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compute mapq; not working for z-split yet

This commit is contained in:
Heng Li 2017-06-29 17:52:48 -04:00
parent 337c2a21cd
commit cc67f1b781
2 changed files with 13 additions and 0 deletions
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1
align.c
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@ -35,6 +35,7 @@ static void mm_reg_split(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *
r2->cnt = r->cnt - n;
r2->score = (int32_t)(r->score * ((float)r2->cnt / r->cnt) + .499);
r2->as = r->as + n;
r2->parent = -2;
mm_reg_set_coor(r2, qlen, a);
r->cnt -= r2->cnt;
r->score -= r2->score;

12
map.c
View File

@ -1,5 +1,6 @@
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "kthread.h"
#include "kvec.h"
#include "kalloc.h"
@ -284,6 +285,16 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int n_regs, mm_reg
kfree(km, aux);
}
void mm_set_mapq(mm_reg1_t *r, int which)
{
if (r->parent == which) {
int mapq;
mapq = (int)(30.0 * (1. - (float)r->subsc / r->score) * logf(r->score));
mapq = mapq > 0? mapq : 0;
r->mapq = mapq < 60? mapq : 60;
} else r->mapq = 0;
}
mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint32_t m_st, uint32_t m_en, const char *qname, int qlen, const char *seq, int *n_regs)
{
int i, n = m_en - m_st, j, n_u;
@ -363,6 +374,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
}
if (opt->flag & MM_F_CIGAR)
regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a);
for (i = 0; i < *n_regs; ++i) mm_set_mapq(&regs[i], i);
// free
kfree(b->km, a);