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r115: set primary tag; still buggy

This commit is contained in:
Heng Li 2017-06-29 23:48:35 -04:00
parent c4871f380c
commit 52b4d8e2c9
4 changed files with 10 additions and 6 deletions
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4
format.c
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@ -76,7 +76,7 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
write_tags(s, r); write_tags(s, r);
if (r->p) { if (r->p) {
uint32_t k; uint32_t k;
mm_sprintf_lite(s, "cg:Z:"); mm_sprintf_lite(s, "\tcg:Z:");
for (k = 0; k < r->p->n_cigar; ++k) for (k = 0; k < r->p->n_cigar; ++k)
mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]); mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
} }
@ -112,7 +112,7 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
s->l = 0; s->l = 0;
if (r->rev) flag |= 0x10; if (r->rev) flag |= 0x10;
if (r->parent != r->id) flag |= 0x100; if (r->parent != r->id) flag |= 0x100;
if (r->id != 0) flag |= 0x800; // TODO: make sure this is always working! else if (!r->sam_pri) flag |= 0x800;
mm_sprintf_lite(s, "%s\t%d\t%s\t%d\t%d\t", t->name, flag, mi->seq[r->rid].name, r->rs+1, r->mapq); mm_sprintf_lite(s, "%s\t%d\t%s\t%d\t%d\t", t->name, flag, mi->seq[r->rid].name, r->rs+1, r->mapq);
if (r->p) { // TODO: using hard clippings if (r->p) { // TODO: using hard clippings
uint32_t k, clip_len = r->rev? t->l_seq - r->qe : r->qs; uint32_t k, clip_len = r->rev? t->l_seq - r->qe : r->qs;

8
hit.c
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@ -27,6 +27,7 @@ void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
if (n <= 0 || n >= r->cnt) return; if (n <= 0 || n >= r->cnt) return;
*r2 = *r; *r2 = *r;
r2->id = -1; r2->id = -1;
r2->sam_pri = 0;
r2->p = 0; r2->p = 0;
r2->cnt = r->cnt - n; r2->cnt = r->cnt - n;
r2->score = (int32_t)(r->score * ((float)r2->cnt / r->cnt) + .499); r2->score = (int32_t)(r->score * ((float)r2->cnt / r->cnt) + .499);
@ -65,7 +66,7 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r) // and compu
void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,parent} in sync; also reset id void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,parent} in sync; also reset id
{ {
int *tmp, i, max_id = -1, n_tmp; int *tmp, i, max_id = -1, n_tmp, n_pri;
if (n_regs <= 0) return; if (n_regs <= 0) return;
for (i = 0; i < n_regs; ++i) for (i = 0; i < n_regs; ++i)
max_id = max_id > regs[i].id? max_id : regs[i].id; max_id = max_id > regs[i].id? max_id : regs[i].id;
@ -74,7 +75,7 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
for (i = 0; i < n_tmp; ++i) tmp[i] = -1; for (i = 0; i < n_tmp; ++i) tmp[i] = -1;
for (i = 0; i < n_regs; ++i) for (i = 0; i < n_regs; ++i)
if (regs[i].id >= 0) tmp[regs[i].id] = i; if (regs[i].id >= 0) tmp[regs[i].id] = i;
for (i = 0; i < n_regs; ++i) { for (i = n_pri = 0; i < n_regs; ++i) {
mm_reg1_t *r = &regs[i]; mm_reg1_t *r = &regs[i];
r->id = i; r->id = i;
if (r->parent == MM_PARENT_TMP_PRI) if (r->parent == MM_PARENT_TMP_PRI)
@ -82,6 +83,9 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
else if (r->parent >= 0 && tmp[r->parent] >= 0) else if (r->parent >= 0 && tmp[r->parent] >= 0)
r->parent = tmp[r->parent]; r->parent = tmp[r->parent];
else r->parent = MM_PARENT_UNSET; else r->parent = MM_PARENT_UNSET;
if (r->id == r->parent) {
if (n_pri++ == 0) r->sam_pri = 1;
}
} }
kfree(km, tmp); kfree(km, tmp);
} }

2
main.c
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@ -10,7 +10,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r114-pre" #define MM_VERSION "2.0-r115-pre"
void liftrlimit() void liftrlimit()
{ {

2
minimap.h
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@ -60,7 +60,7 @@ typedef struct {
int32_t qs, qe, rs, re; int32_t qs, qe, rs, re;
int32_t parent, subsc; int32_t parent, subsc;
int32_t as; int32_t as;
uint32_t mapq:8, split:2, n_sub:22; // TODO: n_sub is not used for now uint32_t mapq:8, split:2, sam_pri:1, n_sub:21; // TODO: n_sub is not used for now
mm_extra_t *p; mm_extra_t *p;
} mm_reg1_t; } mm_reg1_t;