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741 lines (676 loc) · 22.2 KB
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#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include "mbpriv.h"
#include "kalloc.h"
#include "kommon.h"
#include "ksort.h"
#define key_128x(a) ((a).x)
KRADIX_SORT_INIT(mb128x, mb128_t, key_128x, 8)
#define key_64(a) (a)
KRADIX_SORT_INIT(mb64, uint64_t, key_64, 8)
/*****************
* Index loading *
*****************/
mb_idx_t *mb_idx_load(const char *prefix, int32_t is_meth)
{
char *buf;
mb_idx_t *idx = 0;
l2b_t *l2b;
mb_bwt_t *bwt;
buf = kom_calloc(char, strlen(prefix) + 10);
strcat(strcpy(buf, prefix), ".l2b");
l2b = l2b_load(buf);
if (l2b == 0) goto end_idx_load;
if (is_meth) strcat(strcpy(buf, prefix), ".meth.mbw");
else strcat(strcpy(buf, prefix), ".mbw");
bwt = mb_bwt_load(buf);
if (bwt == 0) {
l2b_destroy(l2b);
goto end_idx_load;
}
mb_bwt_cache(bwt, 10); // TODO: don't hard code this
idx = kom_calloc(mb_idx_t, 1);
idx->is_meth = !!is_meth, idx->l2b = l2b, idx->bwt = bwt;
end_idx_load:
free(buf);
return idx;
}
void mb_idx_destroy(mb_idx_t *idx)
{
if (idx == 0) return;
mb_bwt_destroy(idx->bwt);
l2b_destroy(idx->l2b);
free(idx);
}
const char *mb_idx_ctg_name(const mb_idx_t *idx, int32_t tid)
{
return tid >= 0 && tid < idx->l2b->n_ctg? idx->l2b->ctg[tid].name : 0;
}
int64_t mb_idx_ctg_len(const mb_idx_t *idx, int32_t tid)
{
return tid >= 0 && tid < idx->l2b->n_ctg? idx->l2b->ctg[tid].len : -1;
}
/*****************
* Thread buffer *
*****************/
struct mb_tbuf_s {
void *km;
};
mb_tbuf_t *mb_tbuf_init(int no_kalloc)
{
mb_tbuf_t *b;
b = kom_calloc(mb_tbuf_t, 1);
if (!no_kalloc) b->km = km_init();
return b;
}
void *mb_tbuf_km(mb_tbuf_t *b)
{
return b->km;
}
void mb_tbuf_destroy(mb_tbuf_t *b)
{
if (b->km) km_destroy(b->km);
free(b);
}
int32_t mb_tbuf_reset(mb_tbuf_t *b, int64_t max_blk_sz)
{
km_stat_t kmst;
int64_t max_sz = max_blk_sz < 1U<<28? max_blk_sz : 1U<<28;
if (b->km == 0) return 0;
km_stat(b->km, &kmst);
assert(kmst.n_blocks == kmst.n_cores);
if (kmst.largest > max_sz || kmst.capacity > max_sz * 2) {
km_destroy(b->km);
b->km = km_init();
return 1;
}
return 0;
}
/************************
* Basic hit operations *
************************/
int32_t mb_cal_mblen(int32_t n, const mb_anchor_t *a, int32_t *blen_)
{
int32_t i;
int64_t mlen, blen;
*blen_ = 0;
if (n <= 0) return 0;
mlen = blen = a[0].len;
for (i = 1; i < n; ++i) {
int span = a[i].len;
int tl = (int32_t)a[i].tpos - (int32_t)a[i-1].tpos;
int ql = (int32_t)a[i].qpos - (int32_t)a[i-1].qpos;
blen += tl > ql? tl : ql;
mlen += tl > span && ql > span? span : tl < ql? tl : ql;
}
*blen_ = blen;
return mlen;
}
static void mb_cal_fuzzy_len(mb_hit_t *r, const mb_anchor_t *a)
