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r169: output more accurate col. 10&11 to PAF 

In r168, col.10 is smaller than what it should be. This confuses miniasm.
This commit is contained in:
Heng Li 2017-07-11 14:09:51 -04:00
parent 782449975d
commit 801bc84b01
4 changed files with 23 additions and 5 deletions
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5
format.c
View File

@ -56,8 +56,7 @@ static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
{
mm_sprintf_lite(s, "\tcm:i:%d", r->cnt);
if (r->p) mm_sprintf_lite(s, "\ts1:i:%d", r->score);
mm_sprintf_lite(s, "\tcm:i:%d\ts1:i:%d", r->cnt, r->score);
if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
if (r->split) mm_sprintf_lite(s, "\tzd:i:%d", r->split);
if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
@ -71,7 +70,7 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
else mm_sprintf_lite(s, "%d", r->rid);
mm_sprintf_lite(s, "\t%d\t%d\t%d", mi->seq[r->rid].len, r->rs, r->re);
if (r->p) mm_sprintf_lite(s, "\t%d\t%d", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
else mm_sprintf_lite(s, "\t%d\t%d", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
else mm_sprintf_lite(s, "\t%d\t%d", r->fuzzy_mlen, r->fuzzy_blen);
mm_sprintf_lite(s, "\t%d", r->mapq);
write_tags(s, r);
if (r->p) {

18
hit.c
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@ -3,8 +3,23 @@
#include "mmpriv.h"
#include "kalloc.h"
static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
static inline void mm_cal_fuzzy_len(mm_reg1_t *r, const mm128_t *a)
{
int i;
r->fuzzy_mlen = r->fuzzy_blen = 0;
if (r->cnt <= 0) return;
r->fuzzy_mlen = r->fuzzy_blen = a[r->as].y>>32&0xff;
for (i = r->as + 1; i < r->as + r->cnt; ++i) {
int span = a[i].y>>32&0xff;
int tl = (int32_t)a[i].x - (int32_t)a[i-1].x;
int ql = (int32_t)a[i].y - (int32_t)a[i-1].y;
r->fuzzy_blen += tl > ql? tl : ql;
r->fuzzy_mlen += tl > span && ql > span? span : tl < ql? tl : ql;
}
}
static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
{ // NB: r->as and r->cnt MUST BE set correctly for this function to work
int32_t k = r->as, q_span = (int32_t)(a[k].y>>32&0xff);
r->rev = a[k].x>>63;
r->rid = a[k].x<<1>>33;
@ -17,6 +32,7 @@ static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
r->qs = qlen - ((int32_t)a[k + r->cnt - 1].y + 1);
r->qe = qlen - ((int32_t)a[k].y + 1 - q_span);
}
mm_cal_fuzzy_len(r, a);
}
mm_reg1_t *mm_gen_regs(void *km, int qlen, int n_u, uint64_t *u, mm128_t *a) // convert chains to hits

4
main.c
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@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r168-pre"
#define MM_VERSION "2.0-r169-pre"
void liftrlimit()
{
@ -47,6 +47,7 @@ static struct option long_options[] = {
{ "int-rname", no_argument, 0, 0 },
{ "no-kalloc", no_argument, 0, 0 },
{ "print-qname", no_argument, 0, 0 },
{ "no-self", no_argument, 0, 0 },
{ "version", no_argument, 0, 'V' },
{ "min-count", required_argument, 0, 'n' },
{ "min-chain-score",required_argument, 0, 'm' },
@ -99,6 +100,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx == 2) keep_name = 0; // --int-rname
else if (c == 0 && long_idx == 3) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
else if (c == 0 && long_idx == 4) mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
else if (c == 0 && long_idx == 5) opt.flag |= MM_F_NO_SELF;
else if (c == 'V') {
puts(MM_VERSION);
return 0;

1
minimap.h
View File

@ -61,6 +61,7 @@ typedef struct {
int32_t qs, qe, rs, re;
int32_t parent, subsc;
int32_t as;
int32_t fuzzy_mlen, fuzzy_blen;
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_reg1_t;