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/* The MIT License
Copyright (c) 2011 by Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Modified Copyright (C) 2020 Intel Corporation, Heng Li.
Contacts: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Heng Li <hli@jimmy.harvard.edu>
*/
#include <stdlib.h>
#include <stdint.h>
#include <assert.h>
#include "ksw.h"
#include "macro.h"
extern uint64_t tprof[LIM_R][LIM_C];
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x),1)
#define UNLIKELY(x) __builtin_expect((x),0)
#else
#define LIKELY(x) (x)
#define UNLIKELY(x) (x)
#endif
/**
* Initialize the query data structure
*
* @param size Number of bytes used to store a score; valid valures are 1 or 2
* @param qlen Length of the query sequence
* @param query Query sequence
* @param m Size of the alphabet
* @param mat Scoring matrix in a one-dimension array
*
* @return Query data structure
*/
kswq_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const int8_t *mat)
{
kswq_t *q;
int slen, a, tmp, p;
size = size > 1? 2 : 1;
p = 8 * (3 - size); // # values per __m128i
slen = (qlen + p - 1) / p; // segmented length
q = (kswq_t*)malloc(sizeof(kswq_t) + 256 + 16 * slen * (m + 4)); // a single block of memory
assert(q != NULL);
q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory
q->H0 = q->qp + slen * m;
q->H1 = q->H0 + slen;
q->E = q->H1 + slen;
q->Hmax = q->E + slen;
q->slen = slen; q->qlen = qlen; q->size = size;
// compute shift
tmp = m * m;
for (a = 0, q->shift = 127, q->mdiff = 0; a < tmp; ++a) { // find the minimum and maximum score
if (mat[a] < (int8_t)q->shift) q->shift = mat[a];
if (mat[a] > (int8_t)q->mdiff) q->mdiff = mat[a];
}
q->max = q->mdiff;
q->shift = 256 - q->shift; // NB: q->shift is uint8_t
q->mdiff += q->shift; // this is the difference between the min and max scores
// An example: p=8, qlen=19, slen=3 and segmentation:
// {{0,3,6,9,12,15,18,-1},{1,4,7,10,13,16,-1,-1},{2,5,8,11,14,17,-1,-1}}
if (size == 1) {
int8_t *t = (int8_t*)q->qp;
for (a = 0; a < m; ++a) {
int i, k, nlen = slen * p;
const int8_t *ma = mat + a * m;
for (i = 0; i < slen; ++i)
for (k = i; k < nlen; k += slen) // p iterations
*t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;
}
} else {
int16_t *t = (int16_t*)q->qp;
for (a = 0; a < m; ++a) {
int i, k, nlen = slen * p;
const int8_t *ma = mat + a * m;
for (i = 0; i < slen; ++i)
for (k = i; k < nlen; k += slen) // p iterations
*t++ = (k >= qlen? 0 : ma[query[k]]);
}
}
return q;
}
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;
uint64_t *b;
__m128i zero, oe_del, e_del, oe_ins, e_ins, shift, *H0, *H1, *E, *Hmax;
kswr_t r;
#define __max_16(ret, xx) do { \
(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 8)); \
(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 4)); \
(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 2)); \
(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 1)); \
(ret) = _mm_extract_epi16((xx), 0) & 0x00ff; \
} while (0)
// initialization
r = g_defr;
minsc = (xtra & KSW_XSUBO)? xtra & 0xffff : 0x10000;
endsc = (xtra & KSW_XSTOP)? xtra & 0xffff : 0x10000;
m_b = n_b = 0; b = 0;
zero = _mm_set1_epi32(0);
oe_del = _mm_set1_epi8(_o_del + _e_del);
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);
H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
slen = q->slen;
for (i = 0; i < slen; ++i) {
_mm_store_si128(E + i, zero);
_mm_store_si128(H0 + i, zero);
_mm_store_si128(Hmax + i, zero);
}
// the core loop
for (i = 0; i < tlen; ++i) {
int j, k, cmp, imax;
__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_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian
for (j = 0; LIKELY(j < slen); ++j) {
/* SW cells are computed in the following order:
* H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
* E(i+1,j) = max{H(i,j)-q, E(i,j)-r}
* F(i,j+1) = max{H(i,j)-q, F(i,j)-r}
*/
// compute H'(i,j); note that at the beginning, h=H'(i-1,j-1)
h = _mm_adds_epu8(h, _mm_load_si128(S + j));