{
r->mlen = mb_cal_mblen(r->cnt, &a[r->as], &r->blen);
}
static inline void mb_hit_set_coor(mb_hit_t *r, int32_t qlen, const l2b_t *l2b, const mb_anchor_t *a)
{ // NB: r->as and r->cnt MUST BE set correctly for this function to work
int32_t k = r->as;
const mb_anchor_t *ak0 = &a[k];
const mb_anchor_t *ak1 = &a[k + r->cnt - 1];
r->tid = ak0->sid>>1, r->rev = ak0->sid&1;
r->ts = ak0->tpos + 1 - ak0->len;
r->te = ak1->tpos + 1;
if (!r->rev) { // forward strand
r->qs = ak0->qpos + 1 - ak0->len;
r->qe = ak1->qpos + 1;
} else { // reverse strand
r->qs = qlen - (ak1->qpos + 1);
r->qe = qlen - (ak0->qpos + 1 - ak0->len);
}
mb_cal_fuzzy_len(r, a);
}
int32_t mb_cal_high_cov(void *km, int32_t n, const mb_sai_t *sai, int32_t max_occ)
{
int32_t i, n_hi = 0, hi_st, hi_en, hi_cov;
uint64_t *b;
for (i = 0; i < n; ++i)
if (sai[i].size > max_occ)
++n_hi;
if (n_hi == 0) return 0;
b = Kmalloc(km, uint64_t, n_hi);
for (i = 0, n_hi = 0; i < n; ++i)
if (sai[i].size > max_occ)
b[n_hi++] = sai[i].info;
radix_sort_mb64(b, b + n_hi);
hi_st = b[0]>>32, hi_en = (int32_t)b[0], hi_cov = 0;
for (i = 1; i < n_hi; ++i) {
int32_t st = b[i]>>32, en = (int32_t)b[i];
if (st > hi_en) {
hi_cov += hi_en - hi_st;
hi_st = st, hi_en = en;
} else hi_en = hi_en > en? hi_en : en;
}
hi_cov += hi_en - hi_st;
kfree(km, b);
return hi_cov;
}
void mb_sync_high_cov(int32_t n, mb_hit_t *h)
{
int32_t i, max_frac = 0;
for (i = 0; i < n; ++i)
max_frac = max_frac > h[i].frac_high? max_frac : h[i].frac_high;
for (i = 0; i < n; ++i)
h[i].frac_high = max_frac;
}
mb_hit_t *mb_gen_hit(void *km, uint32_t hash, int qlen, const l2b_t *l2b, int n_u, uint64_t *u, mb_anchor_t *a)
{ // convert chains to hits
mb128_t *z, tmp;
mb_hit_t *r;
int i, k;
if (n_u <= 0) return 0;
// sort by score
z = Kmalloc(km, mb128_t, n_u);
for (i = k = 0; i < n_u; ++i) {
uint32_t h;
h = (uint32_t)mb_hash64((mb_hash64(a[k].tpos) + mb_hash64(a[k].qpos)) ^ hash);
z[i].x = u[i] ^ h; // u[i] -- higher 32 bits: chain score; lower 32 bits: number of anchors
z[i].y = (uint64_t)k << 32 | (int32_t)u[i];
k += (int32_t)u[i];
}
radix_sort_mb128x(z, z + n_u);
for (i = 0; i < n_u>>1; ++i) // reverse, s.t. larger score first
tmp = z[i], z[i] = z[n_u-1-i], z[n_u-1-i] = tmp;
// populate r[]
r = (mb_hit_t*)calloc(n_u, sizeof(mb_hit_t));
for (i = 0; i < n_u; ++i) {
mb_hit_t *ri = &r[i];
ri->id = i;
ri->parent = MB_PARENT_UNSET;
ri->score = ri->score0 = z[i].x >> 32;
ri->hash = (uint32_t)z[i].x;
ri->cnt = (int32_t)z[i].y;
ri->as = z[i].y >> 32;
mb_hit_set_coor(ri, qlen, l2b, a);
}
kfree(km, z);
return r;
}
void mb_split_hit(mb_hit_t *r, mb_hit_t *r2, int n, int qlen, mb_anchor_t *a, const l2b_t *l2b)
{
if (n <= 0 || n >= r->cnt) return;
*r2 = *r;
r2->id = -1;
r2->sam_pri = 0;
r2->p = 0;
