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r727: extend seeds with SW

This commit is contained in:
Heng Li 2014-04-24 14:28:40 -04:00
parent b92bbb47e5
commit df65893fb5
3 changed files with 117 additions and 104 deletions
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134
bwamem.c
View File

@ -143,6 +143,7 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, int len, co
typedef struct {
int64_t rbeg;
int32_t qbeg, len;
int score;
} mem_seed_t; // unaligned memory
typedef struct {
@ -214,7 +215,7 @@ void mem_print_chain(const bntseq_t *bns, mem_chain_v *chn)
int is_rev;
pos = bns_depos(bns, p->seeds[j].rbeg, &is_rev);
if (is_rev) pos -= p->seeds[j].len - 1;
err_printf("\t%d;%d,%ld(%s:%c%ld)", p->seeds[j].len, p->seeds[j].qbeg, (long)p->seeds[j].rbeg, bns->anns[p->rid].name, "+-"[is_rev], (long)(pos - bns->anns[p->rid].offset) + 1);
err_printf("\t%d;%d;%d,%ld(%s:%c%ld)", p->seeds[j].score, p->seeds[j].len, p->seeds[j].qbeg, (long)p->seeds[j].rbeg, bns->anns[p->rid].name, "+-"[is_rev], (long)(pos - bns->anns[p->rid].offset) + 1);
}
err_putchar('\n');
}
@ -246,6 +247,7 @@ mem_chain_v mem_chain(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
s.rbeg = tmp.pos = bwt_sa(bwt, p->x[0] + k); // this is the base coordinate in the forward-reverse reference
s.qbeg = p->info>>32;
s.len = slen;
s.score = 0;
rid = bns_intv2rid(bns, s.rbeg, s.rbeg + s.len);
if (rid < 0) continue; // bridging multiple reference sequences or the forward-reverse boundary
if (kb_size(tree)) {
@ -366,6 +368,9 @@ int mem_patch_reg(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
double r;
if (bns == 0 || pac == 0 || query == 0) return 0;
assert(a->rid == b->rid && a->rb <= b->rb);
if (bwa_verbose >= 5)
printf("* test hit merge between [%d,%d)<=>[%ld,%ld) and [%d,%d)<=>[%ld,%ld), @ %s\n",
a->qb, a->qe, (long)a->rb, (long)a->re, b->qb, b->qe, (long)b->rb, (long)b->re, bns->anns[a->rid].name);
if (a->qb >= b->qb || a->qe >= b->qe || a->re >= b->re) return 0; // not colinear
w = (a->re - b->rb) - (a->qe - b->qb); // required bandwidth
w = w > 0? w : -w; // l = abs(l)
@ -374,7 +379,7 @@ int mem_patch_reg(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
if (bwa_verbose >= 4)
printf("* potential hit merge between [%d,%d)<=>[%ld,%ld) and [%d,%d)<=>[%ld,%ld), @ %s; w=%d, r=%.4g\n",
a->qb, a->qe, (long)a->rb, (long)a->re, b->qb, b->qe, (long)b->rb, (long)b->re, bns->anns[a->rid].name, w, r);
if (w > opt->w) return 0; // the bandwidth is too large
if (w > opt->w<<1) return 0; // the bandwidth is too large
if (r >= PATCH_MAX_R_BW) return 0; // relative bandwidth is too large
// global alignment
w += a->w + b->w;
@ -481,6 +486,56 @@ void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t i
free(z.a);
}
/*********************************
* Test if a seed is good enough *
*********************************/
#define MEM_SHORT_EXT 50
#define MEM_SHORT_LEN 200
#define MEM_HSP_COEF 1.1
int mem_seed_sw(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const uint8_t *query, const mem_seed_t *s)
{
int qb, qe, rid;
int64_t rb, re, mid, l_pac = bns->l_pac;
uint8_t *rseq = 0;
kswr_t x;
qb = s->qbeg, qe = s->qbeg + s->len;
rb = s->rbeg, re = s->rbeg + s->len;