h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j)
e = _mm_load_si128(E + j); // e=E'(i,j)
h = _mm_max_epu8(h, e);
h = _mm_max_epu8(h, f); // h=H'(i,j)
max = _mm_max_epu8(max, h); // set max
_mm_store_si128(H1 + j, h); // save to H'(i,j)
// now compute E'(i+1,j)
e = _mm_subs_epu8(e, e_del); // e=E'(i,j) - e_del
t = _mm_subs_epu8(h, oe_del); // h=H'(i,j) - o_del - e_del
e = _mm_max_epu8(e, t); // e=E'(i+1,j)
_mm_store_si128(E + j, e); // save to E'(i+1,j)
// now compute F'(i,j+1)
f = _mm_subs_epu8(f, e_ins);
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
h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
}
// NB: we do not need to set E(i,j) as we disallow adjecent insertion and then deletion
for (k = 0; LIKELY(k < 16); ++k) { // this block mimics SWPS3; NB: H(i,j) updated in the lazy-F loop cannot exceed max
f = _mm_slli_si128(f, 1);
for (j = 0; LIKELY(j < slen); ++j) {
h = _mm_load_si128(H1 + j);
h = _mm_max_epu8(h, f); // h=H'(i,j)
_mm_store_si128(H1 + j, h);
h = _mm_subs_epu8(h, oe_ins);
f = _mm_subs_epu8(f, e_ins);
cmp = _mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(f, h), zero));
if (UNLIKELY(cmp == 0xffff)) goto end_loop16;
}
}
end_loop16:
__max_16(imax, max); // imax is the maximum number in max
if (imax >= minsc) { // write the b array; this condition adds branching unfornately
if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) { // then append
if (n_b == m_b) {
m_b = m_b? m_b<<1 : 8;
b = (uint64_t*) realloc (b, 8 * m_b);
}
b[n_b++] = (uint64_t)imax<<32 | i;
} else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
}
if (imax > gmax) {
gmax = imax; te = i; // te is the end position on the target
for (j = 0; LIKELY(j < slen); ++j) // keep the H1 vector
_mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
if (gmax + q->shift >= 255 || gmax >= endsc) break;
}
S = H1; H1 = H0; H0 = S; // swap H0 and H1
}
r.score = gmax + q->shift < 255? gmax : 255;
r.te = te;
if (r.score != 255) { // get a->qe, the end of query match; find the 2nd best score
int max = -1, tmp, low, high, qlen = slen * 16;
uint8_t *t = (uint8_t*) Hmax;
for (i = 0; i < qlen; ++i, ++t)
if ((int)*t > max) max = *t, r.qe = i / 16 + i % 16 * slen;
else if ((int)*t == max && (tmp = i / 16 + i % 16 * slen) < r.qe) r.qe = tmp;
//printf("%d,%d\n", max, gmax);
if (b) {
i = (r.score + q->max - 1) / q->max;
low = te - i; high = te + i;
for (i = 0; i < n_b; ++i) {
int e = (int32_t)b[i];
if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
r.score2 = b[i]>>32, r.te2 = e;
}
}
}
free(b);
return r;
}
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;
uint64_t *b;
__m128i zero, oe_del, e_del, oe_ins, e_ins, *H0, *H1, *E, *Hmax;
kswr_t r;
#define __max_8(ret, xx) do { \
(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 8)); \
(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 4)); \
(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 2)); \
(ret) = _mm_extract_epi16((xx), 0); \
} while (0)
// initialization
r = g_defr;
minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;
endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
m_b = n_b = 0; b = 0;
zero = _mm_set1_epi32(0);
oe_del = _mm_set1_epi16(_o_del + _e_del);
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;
slen = q->slen;
for (i = 0; i < slen; ++i) {
_mm_store_si128(E + i, zero);
_mm_store_si128(H0 + i, zero);
_mm_store_si128(Hmax + i, zero);
}
// the core loop
for (i = 0; i < tlen; ++i) {
int j, k, imax;
__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_slli_si128(h, 2);
for (j = 0; LIKELY(j < slen); ++j) {
h = _mm_adds_epi16(h, *S++);
e = _mm_load_si128(E + j);
h = _mm_max_epi16(h, e);
h = _mm_max_epi16(h, f);
max = _mm_max_epi16(max, h);
_mm_store_si128(H1 + j, h);
e = _mm_subs_epu16(e, e_del);
t = _mm_subs_epu16(h, oe_del);
e = _mm_max_epi16(e, t);
_mm_store_si128(E + j, e);
f = _mm_subs_epu16(f, e_ins);
t = _mm_subs_epu16(h, oe_ins);
f = _mm_max_epi16(f, t);
h = _mm_load_si128(H0 + j);
}
for (k = 0; LIKELY(k < 16); ++k) {