r2->split_inv = 0;
r2->cnt = r->cnt - n;
r2->score = (int32_t)(r->score * ((float)r2->cnt / r->cnt) + .499);
r2->as = r->as + n;
if (r->parent == r->id) r2->parent = MB_PARENT_TMP_PRI;
mb_hit_set_coor(r2, qlen, l2b, a);
r->cnt -= r2->cnt;
r->score -= r2->score;
mb_hit_set_coor(r, qlen, l2b, a);
r->split |= 1, r2->split |= 2;
}
void mb_sync_hits(void *km, int n_regs, mb_hit_t *regs)
{
int *tmp, i, max_id = -1, n_tmp;
if (n_regs <= 0) return;
for (i = 0; i < n_regs; ++i)
max_id = max_id > regs[i].id? max_id : regs[i].id;
n_tmp = max_id + 1;
tmp = (int*)kmalloc(km, n_tmp * sizeof(int));
for (i = 0; i < n_tmp; ++i) tmp[i] = -1;
for (i = 0; i < n_regs; ++i)
if (regs[i].id >= 0) tmp[regs[i].id] = i;
for (i = 0; i < n_regs; ++i) {
mb_hit_t *r = ®s[i];
r->id = i;
if (r->parent == MB_PARENT_TMP_PRI)
r->parent = i;
else if (r->parent >= 0 && tmp[r->parent] >= 0)
r->parent = tmp[r->parent];
else r->parent = MB_PARENT_UNSET;
}
kfree(km, tmp);
mb_set_sam_pri(n_regs, regs, 0); // this flag will be overwritten later anyway
}
/**********************************
* Set primary and secondary hits *
**********************************/
static int update_sub(mb_hit_t *ri, mb_hit_t *rp, float mask_level, int mask_len, int sub_diff, int uncov_len)
{
int si = ri->qs, ei = ri->qe, sj = rp->qs, ej = rp->qe, min, max, ol;
if (ej <= si || sj >= ei) return 0;
min = ej - sj < ei - si? ej - sj : ei - si;
max = ej - sj > ei - si? ej - sj : ei - si;
ol = ej <= si || sj >= ei? 0 : (ej < ei? ej : ei) - (sj > si? sj : si);
if ((double)ol / min - (double)uncov_len / max > mask_level && uncov_len <= mask_len) {
int cnt_sub = 0, sci = ri->score;
ri->parent = rp->parent;
rp->subsc = rp->subsc > sci? rp->subsc : sci;
if (rp->p && ri->p && (rp->tid != ri->tid || rp->ts != ri->ts || rp->te != ri->te || ol != min)) { // the last condition excludes identical hits after DP
sci = ri->p->dp_max;
rp->p->dp_max2 = rp->p->dp_max2 > sci? rp->p->dp_max2 : sci;
if (rp->p->dp_max - ri->p->dp_max <= sub_diff) cnt_sub = 1;
}
if (cnt_sub) ++rp->n_sub;
return 1;
} else return 0;
}
void mb_set_parent(void *km, float mask_level, int mask_len, int n, mb_hit_t *r, int sub_diff, int hard_mask_level)
{ // TODO: re-examine the logic for variable-length seeds
int i, j, k, *w;
uint64_t *cov;
if (n <= 0) return;
for (i = 0; i < n; ++i) r[i].id = i;
cov = Kmalloc(km, uint64_t, n);
w = Kmalloc(km, int, n);
w[0] = 0, r[0].parent = 0;
for (i = 1, k = 1; i < n; ++i) {
mb_hit_t *ri = &r[i];
int si = ri->qs, ei = ri->qe, n_cov = 0, uncov_len = 0, max_ol, max_j, n_par = 0;
if (hard_mask_level) goto skip_uncov;
for (j = 0; j < k; ++j) {
const mb_hit_t *rp = &r[w[j]];
int sj = rp->qs, ej = rp->qe;
if (ej <= si || sj >= ei) continue;
if (sj < si) sj = si;
