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dev-448: different ins/del penalties

This commit is contained in:
Heng Li 2014-03-28 10:54:23 -04:00
parent 8f9aeef4ec
commit 0c783399e8
3 changed files with 44 additions and 30 deletions
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69
ksw.c
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@ -107,11 +107,11 @@ kswq_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const int8_t
return q; return q;
} }
kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape, int xtra) // the first gap costs -(_o+_e) kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int _e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e)
{ {
int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc; int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;
uint64_t *b; uint64_t *b;
__m128i zero, gapoe, gape, shift, *H0, *H1, *E, *Hmax; __m128i zero, oe_del, e_del, oe_ins, e_ins, shift, *H0, *H1, *E, *Hmax;
kswr_t r; kswr_t r;
#define __max_16(ret, xx) do { \ #define __max_16(ret, xx) do { \
@ -128,8 +128,10 @@ kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape,
endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000; endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
m_b = n_b = 0; b = 0; m_b = n_b = 0; b = 0;
zero = _mm_set1_epi32(0); zero = _mm_set1_epi32(0);
gapoe = _mm_set1_epi8(_gapo + _gape); oe_del = _mm_set1_epi8(_o_del + _e_del);
gape = _mm_set1_epi8(_gape); e_del = _mm_set1_epi8(_e_del);
oe_ins = _mm_set1_epi8(_o_ins + _e_ins);
e_ins = _mm_set1_epi8(_e_ins);
shift = _mm_set1_epi8(q->shift); shift = _mm_set1_epi8(q->shift);
H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax; H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
slen = q->slen; slen = q->slen;
@ -141,7 +143,7 @@ kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape,
// the core loop // the core loop
for (i = 0; i < tlen; ++i) { for (i = 0; i < tlen; ++i) {
int j, k, cmp, imax; int j, k, cmp, imax;
__m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector __m128i e, h, t, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian
for (j = 0; LIKELY(j < slen); ++j) { for (j = 0; LIKELY(j < slen); ++j) {
@ -159,13 +161,14 @@ kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape,
max = _mm_max_epu8(max, h); // set max max = _mm_max_epu8(max, h); // set max
_mm_store_si128(H1 + j, h); // save to H'(i,j) _mm_store_si128(H1 + j, h); // save to H'(i,j)
// now compute E'(i+1,j) // now compute E'(i+1,j)
h = _mm_subs_epu8(h, gapoe); // h=H'(i,j)-gapo e = _mm_subs_epu8(e, e_del); // e=E'(i,j) - e_del
e = _mm_subs_epu8(e, gape); // e=E'(i,j)-gape t = _mm_subs_epu8(h, oe_del); // h=H'(i,j) - o_del - e_del
e = _mm_max_epu8(e, h); // e=E'(i+1,j) e = _mm_max_epu8(e, t); // e=E'(i+1,j)
_mm_store_si128(E + j, e); // save to E'(i+1,j) _mm_store_si128(E + j, e); // save to E'(i+1,j)
// now compute F'(i,j+1) // now compute F'(i,j+1)
f = _mm_subs_epu8(f, gape); f = _mm_subs_epu8(f, e_ins);
f = _mm_max_epu8(f, h); t = _mm_subs_epu8(h, oe_ins); // h=H'(i,j) - o_ins - e_ins
f = _mm_max_epu8(f, t);
// get H'(i-1,j) and prepare for the next j // get H'(i-1,j) and prepare for the next j
h = _mm_load_si128(H0 + j); // h=H'(i-1,j) h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
} }
@ -176,8 +179,8 @@ kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape,
h = _mm_load_si128(H1 + j); h = _mm_load_si128(H1 + j);
h = _mm_max_epu8(h, f); // h=H'(i,j) h = _mm_max_epu8(h, f); // h=H'(i,j)
_mm_store_si128(H1 + j, h); _mm_store_si128(H1 + j, h);
h = _mm_subs_epu8(h, gapoe); h = _mm_subs_epu8(h, oe_ins);