mid = (rb + re) >> 1;
qb -= MEM_SHORT_EXT; qb = qb > 0? qb : 0;
qe += MEM_SHORT_EXT; qe = qe < l_query? qe : l_query;
rb -= MEM_SHORT_EXT; rb = rb > 0? rb : 0;
re += MEM_SHORT_EXT; re = re < l_pac<<1? re : l_pac<<1;
if (rb < l_pac && l_pac < re) {
if (mid < l_pac) re = l_pac;
else rb = l_pac;
}
if (qe - qb >= MEM_SHORT_LEN || re - rb >= MEM_SHORT_LEN) return -1;
rseq = bns_fetch_seq(bns, pac, &rb, mid, &re, &rid);
x = ksw_align2(qe - qb, (uint8_t*)query + qb, re - rb, rseq, 5, opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, KSW_XSTART, 0);
free(rseq);
return x.score;
}
void mem_flt_chained_seeds(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const uint8_t *query, int n_chn, mem_chain_t *a)
{
int i, j, k, min_HSP_score = (int)(opt->min_chain_weight * opt->a * MEM_HSP_COEF + .499);
for (i = 0; i < n_chn; ++i) {
mem_chain_t *c = &a[i];
for (j = k = 0; j < c->n; ++j) {
mem_seed_t *s = &c->seeds[j];
s->score = mem_seed_sw(opt, bns, pac, l_query, query, s);
if (s->score < 0 || s->score >= min_HSP_score)
c->seeds[k++] = *s;
}
c->n = k;
}
}
/****************************************
* Construct the alignment from a chain *
****************************************/
@ -495,70 +550,6 @@ void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t i
* mem_chain2aln_short() is almost never used for short-read alignment.
*/
#define MEM_SHORT_EXT 50
#define MEM_SHORT_LEN 200
#define MEM_HSP_COEF 1.5
#define MAX_BAND_TRY 2
/* mem_test_chain_sw() uses SSE2-SW to align a short chain with 50bp added to
* each end of the chain. If the SW score is below min_HSP_score, it will
* return 0, informing the caller to discard the chain. This heuristic is
* somewhat similar to BLAST which drops a seed hit if ungapped extension is
* below a certain score (true for old BLAST; don't know how BLAST+ works).
*
* For PacBio data, we need to set high matching score and low gap penalties;
* otherwise we are likely to get fragmented alignments. However, with such
* settings, we can often extend most random seed hits to the end. These
* extensions are wasteful and time consuming. By testing the chain with SW,
* we can discard bad chains before performing the expensive extension.
*
* Although probably it is not a bad idea to use this function for
* low-divergence sequences, more testing is needed. For now, I only recommend
* to use mem_test_chain_sw() for PacBio data. It is disabled by default.
*/
int mem_test_chain_sw(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c)
{
int i, qb, qe, rid;
int min_HSP_score = (int)(opt->min_chain_weight * opt->a * MEM_HSP_COEF + .499);
int64_t rb, re, l_pac = bns->l_pac;
uint8_t *rseq = 0;
kswr_t x;
if (c->n == 0) return -1;
qb = l_query; qe = 0;
rb = l_pac<<1; re = 0;
for (i = 0; i < c->n; ++i) {
const mem_seed_t *s = &c->seeds[i];
qb = qb < s->qbeg? qb : s->qbeg;
qe = qe > s->qbeg + s->len? qe : s->qbeg + s->len;
rb = rb < s->rbeg? rb : s->rbeg;
re = re > s->rbeg + s->len? re : s->rbeg + s->len;
}
qb -= MEM_SHORT_EXT; qe += MEM_SHORT_EXT;
qb = qb > 0? qb : 0;
qe = qe < l_query? qe : l_query;
rb -= MEM_SHORT_EXT; re += MEM_SHORT_EXT;
rb = rb > 0? rb : 0;
re = re < l_pac<<1? re : l_pac<<1;
if (rb < l_pac && l_pac < re) {
