sub_epi8(z, vt1)); /* u[r][t..t+15] <- z - v[r-1][t-1..t+14] */ \
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_mm_store_si128(&v[t], _mm_sub_epi8(z, ut)); /* v[r][t..t+15] <- z - u[r-1][t..t+15] */ \
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z = _mm_sub_epi8(z, q_); \
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a = _mm_sub_epi8(a, z); \
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b = _mm_sub_epi8(b, z);
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int r, t, qe = q + e, n_col_, *off = 0, tlen_, qlen_, last_st, last_en, wl, wr, max_sc;
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int with_cigar = !(flag&KSW_EZ_SCORE_ONLY), with_max = !(flag&KSW_EZ_GLOBAL_ONLY);
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int32_t *H = 0, H0 = 0, last_H0_t = 0;
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uint8_t *qr, *sf, *mem, *mem2 = 0;
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__m128i q_, qe2_, zero_, flag1_, flag2_, flag4_, flag32_, sc_mch_, sc_mis_, m1_;
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__m128i *u, *v, *x, *y, *s, *p = 0;
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if (m <= 0 || qlen <= 0 || tlen <= 0 || w < 0 || zdrop < 0) return;
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zero_ = _mm_set1_epi8(0);
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q_ = _mm_set1_epi8(q);
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qe2_ = _mm_set1_epi8((q + e) * 2);
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flag1_ = _mm_set1_epi8(1<<0);
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flag2_ = _mm_set1_epi8(2<<0);
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flag4_ = _mm_set1_epi8(1<<2);
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flag32_ = _mm_set1_epi8(2<<4);
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sc_mch_ = _mm_set1_epi8(mat[0]);
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sc_mis_ = _mm_set1_epi8(mat[1]);
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m1_ = _mm_set1_epi8(m - 1); // wildcard
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ez->max_q = ez->max_t = ez->mqe_t = ez->mte_q = -1;
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ez->max = 0, ez->mqe = ez->mte = KSW_NEG_INF;
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ez->n_cigar = 0;
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wl = wr = w;
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tlen_ = (tlen + 15) / 16;
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n_col_ = ((w + 1 < tlen? w + 1 : tlen) + 15) / 16 + 1;
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qlen_ = (qlen + 15) / 16;
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for (t = 1, max_sc = mat[0]; t < m * m; ++t)
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max_sc = max_sc > mat[t]? max_sc : mat[t];
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mem = (uint8_t*)kcalloc(km, tlen_ * 6 + qlen_ + 1, 16);
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u = (__m128i*)(((size_t)mem + 15) >> 4 << 4); // 16-byte aligned
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v = u + tlen_, x = v + tlen_, y = x + tlen_, s = y + tlen_, sf = (uint8_t*)(s + tlen_), qr = sf + tlen_ * 16;
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if (with_max) {
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H = (int32_t*)kmalloc(km, tlen_ * 16 * 4);
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for (t = 0; t < tlen_ * 16; ++t) H[t] = KSW_NEG_INF;
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}
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if (with_cigar) {
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mem2 = (uint8_t*)kmalloc(km, ((qlen + tlen - 1) * n_col_ + 1) * 16);
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p = (__m128i*)(((size_t)mem2 + 15) >> 4 << 4);
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off = (int*)kmalloc(km, (qlen + tlen - 1) * sizeof(int));
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}
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for (t = 0; t < qlen; ++t) qr[t] = query[qlen - 1 - t];
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memcpy(sf, target, tlen);
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for (r = 0, last_st = last_en = -1; r < qlen + tlen - 1; ++r) {
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int st = 0, en = tlen - 1, st0, en0, st_, en_;
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int8_t x1, v1;