if (ej > ei) ej = ei;
cov[n_cov++] = (uint64_t)sj<<32 | ej;
}
if (n_cov == 0) {
goto add_primary;
} else {
int j, x = si;
radix_sort_mb64(cov, cov + n_cov);
for (j = 0; j < n_cov; ++j) {
if ((int)(cov[j]>>32) > x) uncov_len += (cov[j]>>32) - x;
x = (int32_t)cov[j] > x? (int32_t)cov[j] : x;
}
if (ei > x) uncov_len += ei - x;
}
skip_uncov:
for (j = 0, max_ol = 0, max_j = -1; j < k; ++j) { // find the parent with the maximum overlap
const mb_hit_t *rp = &r[w[j]];
int sj = rp->qs, ej = rp->qe;
int ol = ej <= si || sj >= ei? 0 : (ej < ei? ej : ei) - (sj > si? sj : si);
if (max_ol < ol) max_ol = ol, max_j = j;
}
if (max_j >= 0) {
n_par += update_sub(ri, &r[w[max_j]], mask_level, mask_len, sub_diff, uncov_len);
for (j = 0; j < k && n_par == 0; ++j) // if no parent found on the longest overlap, try more
n_par += update_sub(ri, &r[w[j]], mask_level, mask_len, sub_diff, uncov_len);
}
add_primary:
if (n_par == 0) w[k++] = i, ri->parent = i, ri->n_sub = 0;
}
kfree(km, cov);
kfree(km, w);
}
void mb_set_sam_pri(int32_t n, mb_hit_t *r, int32_t is_primary5)
{
int32_t i, n_pri = 0, min_i = -1, min_qs = -1, first_i = -1;
if (n <= 0) return;
for (i = 0; i < n; ++i) {
r[i].sam_pri = 0;
if (r[i].id != r[i].parent) continue;
if (++n_pri == 1) first_i = i;
if (min_qs < 0 || r[i].qs < min_qs)
min_i = i, min_qs = r[i].qs;
}
assert(n_pri > 0);
if (is_primary5) r[min_i].sam_pri = 1;
else r[first_i].sam_pri = 1;
}
void mb_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_, mb_hit_t *r)
{
if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_, n_2nd = 0;
uint8_t *keep = Kcalloc(km, uint8_t, n);
for (i = 0; i < n; ++i) {
int p = r[i].parent;
if (p == i || r[i].inv) {
keep[i] = 1;
} else if ((r[i].score >= r[p].score * pri_ratio || r[i].score + min_diff >= r[p].score) && n_2nd < best_n) {
if (!(r[i].qs == r[p].qs && r[i].qe == r[p].qe && r[i].tid == r[p].tid && r[i].ts == r[p].ts && r[i].te == r[p].te))
keep[i] = 1, ++n_2nd;
}
}
for (i = k = 0; i < n; ++i) {
if (keep[i]) r[k++] = r[i];
else if (r[i].p) free(r[i].p); // r->p is libc-allocated; free here before the pointer is lost
}
kfree(km, keep);
if (k != n) mb_sync_hits(km, k, r);
*n_ = k;
}
}
void mb_hit_sort(void *km, int *n_regs, mb_hit_t *r)
{
int32_t i, n_aux, n = *n_regs;
mb128_t *aux;
mb_hit_t *t;
if (n <= 1) return;
aux = (mb128_t*)kmalloc(km, (size_t)n * 16);
t = (mb_hit_t*)kmalloc(km, (size_t)n * sizeof(mb_hit_t));
for (i = n_aux = 0; i < n; ++i) {
if (r[i].inv || r[i].cnt >= 0) {
int score = r[i].p? r[i].p->dp_max : r[i].score;
aux[n_aux].x = (uint64_t)score << 32 | r[i].hash;
aux[n_aux++].y = i;
} else if (r[i].p) {
free(r[i].p);
r[i].p = 0;
}
}
radix_sort_mb128x(aux, aux + n_aux);
for (i = n_aux - 1; i >= 0; --i)
