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This commit is contained in:
Heng Li 2017-06-23 22:42:15 -04:00
parent 523a8832ad
commit 35b84f88c6
3 changed files with 90 additions and 33 deletions
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102
align.c
View File

@ -29,26 +29,56 @@ static inline void mm_seq_rev(uint32_t len, uint8_t *seq)
t = seq[i], seq[i] = seq[len - 1 - i], seq[len - 1 - i] = t;
}
static void mm_update_extra(mm_extra_t *p, const uint8_t *qseq, const uint8_t *tseq, uint32_t n_cigar, uint32_t *cigar)
{
uint32_t k, l, toff = 0, qoff = 0;
for (k = 0; k < n_cigar; ++k) {
uint32_t op = cigar[k]&0xf, len = cigar[k]>>4;
if (op == 0) {
for (l = 0; l < len; ++l) {
if (tseq[toff + l] > 3 || qseq[qoff + l] > 3) ++p->n_ambi;
else if (tseq[toff + l] != qseq[qoff + l]) ++p->n_diff;
}
toff += len, qoff += len, p->blen += len;
} else if (op == 1) {
int n_ambi = 0;
for (l = 0; l < len; ++l)
if (qseq[qoff + l] > 3) ++n_ambi;
qoff += len, p->blen += len;
p->n_ambi += n_ambi, p->n_diff += len - n_ambi;
} else if (op == 2) {
int n_ambi = 0;
for (l = 0; l < len; ++l)
if (tseq[toff + l] > 3) ++n_ambi;
toff += len, p->blen += len;
p->n_ambi += n_ambi, p->n_diff += len - n_ambi;
}
}
}
static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) // TODO: this calls the libc realloc()
{
mm_extra_t *p;
if (n_cigar == 0) return;
if (r->cigar == 0) {
uint32_t m_cigar = n_cigar + 2;
kroundup32(m_cigar);
r->cigar = (mm_cigar_t*)malloc(m_cigar * 4);
r->cigar->n = 0, r->cigar->m = m_cigar;
} else if (r->cigar->n + n_cigar > r->cigar->m - 2) {
r->cigar->m = r->cigar->n + n_cigar + 2;
kroundup32(r->cigar->m);
r->cigar = (mm_cigar_t*)realloc(r->cigar, r->cigar->m * 4);
if (r->p == 0) {
uint32_t capacity = n_cigar + sizeof(mm_extra_t);
kroundup32(capacity);
r->p = (mm_extra_t*)malloc(capacity * 4);
r->p->n_cigar = 0, r->p->capacity = capacity;
r->p->n_diff = r->p->n_ambi = 0;
} else if (r->p->n_cigar + n_cigar + sizeof(mm_extra_t) > r->p->capacity) {
r->p->capacity = r->p->n_cigar + n_cigar + sizeof(mm_extra_t);
kroundup32(r->p->capacity);
r->p = (mm_extra_t*)realloc(r->p, r->p->capacity * 4);
}
if (r->cigar->n > 0 && (r->cigar->cigar[r->cigar->n-1]&0xf) == (cigar[0]&0xf)) { // same CIGAR op at the boundary
r->cigar->cigar[r->cigar->n-1] += cigar[0]>>4<<4;
if (n_cigar > 1) memcpy(r->cigar->cigar + r->cigar->n, cigar + 1, (n_cigar - 1) * 4);
r->cigar->n += n_cigar - 1;
p = r->p;
if (p->n_cigar > 0 && (p->cigar[p->n_cigar-1]&0xf) == (cigar[0]&0xf)) { // same CIGAR op at the boundary
p->cigar[p->n_cigar-1] += cigar[0]>>4<<4;
if (n_cigar > 1) memcpy(p->cigar + p->n_cigar, cigar + 1, (n_cigar - 1) * 4);
p->n_cigar += n_cigar - 1;
} else {
memcpy(r->cigar->cigar + r->cigar->n, cigar, n_cigar * 4);
r->cigar->n += n_cigar;
memcpy(p->cigar + p->n_cigar, cigar, n_cigar * 4);
p->n_cigar += n_cigar;
}
}
@ -56,12 +86,13 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
{
int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
uint8_t *tseq, *qseq;
int32_t i, k, l, rs0, re0, qs0, qe0;
int32_t i, l, bw, rs0, re0, qs0, qe0;
int32_t rs, re, qs, qe;
int32_t rs1, qs1;
int32_t rs1, qs1, re1, qe1;
int8_t mat[25];
ksw_gen_simple_mat(5, mat, opt->a, opt->b);
bw = (int)(opt->bw * 1.5 + 1.);
rs = (int32_t)a[r->as].x + 1; // NB: this is the same as r->{rs,re}
re = (int32_t)a[r->as + r->cnt - 1].x + 1;
@ -78,7 +109,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
} else rs0 = rs, qs0 = qs;
if (qe < qlen && re < mi->seq[rid].len) {
l = qlen - re < opt->max_gap? qlen - re : opt->max_gap;
l = qlen - qe < opt->max_gap? qlen - qe : opt->max_gap;
qe0 = qe + l;
l += (l * opt->a - opt->q) / opt->e;
l = l < opt->max_gap? l : opt->max_gap;
@ -86,7 +117,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
re0 = re + l;
} else re0 = re, qe0 = qe;
tseq = (uint8_t*)kmalloc(km, re0 - rs0);
tseq = (uint8_t*)kmalloc(km, re0 - rs0); // TODO: we can allocate a smaller size
if (qs > 0 && rs > 0) { // left extension
uint32_t ql = qs - qs0, tl = rs - rs0;
@ -99,12 +130,15 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
for (k = 0; k < tl; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
for (k = 0; k < ql; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
#endif
ksw_extz2_sse(km, ql, qseq, tl, tseq, 5, mat, opt->q, opt->e, (int)(opt->bw * 1.5 + .499), opt->zdrop, KSW_EZ_EXTZ_ONLY|KSW_EZ_RIGHT|KSW_EZ_REV_CIGAR, ez);
mm_seq_rev(ql, qseq);
ksw_extz2_sse(km, ql, qseq, tl, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_EXTZ_ONLY|KSW_EZ_RIGHT|KSW_EZ_REV_CIGAR, ez);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar);
r->p->score += ez->score;
rs1 = rs - (ez->max_t + 1);
qs1 = qs - (ez->max_q + 1);
mm_seq_rev(ql, qseq);
} else rs1 = rs, qs1 = qs;
assert(qs1 >= 0 && rs1 >= 0);
for (i = 1; i < r->cnt; ++i) { // gap filling
re = (int32_t)a[r->as + i].x + 1;
@ -117,21 +151,37 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
for (k = 0; k < re - rs; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
#endif
ksw_extz2_sse(km, qe-qs, qseq, re-rs, tseq, 5, mat, opt->q, opt->e, (int)(opt->bw * 1.5 + .499), opt->zdrop, KSW_EZ_DYN_BAND, ez);
ksw_extz2_sse(km, qe-qs, qseq, re-rs, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_DYN_BAND, ez);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar);
if (ez->score == KSW_NEG_INF) { // truncated by Z-drop
r->p->score += ez->max;
abort();
} else {
mm_append_cigar(r, ez->n_cigar, ez->cigar);
r->p->score += ez->score;
}
//for (k = 0; k < r->cigar->n; ++k) fprintf(stderr, "%d%c", r->cigar->cigar[k]>>4, "MID"[r->cigar->cigar[k]&0xf]); fputc('\n', stderr);
rs = re, qs = qe;
}
}
if (i == r->cnt) { // right extension
}
if (i == r->cnt && qe < qe0 && re < re0) { // right extension
qseq = &qseq0[rev][qe];
mm_idx_getseq(mi, rid, re, re0, tseq);
ksw_extz2_sse(km, qe0-qe, qseq, re0-re, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_EXTZ_ONLY, ez);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar);
r->p->score += ez->score;
re1 = re + (ez->max_t + 1);
qe1 = qe + (ez->max_q + 1);
} else re1 = re, qe1 = qe;
assert(qe1 <= qlen);
for (i = 0; i < r->cigar->n; ++i) fprintf(stderr, "%d%c", r->cigar->cigar[i]>>4, "MID"[r->cigar->cigar[i]&0xf]); fputc('\n', stderr);
r->rs = rs1, r->re = re1;
if (rev) r->qs = qlen - qe1, r->qe = qlen - qs1;
else r->qs = qs1, r->qe = qe1;
// for (i = 0; i < r->p->n_cigar; ++i) fprintf(stderr, "%d%c", r->p->cigar[i]>>4, "MID"[r->p->cigar[i]&0xf]); fputc('\n', stderr);
kfree(km, tseq);
}