f = _mm_slli_si128(f, 2);
for (j = 0; LIKELY(j < slen); ++j) {
h = _mm_load_si128(H1 + j);
h = _mm_max_epi16(h, f);
_mm_store_si128(H1 + j, h);
h = _mm_subs_epu16(h, oe_ins);
f = _mm_subs_epu16(f, e_ins);
if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
}
}
end_loop8:
__max_8(imax, max);
if (imax >= minsc) {
if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) {
if (n_b == m_b) {
m_b = m_b? m_b<<1 : 8;
b = (uint64_t*)realloc(b, 8 * m_b);
}
b[n_b++] = (uint64_t)imax<<32 | i;
} else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
}
if (imax > gmax) {
gmax = imax; te = i;
for (j = 0; LIKELY(j < slen); ++j)
_mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
if (gmax >= endsc) break;
}
S = H1; H1 = H0; H0 = S;
}
r.score = gmax; r.te = te;
{
int max = -1, tmp, low, high, qlen = slen * 8;
uint16_t *t = (uint16_t*)Hmax;
for (i = 0, r.qe = -1; i < qlen; ++i, ++t)
if ((int)*t > max) max = *t, r.qe = i / 8 + i % 8 * slen;
else if ((int)*t == max && (tmp = i / 8 + i % 8 * slen) < r.qe) r.qe = tmp;
if (b) {
i = (r.score + q->max - 1) / q->max;
low = te - i; high = te + i;
for (i = 0; i < n_b; ++i) {
int e = (int32_t)b[i];
if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
r.score2 = b[i]>>32, r.te2 = e;
}
}
}
free(b);
return r;
}
static inline void revseq(int l, uint8_t *s)
{
int i, t;
for (i = 0; i < l>>1; ++i)
t = s[i], s[i] = s[l - 1 - i], s[l - 1 - i] = t;
}
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 tid = omp_get_thread_num();
int size;
kswq_t *q;
kswr_t r, rr;
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(2, qlen, query, m, mat); //test
if (qry && *qry == 0) *qry = q;
func = q->size == 2? ksw_i16 : ksw_u8;
size = q->size;
r = func(q, tlen, target, o_del, e_del, o_ins, e_ins, xtra);
if (qry == 0) free(q);
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
q = ksw_qinit(size, r.qe + 1, query, m, mat);
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);
free(q);
if (r.score == rr.score) {
r.tb = r.te - rr.te, r.qb = r.qe - rr.qe;
}
return r;
}
kswr_t ksw_align2_orig_bak(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 tid = omp_get_thread_num();
int size;
kswq_t *q;
kswr_t r, rr;
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);
if (qry && *qry == 0) *qry = q;
func = q->size == 2? ksw_i16 : ksw_u8;
size = q->size;
// uint64_t tim = __rdtsc();
r = func(q, tlen, target, o_del, e_del, o_ins, e_ins, xtra);
// tprof[ALIGN1][tid] += __rdtsc() - tim;
if (qry == 0) free(q);
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
q = ksw_qinit(size, r.qe + 1, query, m, mat);
// tim = __rdtsc();
rr = func(q, tlen, target, o_del, e_del, o_ins, e_ins, KSW_XSTOP | r.score);
// tprof[ALIGN1][tid] += __rdtsc() - tim;
revseq(r.qe + 1, query); revseq(r.te + 1, target);
free(q);
if (r.score == rr.score)
r.tb = r.te - rr.te, r.qb = r.qe - rr.qe;
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 ***
********************/
typedef struct {
int32_t h, e;
} eh_t;
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)
{
eh_t *eh; // score array
int8_t *qp; // query profile
int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
assert(h0 > 0);
// allocate memory
qp = (int8_t *) malloc(qlen * m);
assert(qp != NULL);
eh = (eh_t *) calloc(qlen + 1, 8);
assert(eh != NULL);
// generate the query profile
for (k = i = 0; k < m; ++k) {
const int8_t *p = &mat[k * m];
for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];
}
// fill the first row
eh[0].h = h0; eh[1].h = h0 > oe_ins? h0 - oe_ins : 0;
for (j = 2; j <= qlen && eh[j-1].h > e_ins; ++j)
eh[j].h = eh[j-1].h - e_ins;
// adjust $w if it is too large
k = m * m;
for (i = 0, max = 0; i < k; ++i) // get the max score
max = max > mat[i]? max : mat[i];
max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
max_ins = max_ins > 1? max_ins : 1;
w = w < max_ins? w : max_ins;
max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
max_del = max_del > 1? max_del : 1;
w = w < max_del? w : max_del; // TODO: is this necessary?