t[n_aux - 1 - i] = r[aux[i].y];
memcpy(r, t, sizeof(mb_hit_t) * n_aux);
*n_regs = n_aux;
kfree(km, aux);
kfree(km, t);
}
void mb_filter_hits(const mb_opt_t *opt, int qlen, int *n_regs, mb_hit_t *regs)
{
int i, k;
for (i = k = 0; i < *n_regs; ++i) {
mb_hit_t *r = ®s[i];
int flt = r->flt;
if (r->p) {
if (r->mlen < opt->min_chain_score) flt = 1;
else if (r->p->dp_max < opt->min_dp_max * opt->a) flt = 1;
if (flt) free(r->p);
}
if (!flt) {
if (k < i) regs[k++] = regs[i];
else ++k;
}
}
*n_regs = k;
}
int mb_squeeze_a(void *km, int n_regs, mb_hit_t *regs, mb_anchor_t *a)
{
int i, as = 0;
uint64_t *aux;
aux = (uint64_t*)kmalloc(km, (size_t)n_regs * 8);
for (i = 0; i < n_regs; ++i)
aux[i] = (uint64_t)regs[i].as << 32 | i;
radix_sort_mb64(aux, aux + n_regs);
for (i = 0; i < n_regs; ++i) {
mb_hit_t *r = ®s[(int32_t)aux[i]];
if (r->as != as) {
memmove(&a[as], &a[r->as], (size_t)r->cnt * sizeof(mb_anchor_t));
r->as = as;
}
as += r->cnt;
}
kfree(km, aux);
return as;
}
/*******************
* Mapping quality *
*******************/
static void mb_set_inv_mapq(void *km, int n_regs, mb_hit_t *regs)
{
int i, n_aux;
mb128_t *aux;
if (n_regs < 3) return;
for (i = 0; i < n_regs; ++i)
if (regs[i].inv) break;
if (i == n_regs) return; // no inversion hits
aux = Kmalloc(km, mb128_t, n_regs);
for (i = n_aux = 0; i < n_regs; ++i)
if (regs[i].parent == i || regs[i].parent < 0)
aux[n_aux].y = i, aux[n_aux++].x = (uint64_t)regs[i].tid << 32 | regs[i].ts;
radix_sort_mb128x(aux, aux + n_aux);
for (i = 1; i < n_aux - 1; ++i) {
mb_hit_t *inv = ®s[aux[i].y];
if (inv->inv) {
mb_hit_t *l = ®s[aux[i-1].y];
mb_hit_t *r = ®s[aux[i+1].y];
inv->mapq = l->mapq < r->mapq? l->mapq : r->mapq;
}
}
kfree(km, aux);
}
void mb_set_mapq(void *km, int32_t qlen, int n_regs, mb_hit_t *regs, int min_chain_sc, int match_sc, int is_sr, int max_sr_len)
{
const int32_t mapQ_coef_len = 50;
const double mapQ_coef_fac = 3.0; // should be log(mapQ_coef_len)), but bwa-mem uses 3.0 due to a bug. Let's match bwa-mem
const double q_coef = 40.0f;
int i;
if (n_regs == 0) return;
for (i = 0; i < n_regs; ++i) {
mb_hit_t *r = ®s[i];
if (r->inv) {
r->mapq = 0;
} else if (r->parent == r->id) {
int mapq, mapq_sr, mapq_lr, subsc;
double pen_chn = r->score > qlen * 0.1? 1.0 : 10.0 * r->score / qlen; // penalize chains with few matching bases
subsc = r->subsc > min_chain_sc? r->subsc : min_chain_sc;
if (r->p && r->p->dp_max2 > 0 && r->p->dp_max > 0) {
double x, identity = (double)r->mlen / r->blen;
// BWA-MEM formula for short reads
x = r->blen < mapQ_coef_len? 1. : mapQ_coef_fac / log(r->blen);
x *= identity * identity;
mapq_sr = (int)(6.02 * x * x * (r->p->dp_max - r->p->dp_max2) / match_sc + .499f);
// minimap2 formula for long reads
x = (double)r->p->dp_max2 / r->p->dp_max;