11
map.c
View File

@ -16,7 +16,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->sdust_thres = 0;
opt->min_score = 40;
opt->bw = 500;
opt->bw = 1000;
opt->max_gap = 10000;
opt->max_skip = 15;
@ -381,11 +381,14 @@ static void *worker_pipeline(void *shared, int step, void *in)
printf("%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
if (mi->seq[r->rid].name) fputs(mi->seq[r->rid].name, stdout);
else printf("%d", r->rid + 1);
printf("\t%d\t%d\t%d\t%d\t%d\t255\tcm:i:%d", mi->seq[r->rid].len, r->rs, r->re, r->score,
r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs, r->cnt);
printf("\t%d\t%d\t%d", mi->seq[r->rid].len, r->rs, r->re);
if (r->p) printf("\t%d\t%d\t255", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
else printf("\t%d\t%d\t255", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
printf("\tcm:i:%d", r->cnt);
if (r->parent == j) printf("\tss:i:%d", r->subsc);
if (r->p) printf("\tNM:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->score, r->p->n_ambi);
putchar('\n');
free(r->cigar);
free(r->p);
}
free(s->reg[i]);
free(s->seq[i].seq); free(s->seq[i].name);

10
minimap.h
View File

@ -42,9 +42,13 @@ typedef struct {
} mm_idx_t;
typedef struct {
uint32_t n, m;
uint32_t capacity;
int32_t score;
uint32_t blen;
uint32_t n_diff, n_ambi;
uint32_t n_cigar;
uint32_t cigar[];
} mm_cigar_t;
} mm_extra_t;
typedef struct {
uint32_t cnt:31, rev:1;
@ -53,7 +57,7 @@ typedef struct {
int32_t qs, qe, rs, re;
int32_t parent, subsc;
int32_t as;
mm_cigar_t *cigar;
mm_extra_t *p;
} mm_reg1_t;
typedef struct {