f = _mm_subs_epu8(f, gape); f = _mm_subs_epu8(f, e_ins);
cmp = _mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(f, h), zero)); cmp = _mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(f, h), zero));
if (UNLIKELY(cmp == 0xffff)) goto end_loop16; if (UNLIKELY(cmp == 0xffff)) goto end_loop16;
} }
@ -225,11 +228,11 @@ end_loop16:
return r; return r;
} }
kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape, int xtra) // the first gap costs -(_o+_e) kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int _e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e)
{ {
int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc; int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;
uint64_t *b; uint64_t *b;
__m128i zero, gapoe, gape, *H0, *H1, *E, *Hmax; __m128i zero, oe_del, e_del, oe_ins, e_ins, *H0, *H1, *E, *Hmax;
kswr_t r; kswr_t r;
#define __max_8(ret, xx) do { \ #define __max_8(ret, xx) do { \
@ -245,8 +248,10 @@ kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape,
endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000; endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
m_b = n_b = 0; b = 0; m_b = n_b = 0; b = 0;
zero = _mm_set1_epi32(0); zero = _mm_set1_epi32(0);
gapoe = _mm_set1_epi16(_gapo + _gape); oe_del = _mm_set1_epi16(_o_del + _e_del);
gape = _mm_set1_epi16(_gape); e_del = _mm_set1_epi16(_e_del);
oe_ins = _mm_set1_epi16(_o_ins + _e_ins);
e_ins = _mm_set1_epi16(_e_ins);
H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax; H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
slen = q->slen; slen = q->slen;
for (i = 0; i < slen; ++i) { for (i = 0; i < slen; ++i) {
@ -257,7 +262,7 @@ kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape,
// the core loop // the core loop
for (i = 0; i < tlen; ++i) { for (i = 0; i < tlen; ++i) {
int j, k, imax; int j, k, imax;
__m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector __m128i e, t, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
h = _mm_slli_si128(h, 2); h = _mm_slli_si128(h, 2);
for (j = 0; LIKELY(j < slen); ++j) { for (j = 0; LIKELY(j < slen); ++j) {
@ -267,12 +272,13 @@ kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape,
h = _mm_max_epi16(h, f); h = _mm_max_epi16(h, f);
max = _mm_max_epi16(max, h); max = _mm_max_epi16(max, h);
_mm_store_si128(H1 + j, h); _mm_store_si128(H1 + j, h);
h = _mm_subs_epu16(h, gapoe); e = _mm_subs_epu16(e, e_del);
e = _mm_subs_epu16(e, gape); t = _mm_subs_epu16(h, oe_del);
e = _mm_max_epi16(e, h); e = _mm_max_epi16(e, t);
_mm_store_si128(E + j, e); _mm_store_si128(E + j, e);
f = _mm_subs_epu16(f, gape); f = _mm_subs_epu16(f, e_ins);
f = _mm_max_epi16(f, h); t = _mm_subs_epu16(h, oe_ins);
f = _mm_max_epi16(f, t);
h = _mm_load_si128(H0 + j); h = _mm_load_si128(H0 + j);
} }
for (k = 0; LIKELY(k < 16); ++k) { for (k = 0; LIKELY(k < 16); ++k) {
@ -281,8 +287,8 @@ kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape,
h = _mm_load_si128(H1 + j); h = _mm_load_si128(H1 + j);
h = _mm_max_epi16(h, f); h = _mm_max_epi16(h, f);
_mm_store_si128(H1 + j, h); _mm_store_si128(H1 + j, h);
h = _mm_subs_epu16(h, gapoe); h = _mm_subs_epu16(h, oe_ins);
f = _mm_subs_epu16(f, gape); f = _mm_subs_epu16(f, e_ins);
if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8; if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
} }
} }
@ -326,30 +332,30 @@ end_loop8:
return r; return r;
} }
static void revseq(int l, uint8_t *s) static inline void revseq(int l, uint8_t *s)
{ {
int i, t; int i, t;
for (i = 0; i < l>>1; ++i) for (i = 0; i < l>>1; ++i)
t = s[i], s[i] = s[l - 1 - i], s[l - 1 - i] = t; t = s[i], s[i] = s[l - 1 - i], s[l - 1 - i] = t;