if (subsc > r->score0) x *= (double)subsc / r->score0;
mapq_lr = (int)(pen_chn * identity * q_coef * (1.0 - x * x) * log((double)r->p->dp_max / match_sc));
// final mapq
if (is_sr) mapq = mapq_sr;
else if (max_sr_len < 0) mapq = mapq_lr;
else mapq = qlen < max_sr_len? mapq_sr : (int32_t)(mapq_lr - (mapq_lr - mapq_sr) * pow(2.0, 1.0 - (double)qlen / max_sr_len) + .499);
} else { // minimap2 formula
double x = (double)subsc / r->score0;
if (r->p) {
double identity = (double)r->mlen / r->blen;
mapq = (int)(pen_chn * identity * q_coef * (1.0f - x) * log((double)r->p->dp_max / match_sc));
} else {
mapq = (int)(pen_chn * q_coef * (1.0f - x) * log(r->score));
}
}
mapq -= (int)(4.343f * log(r->n_sub + 1) + .499f);
mapq = mapq > 0? mapq : 0;
if (r->seed_ratio < 50) mapq *= (double)r->seed_ratio * r->seed_ratio / 2500.0;
r->mapq = mapq < 60? mapq : 60;
if (r->p && r->p->dp_max > r->p->dp_max2 && r->mapq == 0) r->mapq = 1;
} else r->mapq = 0;
}
mb_set_inv_mapq(km, n_regs, regs);
}
/************************
* Core mapping routine *
************************/
static void mb_dbg_seed(int64_t n, const mb_sai_t *u, const char *qname)
{
int64_t i;
for (i = 0; i < n; ++i) {
const mb_sai_t *p = &u[i];
fprintf(stderr, "SD\t%s\t%d\t%d\t%ld\n", qname? qname : "*", (int32_t)(p->info>>32), (int32_t)p->info, (long)p->size);
}
}
static void mb_dbg_anchor(const mb_idx_t *idx, int qlen, int64_t n, const mb_anchor_t *a, const char *qname)
{
int64_t i;
for (i = 0; i < n; ++i) {
const mb_anchor_t *ai = &a[i];
int rid = ai->sid >> 1;
int rev = ai->sid & 1;
int32_t qs = rev? qlen - 1 - ai->qpos : ai->qpos + 1 - ai->len;
int64_t ts = ai->tpos + 1 - ai->len;
fprintf(stderr, "AC\t%s\t%d\t%c\t%s\t%ld\t%d\n", qname? qname : "*", qs, "+-"[rev], idx->l2b->ctg[rid].name, (long)ts, ai->len);
}
}
mb_hit_t *mb_map_sai(const mb_opt_t *opt, const mb_idx_t *idx, int64_t qlen, const char *seq0, l2b_meth_t mt, mb_sai_v *u, int32_t *n_hit_, mb_tbuf_t *b, const char *qname)
{
const int32_t min_rechain_len = 1000;
const double min_rechain_ratio = 0.1;
uint32_t hash;
int32_t i, n_hit, hi_cov, is_sr;
int32_t sub_diff = opt->a + opt->b > opt->q + opt->e? opt->a + opt->b : opt->q + opt->e;
uint64_t *w;
double chn_pen_gap, seed_ratio;
uint8_t *seq;
mb_anchor_v v = {0,0,0};
mb_anchor_t *a;
mb_hit_t *hit;
if (kom_dbg_flag & MB_DBG_QNAME) fprintf(stderr, "QN\t%s\n", qname);
*n_hit_ = 0;
if (u->n == 0) {
kfree(b->km, u->a);
return 0;
}
hash = qname? mb_hash_str(qname) : 0;
hash ^= mb_hash64(qlen) + mb_hash64(opt->seed);
hash = mb_hash64(hash);
seq = kmalloc(b->km, qlen);
for (i = 0; i < qlen; ++i) seq[i] = kom_nt4_table[(uint8_t)seq0[i]];
hi_cov = mb_cal_high_cov(b->km, u->n, u->a, opt->max_occ);
is_sr = mb_is_sr_mode(opt, qlen);
