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minor improvement to mapQ approx. 

That is not good enough, but I am tired and need rest...
This commit is contained in:
Heng Li 2013-02-07 22:09:58 -05:00
parent d8e4d57956
commit 245505deed
1 changed files with 11 additions and 2 deletions
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11
bwamem.c
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@ -457,6 +457,7 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
if (s->qual) kputsn(s->qual, s->l_seq, &str); if (s->qual) kputsn(s->qual, s->l_seq, &str);
else kputc('*', &str); else kputc('*', &str);
kputc('\n', &str); kputc('\n', &str);
goto ret_sam_se;
} }
for (k = 0; k < m; ++k) { for (k = 0; k < m; ++k) {
uint32_t *cigar = 0; uint32_t *cigar = 0;
@ -470,8 +471,14 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
if (n_cigar == 0) flag |= 8; if (n_cigar == 0) flag |= 8;
kputs(s->name, &str); kputc('\t', &str); kputw(flag, &str); kputc('\t', &str); kputs(s->name, &str); kputc('\t', &str); kputw(flag, &str); kputc('\t', &str);
kputs(bns->anns[rid].name, &str); kputc('\t', &str); kputuw(pos - bns->anns[rid].offset + 1, &str); kputc('\t', &str); kputs(bns->anns[rid].name, &str); kputc('\t', &str); kputuw(pos - bns->anns[rid].offset + 1, &str); kputc('\t', &str);
mapq = p->score? (int)(MAPQ_COEF * (1. - (float)(p->sub? p->sub : opt->min_seed_len * opt->a) / p->score) * log(p->score / opt->a) + .499) : 0; { // approximate mapQ
int sub = p->sub? p->sub : opt->min_seed_len * opt->a;
double identity;
mapq = p->score? (int)(MAPQ_COEF * (1. - (float)sub / p->score) * log(p->score / opt->a) + .499) : 0;
identity = (double)p->score / opt->a / (p->qe - p->qb);
mapq = identity < 0.95? (int)(mapq * identity * identity + .499) : mapq;
if (mapq > 60) mapq = 60; if (mapq > 60) mapq = 60;
}
kputw(mapq, &str); kputc('\t', &str); kputw(mapq, &str); kputc('\t', &str);
if (n_cigar) { if (n_cigar) {
int clip5, clip3; int clip5, clip3;
@ -495,6 +502,8 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
kputc('\n', &str); kputc('\n', &str);
free(cigar); free(cigar);
} }
ret_sam_se:
free(seq); free(seq);
s->sam = str.s; s->sam = str.s;
} }