// DP loop
max = h0, max_i = max_j = -1; max_ie = -1, gscore = -1;
max_off = 0;
beg = 0, end = qlen;
for (i = 0; LIKELY(i < tlen); ++i) {
int t, f = 0, h1, m = 0, mj = -1;
int8_t *q = &qp[target[i] * qlen];
// apply the band and the constraint (if provided)
if (beg < i - w) beg = i - w;
if (end > i + w + 1) end = i + w + 1;
if (end > qlen) end = qlen;
// compute the first column
if (beg == 0) {
h1 = h0 - (o_del + e_del * (i + 1));
if (h1 < 0) h1 = 0;
} else h1 = 0;
for (j = beg; LIKELY(j < end); ++j) {
// At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
// Similar to SSE2-SW, cells are computed in the following order:
// H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
// E(i+1,j) = max{H(i,j)-gapo, E(i,j)} - gape
// F(i,j+1) = max{H(i,j)-gapo, F(i,j)} - gape
eh_t *p = &eh[j];
int h, M = p->h, e = p->e; // get H(i-1,j-1) and E(i-1,j)
p->h = h1; // set H(i,j-1) for the next row
M = M? M + q[j] : 0;// separating H and M to disallow a cigar like "100M3I3D20M"
h = M > e? M : e; // e and f are guaranteed to be non-negative, so h>=0 even if M<0
h = h > f? h : f;
h1 = h; // save H(i,j) to h1 for the next column
mj = m > h? mj : j; // record the position where max score is achieved
m = m > h? m : h; // m is stored at eh[mj+1]
t = M - oe_del;
t = t > 0? t : 0;
e -= e_del;
e = e > t? e : t; // computed E(i+1,j)
p->e = e; // save E(i+1,j) for the next row
t = M - oe_ins;
t = t > 0? t : 0;
f -= e_ins;
f = f > t? f : t; // computed F(i,j+1)
}
eh[end].h = h1; eh[end].e = 0;
if (j == qlen) {
max_ie = gscore > h1? max_ie : i;
gscore = gscore > h1? gscore : h1;
}
if (m == 0) break;
if (m > max) {
max = m, max_i = i, max_j = mj;
max_off = max_off > abs(mj - i)? max_off : abs(mj - i);
} else if (zdrop > 0) {
if (i - max_i > mj - max_j) {
if (max - m - ((i - max_i) - (mj - max_j)) * e_del > zdrop) break;
} else {
if (max - m - ((mj - max_j) - (i - max_i)) * e_ins > zdrop) break;
}
}
// update beg and end for the next round
for (j = beg; LIKELY(j < end) && eh[j].h == 0 && eh[j].e == 0; ++j);
beg = j;
for (j = end; LIKELY(j >= beg) && eh[j].h == 0 && eh[j].e == 0; --j);
end = j + 2 < qlen? j + 2 : qlen;
//beg = 0; end = qlen; // uncomment this line for debugging
}
free(eh); free(qp);
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;
}
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)
{
return ksw_extend2(qlen, query, tlen, target, m, mat, gapo, gape, gapo, gape, w, end_bonus, zdrop, h0, qle, tle, gtle, gscore, max_off);
}
/********************
* Global alignment *
********************/
#define MINUS_INF -0x40000000
static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len)
{
if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
if (*n_cigar == *m_cigar) {
*m_cigar = *m_cigar? (*m_cigar)<<1 : 4;
cigar = (uint32_t *) realloc(cigar, (*m_cigar) << 2);
}
cigar[(*n_cigar)++] = len<<4 | op;
} else cigar[(*n_cigar)-1] += len<<4;
return 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_)
{
eh_t *eh;
int8_t *qp; // query profile
int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, score, n_col;
uint8_t *z; // backtrack matrix; in each cell: f<<4|e<<2|h; in principle, we can halve the memory, but backtrack will be a little more complex