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uint8_t *qrr = qr + (qlen - 1 - r), *u8 = (uint8_t*)u, *v8 = (uint8_t*)v;
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__m128i x1_, v1_;
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// find the boundaries
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if (st < r - qlen + 1) st = r - qlen + 1;
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if (en > r) en = r;
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if (st < (r-wr+1)>>1) st = (r-wr+1)>>1; // take the ceil
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if (en > (r+wl)>>1) en = (r+wl)>>1; // take the floor
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st0 = st, en0 = en;
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st = st / 16 * 16, en = (en + 16) / 16 * 16 - 1;
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// set boundary conditions
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if (st > 0) {
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if (st - 1 >= last_st && st - 1 <= last_en)
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x1 = ((uint8_t*)x)[st - 1], v1 = v8[st - 1]; // (r-1,s-1) calculated in the last round
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else x1 = v1 = 0; // not calculated; set to zeros
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} else x1 = 0, v1 = r? q : 0;
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if (en >= r) ((uint8_t*)y)[r] = 0, u8[r] = r? q : 0;
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// loop fission: set scores first
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if (!(flag & KSW_EZ_GENERIC_SC)) {
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for (t = st0; t <= en0; t += 16) {
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__m128i sq, st, tmp, mask;
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sq = _mm_loadu_si128((__m128i*)&sf[t]);
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st = _mm_loadu_si128((__m128i*)&qrr[t]);
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mask = _mm_or_si128(_mm_cmpeq_epi8(sq, m1_), _mm_cmpeq_epi8(st, m1_));
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tmp = _mm_cmpeq_epi8(sq, st);
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#ifdef __SSE4_1__
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tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);
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#else
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tmp = _mm_or_si128(_mm_andnot_si128(tmp, sc_mis_), _mm_and_si128(tmp, sc_mch_));
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#endif
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tmp = _mm_andnot_si128(mask, tmp);
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_mm_storeu_si128((__m128i*)((uint8_t*)s + t), tmp);
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}
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} else {
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for (t = st0; t <= en0; ++t)
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((uint8_t*)s)[t] = mat[sf[t] * m + qrr[t]];
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}
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// core loop
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x1_ = _mm_cvtsi32_si128(x1);
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v1_ = _mm_cvtsi32_si128(v1);
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st_ = st / 16, en_ = en / 16;
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if (!with_cigar) { // score only
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for (t = st_; t <= en_; ++t) {
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__m128i z, a, b, xt1, vt1, ut, tmp;
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__dp_code_block1;
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#ifdef __SSE4_1__
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z = _mm_max_epi8(z, a); // z = z > a? z : a (signed)
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#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8()
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z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_)); // z = z > 0? z : 0;
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z = _mm_max_epu8(z, a); // z = max(z, a); this works because both are non-negative
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#endif
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__dp_code_block2;
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#ifdef __SSE4_1__
