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r891: compute gap-compressed divergence

This commit is contained in:
Heng Li 2018-11-24 21:50:49 -05:00
parent 1b3a6a0fe5
commit 128476efc9
3 changed files with 22 additions and 5 deletions
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22
format.c
View File

@ -261,6 +261,18 @@ int mm_gen_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_r
return mm_gen_cs_or_MD(km, buf, max_len, mi, r, seq, 1, 0); return mm_gen_cs_or_MD(km, buf, max_len, mi, r, seq, 1, 0);
} }
double mm_event_identity(const mm_reg1_t *r)
{
int32_t i, n_gapo = 0, n_gap = 0;
if (r->p == 0) return -1.0f;
for (i = 0; i < r->p->n_cigar; ++i) {
int32_t op = r->p->cigar[i] & 0xf, len = r->p->cigar[i] >> 4;
if (op == 1 || op == 2)
++n_gapo, n_gap += len;
}
return (double)r->mlen / (r->blen - r->p->n_ambi - n_gap + n_gapo);
}
static inline void write_tags(kstring_t *s, const mm_reg1_t *r) static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
{ {
int type; int type;
@ -273,10 +285,14 @@ static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
} }
mm_sprintf_lite(s, "\ttp:A:%c\tcm:i:%d\ts1:i:%d", type, r->cnt, r->score); mm_sprintf_lite(s, "\ttp:A:%c\tcm:i:%d\ts1:i:%d", type, r->cnt, r->score);
if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc); if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
if (r->div >= 0.0f && r->div <= 1.0f) { if (r->p) {
char buf[8]; char buf[16];
snprintf(buf, 16, "%.4f", 1.0 - mm_event_identity(r));
mm_sprintf_lite(s, "\tde:f:%s", buf);
} else if (r->div >= 0.0f && r->div <= 1.0f) {
char buf[16];
if (r->div == 0.0f) buf[0] = '0', buf[1] = 0; if (r->div == 0.0f) buf[0] = '0', buf[1] = 0;
else sprintf(buf, "%.4f", r->div); else snprintf(buf, 16, "%.4f", r->div);
mm_sprintf_lite(s, "\tdv:f:%s", buf); mm_sprintf_lite(s, "\tdv:f:%s", buf);
} }
if (r->split) mm_sprintf_lite(s, "\tzd:i:%d", r->split); if (r->split) mm_sprintf_lite(s, "\tzd:i:%d", r->split);

2
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.14-r890-dirty" #define MM_VERSION "2.14-r891-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

3
minimap2.1
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@ -1,4 +1,4 @@
.TH minimap2 1 "5 November 2018" "minimap2-2.14 (r883)" "Bioinformatics tools" .TH minimap2 1 "5 November 2018" "minimap2-2.14-dirty (r891)" "Bioinformatics tools"
.SH NAME .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences minimap2 - mapping and alignment between collections of DNA sequences
@ -604,6 +604,7 @@ ts A Transcript strand (splice mode only)
cg Z CIGAR string (only in PAF) cg Z CIGAR string (only in PAF)
cs Z Difference string cs Z Difference string
dv f Approximate per-base sequence divergence dv f Approximate per-base sequence divergence
de f Gap-compressed per-base sequence divergence
.TE .TE
.PP .PP