} }
kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry) kswr_t ksw_align2(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int xtra, kswq_t **qry)
{ {
int size; int size;
kswq_t *q; kswq_t *q;
kswr_t r, rr; kswr_t r, rr;
kswr_t (*func)(kswq_t*, int, const uint8_t*, int, int, int); kswr_t (*func)(kswq_t*, int, const uint8_t*, int, int, int, int, int);
q = (qry && *qry)? *qry : ksw_qinit((xtra&KSW_XBYTE)? 1 : 2, qlen, query, m, mat); q = (qry && *qry)? *qry : ksw_qinit((xtra&KSW_XBYTE)? 1 : 2, qlen, query, m, mat);
if (qry && *qry == 0) *qry = q; if (qry && *qry == 0) *qry = q;
func = q->size == 2? ksw_i16 : ksw_u8; func = q->size == 2? ksw_i16 : ksw_u8;
size = q->size; size = q->size;
r = func(q, tlen, target, gapo, gape, xtra); r = func(q, tlen, target, o_del, e_del, o_ins, e_ins, xtra);
if (qry == 0) free(q); if (qry == 0) free(q);
if ((xtra&KSW_XSTART) == 0 || ((xtra&KSW_XSUBO) && r.score < (xtra&0xffff))) return r; if ((xtra&KSW_XSTART) == 0 || ((xtra&KSW_XSUBO) && r.score < (xtra&0xffff))) return r;
revseq(r.qe + 1, query); revseq(r.te + 1, target); // +1 because qe/te points to the exact end, not the position after the end revseq(r.qe + 1, query); revseq(r.te + 1, target); // +1 because qe/te points to the exact end, not the position after the end
q = ksw_qinit(size, r.qe + 1, query, m, mat); q = ksw_qinit(size, r.qe + 1, query, m, mat);
rr = func(q, tlen, target, gapo, gape, KSW_XSTOP | r.score); rr = func(q, tlen, target, o_del, e_del, o_ins, e_ins, KSW_XSTOP | r.score);
revseq(r.qe + 1, query); revseq(r.te + 1, target); revseq(r.qe + 1, query); revseq(r.te + 1, target);
free(q); free(q);
if (r.score == rr.score) if (r.score == rr.score)
@ -357,6 +363,11 @@ kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, con
return r; return r;
} }
kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry)
{
return ksw_align2(qlen, query, tlen, target, m, mat, gapo, gape, gapo, gape, xtra, qry);
}
/******************** /********************
*** SW extension *** *** SW extension ***
********************/ ********************/

3
ksw.h
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@ -61,6 +61,7 @@ extern "C" {
* query profile will be deallocated in ksw_align(). * query profile will be deallocated in ksw_align().
*/ */
kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry); kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry);
kswr_t ksw_align2(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int xtra, kswq_t **qry);
/** /**
* Banded global alignment * Banded global alignment
@ -80,6 +81,7 @@ extern "C" {
* @return score of the alignment * @return score of the alignment
*/ */
int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar, uint32_t **cigar); int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar, uint32_t **cigar);
int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int *n_cigar, uint32_t **cigar);
/** /**
* Extend alignment * Extend alignment
@ -103,6 +105,7 @@ extern "C" {
* @return best semi-local alignment score * @return best semi-local alignment score
*/ */
int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int end_bonus, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off); int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int end_bonus, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off);
int ksw_extend2(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off);
#ifdef __cplusplus #ifdef __cplusplus
} }

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.7+dev-r442" #define PACKAGE_VERSION "0.7.7+dev-r448"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);