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This commit is contained in:
Heng Li 2017-06-23 15:13:53 -04:00
parent 4ae0b46972
commit 990f7b0b71
3 changed files with 47 additions and 23 deletions
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68
align.c
View File

@ -2,10 +2,52 @@
#include "minimap.h"
#include "ksw2.h"
static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r_split, mm128_t *a)
{
int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
uint8_t *tseq0, *tseq, *qseq;
int32_t i, l, rs0, re0;
int32_t rs, re, qs, qe, ret;
l = r->qs < opt->max_gap? r->qs : opt->max_gap;
l = (l * opt->a - opt->q) / opt->e;
l = l < opt->max_gap? l : opt->max_gap;
l = l < r->rs? l : r->rs;
rs0 = r->rs - l;
l = qlen - r->re < opt->max_gap? qlen - r->re : opt->max_gap;
l = (l * opt->a - opt->q) / opt->e;
l = l < opt->max_gap? l : opt->max_gap;
l = l < mi->seq[rid].len - r->re? l : mi->seq[rid].len - r->re;
re0 = r->re + l;
tseq0 = (uint8_t*)kmalloc(km, re0 - rs0);
ret = mm_idx_getseq(mi, rid, rs0, re0, tseq0);
assert(ret > 0);
rs = (int32_t)a[r->as].x + 1;
qs = (int32_t)a[r->as].y + 1;
for (i = 1; i < r->cnt; ++i) {
re = (int32_t)a[r->as + i].x + 1;
qe = (int32_t)a[r->as + i].y + 1;
if (i == r->cnt - 1 || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
qseq = &qseq0[rev][qs];
tseq = &tseq0[rs - rs0];
#if 0
fprintf(stderr, "===> [%d] %d-%d %c (%s:%d-%d) <===\n", i, qs, qe, "+-"[rev], mi->seq[rid].name, rs, re);
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
rs = re, qs = qe;
}
}
kfree(km, tseq0);
}
void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int n_regs, mm_reg1_t *regs, mm128_t *a)
{
extern unsigned char seq_nt4_table[256];
int i, k, reg;
int i, reg;
uint8_t *qseq0[2];
qseq0[0] = (uint8_t*)kmalloc(km, qlen);
@ -16,28 +58,8 @@ void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
}
for (reg = 0; reg < n_regs; ++reg) {
mm_reg1_t *r = &regs[reg];
int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
uint8_t *tseq0, *tseq, *qseq;
int32_t rs, re, qs, qe, ret;
tseq0 = (uint8_t*)kmalloc(km, r->re - r->rs);
ret = mm_idx_getseq(mi, rid, r->rs, r->re, tseq0);
assert(ret > 0);
rs = (int32_t)a[r->as].x + 1;
qs = (int32_t)a[r->as].y + 1;
for (i = 1; i < r->cnt; ++i) {
re = (int32_t)a[r->as + i].x + 1;
qe = (int32_t)a[r->as + i].y + 1;
if (qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
qseq = &qseq0[rev][qs];
tseq = &tseq0[rs - r->rs];
fprintf(stderr, "===> [%d,%d] %d-%d %c (%s:%d-%d) <===\n", reg, i, qs, qe, "+-"[rev], mi->seq[rid].name, rs, re);
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);
rs = re, qs = qe;
}
}
kfree(km, tseq0);
mm_reg1_t r_split;
mm_align1(km, opt, mi, qlen, qseq0, &regs[reg], &r_split, a);
}
kfree(km, qseq0[0]); kfree(km, qseq0[1]);

1
map.c
View File

@ -24,6 +24,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->mask_level = 0.5f;
opt->a = 1, opt->b = 1, opt->q = 1, opt->e = 1;
opt->zdrop = 100;
opt->min_ksw_len = 100;
}

1
minimap.h
View File

@ -62,6 +62,7 @@ typedef struct {
float pri_ratio;
float mask_level;
int a, b, q, e; // matching score, mismatch, gap-open and gap-ext penalties
int zdrop;
int max_occ;
int mid_occ;