if (n_cigar_) *n_cigar_ = 0;
// allocate memory
n_col = qlen < 2*w+1? qlen : 2*w+1; // maximum #columns of the backtrack matrix
if (n_cigar_ && cigar_) {
z = (uint8_t *) malloc((long)n_col * tlen);
assert(z != NULL);
}
else {
z = 0;
}
qp = (int8_t *) malloc(qlen * m);
assert(qp != NULL);
eh = (eh_t *) calloc(qlen + 1, 8);
assert(eh != NULL);
// generate the query profile
for (k = i = 0; k < m; ++k) {
const int8_t *p = &mat[k * m];
for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];
}
// fill the first row
eh[0].h = 0; eh[0].e = MINUS_INF;
for (j = 1; j <= qlen && j <= w; ++j)
eh[j].h = -(o_ins + e_ins * j), eh[j].e = MINUS_INF;
for (; j <= qlen; ++j) eh[j].h = eh[j].e = MINUS_INF; // everything is -inf outside the band
// DP loop
for (i = 0; LIKELY(i < tlen); ++i) { // target sequence is in the outer loop
int32_t f = MINUS_INF, h1, beg, end, t;
int8_t *q = &qp[target[i] * qlen];
beg = i > w? i - w : 0;
end = i + w + 1 < qlen? i + w + 1 : qlen; // only loop through [beg,end) of the query sequence
h1 = beg == 0? -(o_del + e_del * (i + 1)) : MINUS_INF;
if (n_cigar_ && cigar_) {
uint8_t *zi = &z[(long)i * n_col];
for (j = beg; LIKELY(j < end); ++j) {
// At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
// Cells are computed in the following order:
// M(i,j) = H(i-1,j-1) + S(i,j)
// H(i,j) = max{M(i,j), E(i,j), F(i,j)}
// E(i+1,j) = max{M(i,j)-gapo, E(i,j)} - gape
// F(i,j+1) = max{M(i,j)-gapo, F(i,j)} - gape
// We have to separate M(i,j); otherwise the direction may not be recorded correctly.
// However, a CIGAR like "10M3I3D10M" allowed by local() is disallowed by global().
// Such a CIGAR may occur, in theory, if mismatch_penalty > 2*gap_ext_penalty + 2*gap_open_penalty/k.
// In practice, this should happen very rarely given a reasonable scoring system.
eh_t *p = &eh[j];
int32_t h, m = p->h, e = p->e;
uint8_t d; // direction
p->h = h1;
m += q[j];
d = m >= e? 0 : 1;
h = m >= e? m : e;
d = h >= f? d : 2;
h = h >= f? h : f;
h1 = h;
t = m - oe_del;
e -= e_del;
d |= e > t? 1<<2 : 0;
e = e > t? e : t;
p->e = e;
t = m - oe_ins;
f -= e_ins;
d |= f > t? 2<<4 : 0; // if we want to halve the memory, use one bit only, instead of two
f = f > t? f : t;
zi[j - beg] = d; // z[i,j] keeps h for the current cell and e/f for the next cell
}
} else {
for (j = beg; LIKELY(j < end); ++j) {
eh_t *p = &eh[j];
int32_t h, m = p->h, e = p->e;
p->h = h1;
m += q[j];
h = m >= e? m : e;
h = h >= f? h : f;
h1 = h;
t = m - oe_del;
e -= e_del;
e = e > t? e : t;
p->e = e;
t = m - oe_ins;
f -= e_ins;
f = f > t? f : t;
}
}
eh[end].h = h1; eh[end].e = MINUS_INF;
}
score = eh[qlen].h;
if (n_cigar_ && cigar_) { // backtrack
int n_cigar = 0, m_cigar = 0, which = 0;
uint32_t *cigar = 0, tmp;
i = tlen - 1; k = (i + w + 1 < qlen? i + w + 1 : qlen) - 1; // (i,k) points to the last cell
while (i >= 0 && k >= 0) {
which = z[(long)i * n_col + (k - (i > w? i - w : 0))] >> (which<<1) & 3;
if (which == 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k;
else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i;
else cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k;
