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min_ksw_len

This commit is contained in:
Heng Li 2017-06-23 14:38:28 -04:00
parent 9cd313eae1
commit 4ae0b46972
3 changed files with 24 additions and 16 deletions
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25
align.c
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@ -18,23 +18,26 @@ void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
for (reg = 0; reg < n_regs; ++reg) { for (reg = 0; reg < n_regs; ++reg) {
mm_reg1_t *r = &regs[reg]; mm_reg1_t *r = &regs[reg];
int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63; int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
uint8_t *tseq; uint8_t *tseq0, *tseq, *qseq;
tseq = (uint8_t*)kmalloc(km, r->re - r->rs);
for (i = 0; i < r->cnt - 1; ++i) {
uint8_t *qseq;
int32_t rs, re, qs, qe, ret; int32_t rs, re, qs, qe, ret;
rs = (int32_t)a[r->as + i].x + 1; tseq0 = (uint8_t*)kmalloc(km, r->re - r->rs);
re = (int32_t)a[r->as + i + 1].x + 1; ret = mm_idx_getseq(mi, rid, r->rs, r->re, tseq0);
qs = (int32_t)a[r->as + i].y + 1;
qe = (int32_t)a[r->as + i + 1].y + 1;
qseq = &qseq0[rev][qs];
ret = mm_idx_getseq(mi, rid, rs, re, tseq);
assert(ret > 0); 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); 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 < 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); for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
rs = re, qs = qe;
} }
kfree(km, tseq); }
kfree(km, tseq0);
} }
kfree(km, qseq0[0]); kfree(km, qseq0[1]); kfree(km, qseq0[0]); kfree(km, qseq0[1]);

3
map.c
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@ -22,6 +22,9 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->pri_ratio = 2.0f; opt->pri_ratio = 2.0f;
opt->mask_level = 0.5f; opt->mask_level = 0.5f;
opt->a = 1, opt->b = 1, opt->q = 1, opt->e = 1;
opt->min_ksw_len = 100;
} }
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi) void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)

2
minimap.h
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@ -61,9 +61,11 @@ typedef struct {
int min_score; int min_score;
float pri_ratio; float pri_ratio;
float mask_level; float mask_level;
int a, b, q, e; // matching score, mismatch, gap-open and gap-ext penalties
int max_occ; int max_occ;
int mid_occ; int mid_occ;
int min_ksw_len;
} mm_mapopt_t; } mm_mapopt_t;
extern int mm_verbose; extern int mm_verbose;