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_mm_store_si128(&x[t], _mm_max_epi8(a, zero_));
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_mm_store_si128(&y[t], _mm_max_epi8(b, zero_));
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#else
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tmp = _mm_cmpgt_epi8(a, zero_);
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_mm_store_si128(&x[t], _mm_and_si128(a, tmp));
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tmp = _mm_cmpgt_epi8(b, zero_);
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_mm_store_si128(&y[t], _mm_and_si128(b, tmp));
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#endif
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}
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} else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment
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__m128i *pr = p + r * n_col_ - st_;
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off[r] = st;
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for (t = st_; t <= en_; ++t) {
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__m128i d, z, a, b, xt1, vt1, ut, tmp;
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__dp_code_block1;
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d = _mm_and_si128(_mm_cmpgt_epi8(a, z), flag1_); // d = a > z? 1 : 0
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#ifdef __SSE4_1__
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z = _mm_max_epi8(z, a); // z = z > a? z : a (signed)
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tmp = _mm_cmpgt_epi8(b, z);
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d = _mm_blendv_epi8(d, flag2_, tmp); // d = b > z? 2 : d
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#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()
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z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_)); // z = z > 0? z : 0;
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z = _mm_max_epu8(z, a); // z = max(z, a); this works because both are non-negative
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tmp = _mm_cmpgt_epi8(b, z);
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d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, flag2_)); // d = b > z? 2 : d; emulating blendv
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#endif
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__dp_code_block2;
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tmp = _mm_cmpgt_epi8(a, zero_);
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_mm_store_si128(&x[t], _mm_and_si128(tmp, a));
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d = _mm_or_si128(d, _mm_and_si128(tmp, flag4_)); // d = a > 0? 1<<2 : 0
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tmp = _mm_cmpgt_epi8(b, zero_);
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_mm_store_si128(&y[t], _mm_and_si128(tmp, b));
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d = _mm_or_si128(d, _mm_and_si128(tmp, flag32_)); // d = b > 0? 2<<4 : 0
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_mm_store_si128(&pr[t], d);
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}
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} else { // gap right-alignment
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__m128i *pr = p + r * n_col_ - st_;
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off[r] = st;
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for (t = st_; t <= en_; ++t) {
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__m128i d, z, a, b, xt1, vt1, ut, tmp;
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__dp_code_block1;
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d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), flag1_); // d = z > a? 0 : 1
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#ifdef __SSE4_1__
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||||
z = _mm_max_epi8(z, a); // z = z > a? z : a (signed)
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tmp = _mm_cmpgt_epi8(z, b);
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d = _mm_blendv_epi8(flag2_, d, tmp); // d = z > b? d : 2
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#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()
|
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z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_)); // z = z > 0? z : 0;
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||||