// collect anchors
chn_pen_gap = opt->chain_gap_scale * .01 * opt->min_len;
if (kom_dbg_flag & MB_DBG_SEED) mb_dbg_seed(u->n, u->a, qname);
seed_ratio = mb_anchor(b->km, idx, u, opt->min_len, qlen, seq, mt, opt->max_occ, &v);
kfree(b->km, u->a); // no longer needed
u->n = 0, u->a = 0;
// initial chaining
if (kom_dbg_flag & MB_DBG_ANCHOR) mb_dbg_anchor(idx, qlen, v.n, v.a, qname);
a = mb_lchain_dp(b->km, idx->l2b, opt->max_gap, opt->max_gap, opt->bw, opt->max_chain_skip, opt->max_chain_iter,
opt->min_chain_score, chn_pen_gap, v.n, v.a, &n_hit, &w);
v.a = 0; v.n = v.m = 0; // ownership transferred to a
// re-chaining
if (opt->bw_long > opt->bw * 2 && !is_sr && n_hit > 0) {
int64_t n_a, as, st, en;
int32_t best;
// chains in w[] are sorted by tpos of first anchor, not by score; find the best
for (i = 1, best = 0; i < n_hit; ++i)
if ((w[i] >> 32) > (w[best] >> 32)) best = i;
for (i = 0, as = 0; i < best; ++i) as += (int32_t)w[i];
st = a[as].qpos + 1 - a[as].len;
en = a[as + (int32_t)w[best] - 1].qpos + 1;
if (qlen - (en - st) > min_rechain_len && en - st > qlen * min_rechain_ratio) {
for (i = 0, n_a = 0; i < n_hit; ++i) n_a += (int32_t)w[i];
kfree(b->km, w);
mb_anchor_sort(idx->l2b, n_a, a);
a = mb_lchain_dp(b->km, idx->l2b, opt->max_gap, opt->max_gap, opt->bw_long, opt->max_chain_skip, opt->max_chain_iter,
opt->min_chain_score, chn_pen_gap, n_a, a, &n_hit, &w);
}
}
// chain ordering
hit = mb_gen_hit(b->km, hash, qlen, idx->l2b, n_hit, w, a);
kfree(b->km, w);
mb_set_parent(b->km, opt->mask_level, opt->mask_len, n_hit, hit, sub_diff, 0);
mb_select_sub(b->km, opt->pri_ratio, opt->min_len * 2, opt->best_n, &n_hit, hit);
// base alignment
if (!(opt->flag & MB_F_NO_ALN)) {
hit = mb_align_skeleton(b->km, opt, idx, qlen, seq, mt, &n_hit, hit, a);
mb_set_parent(b->km, opt->mask_level, opt->mask_len, n_hit, hit, sub_diff, 0);
mb_select_sub(b->km, opt->pri_ratio, opt->min_len * 2, opt->best_n, &n_hit, hit);
mb_set_sam_pri(n_hit, hit, !!(opt->flag & MB_F_PRIMARY5));
}
for (i = 0; i < n_hit; ++i) {
hit[i].frac_high = (int32_t)(255. * hi_cov / qlen);
hit[i].seed_ratio = (int32_t)(255. * seed_ratio + .499);
if (hit[i].seed_ratio == 0) hit[i].seed_ratio = 1;
}
mb_set_mapq(b->km, qlen, n_hit, hit, opt->min_chain_score, opt->a, is_sr, opt->max_sr_len);
// clean up
kfree(b->km, a);
kfree(b->km, seq);
*n_hit_ = n_hit;
return hit;
}
/*************************
* Public alignment APIs *
*************************/
mb_hit_t *mb_map(const
8EFB
mb_opt_t *opt, const mb_idx_t *idx, int32_t qlen, const char *seq0, int32_t mt0, int32_t *n_hit_, mb_tbuf_t *b0, const char *qname)
{
mb_opt_t opt_adap;
mb_hit_t *ret;
mb_sai_v u = {0,0,0};
mb_tbuf_t *b;
uint8_t *seq;
int32_t i;