}
if (i >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1);
if (k >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1);
for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
*n_cigar_ = n_cigar, *cigar_ = cigar;
}
free(eh); free(qp); free(z);
return score;
}
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_)
{
return ksw_global2(qlen, query, tlen, target, m, mat, gapo, gape, gapo, gape, w, n_cigar_, cigar_);
}
/*******************************************
* Main function (not compiled by default) *
*******************************************/
#ifdef _KSW_MAIN
#include <unistd.h>
#include <stdio.h>
#include <zlib.h>
#include "kseq.h"
KSEQ_INIT(gzFile, err_gzread)
unsigned char seq_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
int main(int argc, char *argv[])
{
int c, sa = 1, sb = 3, i, j, k, forward_only = 0, max_rseq = 0;
int8_t mat[25];
int gapo = 5, gape = 2, minsc = 0, xtra = KSW_XSTART;
uint8_t *rseq = 0;
gzFile fpt, fpq;
kseq_t *kst, *ksq;
// parse command line
while ((c = getopt(argc, argv, "a:b:q:r:ft:1")) >= 0) {
switch (c) {
case 'a': sa = atoi(optarg); break;
case 'b': sb = atoi(optarg); break;
case 'q': gapo = atoi(optarg); break;
case 'r': gape = atoi(optarg); break;
case 't': minsc = atoi(optarg); break;
case 'f': forward_only = 1; break;
case '1': xtra |= KSW_XBYTE; break;
}
}
if (optind + 2 > argc) {
fprintf(stderr, "Usage: ksw [-1] [-f] [-a%d] [-b%d] [-q%d] [-r%d] [-t%d] <target.fa> <query.fa>\n", sa, sb, gapo, gape, minsc);
return 1;
}
if (minsc > 0xffff) minsc = 0xffff;
xtra |= KSW_XSUBO | minsc;
// initialize scoring matrix
for (i = k = 0; i < 4; ++i) {
for (j = 0; j < 4; ++j)
mat[k++] = i == j? sa : -sb;
mat[k++] = 0; // ambiguous base
}
for (j = 0; j < 5; ++j) mat[k++] = 0;
// open file
fpt = xzopen(argv[optind], "r"); kst = kseq_init(fpt);
fpq = xzopen(argv[optind+1], "r"); ksq = kseq_init(fpq);
// all-pair alignment
while (kseq_read(ksq) > 0) {
kswq_t *q[2] = {0, 0};
kswr_t r;
for (i = 0; i < (int)ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]];
if (!forward_only) { // reverse
if ((int)ksq->seq.m > max_rseq) {
max_rseq = ksq->seq.m;
rseq = (uint8_t*)realloc(rseq, max_rseq);
}
for (i = 0, j = ksq->seq.l - 1; i < (int)ksq->seq.l; ++i, --j)
rseq[j] = ksq->seq.s[i] == 4? 4 : 3 - ksq->seq.s[i];
}
gzrewind(fpt); kseq_rewind(kst);
while (kseq_read(kst) > 0) {
for (i = 0; i < (int)kst->seq.l; ++i) kst->seq.s[i] = seq_nt4_table[(int)kst->seq.s[i]];
r = ksw_align(ksq->seq.l, (uint8_t*)ksq->seq.s, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[0]);
if (r.score >= minsc)
err_printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, r.qb, r.qe+1, r.score, r.score2, r.te2);
if (rseq) {
r = ksw_align(ksq->seq.l, rseq, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[1]);
if (r.score >= minsc)
err_printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, (int)ksq->seq.l - r.qb, (int)ksq->seq.l - 1 - r.qe, r.score, r.score2, r.te2);
}
}
free(q[0]); free(q[1]);
}
free(rseq);
kseq_destroy(kst); err_gzclose(fpt);
kseq_destroy(ksq); err_gzclose(fpq);
return 0;
}
#endif
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