z = _mm_max_epu8(z, a); // z = max(z, a); this works because both are non-negative
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||||
tmp = _mm_cmpgt_epi8(z, b);
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||||
d = _mm_or_si128(_mm_andnot_si128(tmp, flag2_), _mm_and_si128(tmp, d)); // d = z > b? d : 2; emulating blendv
|
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#endif
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||||
__dp_code_block2;
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||||
tmp = _mm_cmpgt_epi8(zero_, a);
|
||||
_mm_store_si128(&x[t], _mm_andnot_si128(tmp, a));
|
||||
d = _mm_or_si128(d, _mm_andnot_si128(tmp, flag4_)); // d = 0 > a? 0 : 1<<2
|
||||
tmp = _mm_cmpgt_epi8(zero_, b);
|
||||
_mm_store_si128(&y[t], _mm_andnot_si128(tmp, b));
|
||||
d = _mm_or_si128(d, _mm_andnot_si128(tmp, flag32_)); // d = 0 > b? 0 : 2<<4
|
||||
_mm_store_si128(&pr[t], d);
|
||||
}
|
||||
}
|
||||
if (with_max) {
|
||||
int32_t max_H, max_t;
|
||||
// compute H[], max_H and max_t
|
||||
if (r > 0) {
|
||||
int32_t HH[4], tt[4], en1 = st0 + (en0 - st0) / 4 * 4, i;
|
||||
__m128i max_H_, max_t_, qe_;
|
||||
max_H = H[en0] = H[en0-1] + u8[en0] - qe, max_t = en0; // special casing last H
|
||||
max_H_ = _mm_set1_epi32(max_H);
|
||||
max_t_ = _mm_set1_epi32(max_t);
|
||||
qe_ = _mm_set1_epi32(q + e);
|
||||
for (t = st0; t < en1; t += 4) { // this implements: H[t]+=v8[t]-qe; if(H[t]>max_H) max_H=H[t],max_t=t;
|
||||
__m128i H1, tmp, t_;
|
||||
H1 = _mm_loadu_si128((__m128i*)&H[t]);
|
||||
t_ = _mm_setr_epi32(v8[t], v8[t+1], v8[t+2], v8[t+3]);
|
||||
H1 = _mm_add_epi32(H1, t_);
|
||||
H1 = _mm_sub_epi32(H1, qe_);
|
||||
_mm_storeu_si128((__m128i*)&H[t], H1);
|
||||
t_ = _mm_set1_epi32(t);
|
||||
tmp = _mm_cmpgt_epi32(H1, max_H_);
|
||||
#ifdef __SSE4_1__
|
||||
max_H_ = _mm_blendv_epi8(max_H_, H1, tmp);
|
||||
max_t_ = _mm_blendv_epi8(max_t_, t_, tmp);
|
||||
#else
|
||||
max_H_ = _mm_or_si128(_mm_and_si128(tmp, H1), _mm_andnot_si128(tmp, max_H_));
|
||||
max_t_ = _mm_or_si128(_mm_and_si128(tmp, t_), _mm_andnot_si128(tmp, max_t_));
|
||||
#endif
|
||||
}
|
||||
_mm_storeu_si128((__m128i*)HH, max_H_);
|
||||
_mm_storeu_si128((__m128i*)tt, max_t_);
|
||||
for (i = 0; i < 4; ++i)
|
||||
if (max_H < HH[i]) max_H = HH[i], max_t = tt[i] + i;
|
||||
for (; t < en0; ++t) { // for the rest of values that haven't been computed with SSE
|
||||
H[t] += (int32_t)v8[t] - qe;
|
||||
if (H[t] > max_H)
|
||||
max_H = H[t], max_t = t;
|
||||
}
|
||||
} else H[0] = v8[0] - qe - qe, max_H = H[0], max_t = 0; // special casing r==0
|
||||
// update ez
|
||||
if (en0 == tlen - 1 && H[en0] > ez->mte)
|
||||
ez->mte = H[en0], ez->mte_q = r - en;
|
||||
if (r - st0 == qlen - 1 && H[st0] > ez->mqe)
|
||||
ez->mqe = H[st0], ez->mqe_t = st0;
|
||||
if (max_H > ez->max) {
|
||||
ez->max = max_H, ez->max_t = max_t, ez->max_q = r - max_t;
|
||||
} else if (max_t >= ez->max_t && r - max_t >= ez->max_q) {
|
||||
int tl = max_t - ez->max_t, ql = (r - max_t) - ez->max_q, l;
|
||||
l = tl > ql? tl - ql : ql - tl;
|
||||
if (ez->max - max_H > zdrop + l * e)
|
||||
break;
|
||||
}
|
||||
if (r == qlen + tlen - 2 && en0 == tlen - 1)
|
||||
ez->score = H[tlen - 1];
|
||||
if (flag & KSW_EZ_DYN_BAND) { // update band width
|
||||
int lq, lt, l;
|
||||
lt = tlen - st0, lq = qlen - (r - st0);
|
||||
l = lt < lq? lt : lq;
|
||||
if (H[st0] + l * max_sc < ez->max - zdrop && wr > 1) --wr;
|
||||
lt = tlen - en0, lq = qlen - (r - en0);
|
||||
l = lt < lq? lt : lq;
|
||||
if (H[en0] + l * max_sc < ez->max - zdrop && wl > 1) --wl;
|
||||
}
|
||||
} else {
|
||||
if (r > 0) {
|
||||
if (last_H0_t >= st0 && last_H0_t <= en0)
|
||||
H0 += v8[last_H0_t] - qe;
|
||||
else ++last_H0_t, H0 += u8[last_H0_t] - qe;
|
||||
} else H0 = v8[0] - qe - qe, last_H0_t = 0;
|
||||
if (r == qlen + tlen - 2 && en0 == tlen - 1)
|
||||
ez->score = H0;
|
||||
}
|
||||
last_st = st, last_en = en;
|
||||
//for (t = st0; t <= en0; ++t) printf("(%d,%d)\t(%d,%d,%d,%d)\t%d\n", r, t, ((int8_t*)u)[t], ((int8_t*)v)[t], ((int8_t*)x)[t], ((int8_t*)y)[t], H[t]); // for debugging
|
||||
}
|
||||
kfree(km, mem);
|
||||
if (with_max) kfree(km, H);
|
||||
if (with_cigar) { // backtrack
|
||||
if (ez->score > KSW_NEG_INF) ksw_backtrack(km, 1, (uint8_t*)p, off, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
|
||||
else ksw_backtrack(km, 1, (uint8_t*)p, off, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
|
||||
kfree(km, mem2); kfree(km, off);
|
||||
}
|
||||
}
|
||||
#endif // __SSE2__
|
||||
Loading…
Reference in New Issue