if (c->seeds[0].rbeg < l_pac) re = l_pac;
else rb = l_pac;
}
if ((re - rb) - (qe - qb) > MEM_SHORT_EXT || (qe - qb) - (re - rb) > MEM_SHORT_EXT) return 1;
if (qe - qb >= opt->w * 4 || re - rb >= opt->w * 4) return 1;
if (qe - qb >= MEM_SHORT_LEN || re - rb >= MEM_SHORT_LEN) return 1;
rseq = bns_fetch_seq(bns, pac, &rb, c->seeds[0].rbeg, &re, &rid);
assert(c->rid == rid);
x = ksw_align2(qe - qb, (uint8_t*)query + qb, re - rb, rseq, 5, opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, KSW_XSTART, 0);
free(rseq);
if (x.score >= min_HSP_score) return 1;
if (bwa_verbose >= 4) printf("** give up the chain due to small HSP score %d.\n", x.score);
return 0;
}
int mem_chain2aln_short(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c, mem_alnreg_v *av)
{
int i, qb, qe, xtra, rid;
@ -617,6 +608,8 @@ static inline int cal_max_gap(const mem_opt_t *opt, int qlen)
return l < opt->w<<1? l : opt->w<<1;
}
#define MAX_BAND_TRY 2
void mem_chain2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c, mem_alnreg_v *av)
{
int i, k, rid, max_off[2], aw[2]; // aw: actual bandwidth used in extension
@ -649,7 +642,7 @@ void mem_chain2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
srt = malloc(c->n * 8);
for (i = 0; i < c->n; ++i)
srt[i] = (uint64_t)c->seeds[i].len<<32 | i;
srt[i] = (uint64_t)c->seeds[i].score<<32 | i;
ks_introsort_64(c->n, srt);
for (k = c->n - 1; k >= 0; --k) {
@ -989,15 +982,16 @@ mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntse
chn = mem_chain(opt, bwt, bns, l_seq, (uint8_t*)seq);
chn.n = mem_chain_flt(opt, chn.n, chn.a);
if (opt->min_chain_weight > 0) mem_flt_chained_seeds(opt, bns, pac, l_seq, (uint8_t*)seq, chn.n, chn.a);
if (bwa_verbose >= 4) mem_print_chain(bns, &chn);
kv_init(regs);
for (i = 0; i < chn.n; ++i) {
mem_chain_t *p = &chn.a[i];
int ret;
int ret = 1;
if (bwa_verbose >= 4) err_printf("* ---> Processing chain(%d) <---\n", i);
if (opt->min_chain_weight > 0) ret = mem_test_chain_sw(opt, bns, pac, l_seq, (uint8_t*)seq, p);
else ret = mem_chain2aln_short(opt, bns, pac, l_seq, (uint8_t*)seq, p, &regs);
if (opt->min_chain_weight == 0)
ret = mem_chain2aln_short(opt, bns, pac, l_seq, (uint8_t*)seq, p, &regs);
if (ret > 0) mem_chain2aln(opt, bns, pac, l_seq, (uint8_t*)seq, p, &regs);
free(chn.a[i].seeds);
}

85
ksw.c
View File

@ -510,7 +510,7 @@ int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
if (n_cigar_) *n_cigar_ = 0;
// allocate memory
n_col = qlen < 2*w+1? qlen : 2*w+1; // maximum #columns of the backtrack matrix
z = malloc(n_col * tlen);
z = n_cigar_ && cigar_? malloc(n_col * tlen) : 0;
qp = malloc(qlen * m);
eh = calloc(qlen + 1, 8);
// generate the query profile
@ -527,41 +527,60 @@ int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
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];
uint8_t *zi = &z[i * n_col];
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;
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
if (n_cigar_ && cigar_) {
uint8_t *zi = &z[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;
}

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r726-dirty"
#define PACKAGE_VERSION "0.7.8-r727-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);