l2b_meth_t mt = mt0 == 0? L2B_METH_NONE : mt0 == 1? L2B_METH_C2T : L2B_METH_G2A;
b = b0? b0 : mb_tbuf_init(1);
mb_opt_adap(opt, qlen, &opt_adap);
seq = Kmalloc(b->km, uint8_t, qlen);
for (i = 0; i < qlen; ++i)
seq[i] = kom_nt4_table[(uint8_t)seq0[i]];
mb_seed_intv(b->km, idx->bwt, qlen, seq, opt->min_len, opt->max_sub_occ, &u);
kfree(b->km, seq);
ret = mb_map_sai(&opt_adap, idx, qlen, seq0, mt, &u, n_hit_, b, qname);
if (b0 == 0) mb_tbuf_destroy(b);
return ret;
}
mb_hit_t **mb_map_batch(const mb_opt_t *opt, const mb_idx_t *idx, int32_t n_seq, const int32_t *qlen, const char **seq, int32_t *n_hit, mb_tbuf_t *b0, const char **qname)
{
mb_tbuf_t *b;
mb_hit_t **hit;
mb_sai_v *sai;
uint8_t **seq4;
void *km;
int32_t i, j, k, sb_st, sb_len, sb_max, is_pe = !!(opt->flag & MB_F_PE);
if (n_seq <= 0) return 0;
b = b0? b0 : mb_tbuf_init(0);
km = mb_tbuf_km(b);
hit = (mb_hit_t**)calloc(n_seq, sizeof(mb_hit_t*));
// pre-allocate for sub-batch processing
sb_max = opt->sb_seq < n_seq? opt->sb_seq : n_seq;
seq4 = Kmalloc(km, uint8_t*, sb_max);
sai = Kmalloc(km, mb_sai_v, sb_max);
// process in sub-batches
for (i = 0, sb_st = 0, sb_len = 0; i <= n_seq; ++i) {
if (i == n_seq || sb_len >= opt->sb_len || i - sb_st >= opt->sb_seq) {
int32_t sb_n = i - sb_st;
if (sb_n == 0) { sb_st = i; sb_len = 0; continue; }
// convert sub-batch to 4-bit encoding
for (k = 0; k < sb_n; ++k) {
int32_t idx_k = sb_st + k;
seq4[k] = Kmalloc(km, uint8_t, qlen[idx_k]);
for (j = 0; j < qlen[idx_k]; ++j)
seq4[k][j] = kom_nt4_table[(uint8_t)seq[idx_k][j]];
}
// batch SMEM for sub-batch
memset(sai, 0, sb_n * sizeof(mb_sai_v));
mb_seed_intv_batch(km, idx->bwt, sb_n, &qlen[sb_st], seq4, opt->min_len, opt->max_sub_occ, sai);
for (k = 0; k < sb_n; ++k) kfree(km, seq4[k]);
// map each sequence in sub-batch
for (k = 0; k < sb_n; ++k) {
int32_t idx_k = sb_st + k;
mb_opt_t opt_adap;
l2b_meth_t mt = L2B_METH_NONE;
mb_opt_adap(opt, qlen[idx_k], &opt_adap);
if (opt->flag & MB_F_METH) {
if (is_pe) mt = (idx_k&1) == 0? L2B_METH_C2T : L2B_METH_G2A;
else mt = L2B_METH_C2T;
}
hit[idx_k] = mb_map_sai(&opt_adap, idx, qlen[idx_k], seq[idx_k], mt, &sai[k], &n_hit[idx_k], b, qname? qname[idx_k] : 0);
}
sb_st = i;
sb_len = 0;
}
if (i < n_seq) sb_len += qlen[i];
}
kfree(km, sai);
kfree(km, seq4);
// paired-end processing
if (is_pe && n_seq >= 2) {
mb_pestat_t pes[4];
for (i = 0; i < 4; ++i) pes[i].failed = 1;
pes[1].failed = 0;
pes[1].avg = opt->pe_avg, pes[1].std = opt->pe_std;
pes[1].lo = opt->pe_lo, pes[1].hi = opt->pe_hi;
for (i = 0; i + 1 < n_seq; i += 2) {
int32_t len2[2] = { qlen[i], qlen[i+1] };
char *seq2[2] = { (char*)seq[i], (char*)seq[i+1] };
mb_pair(km, opt, idx->l2b, &n_hit[i], &hit[i], pes, len2, seq2);
}
}
if (b0 == 0) mb_tbuf_destroy(b);
return hit;
}