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r112: output z-drop

This commit is contained in:
Heng Li 2017-06-29 22:08:46 -04:00
parent 3825feeeac
commit 11167f511b
5 changed files with 22 additions and 16 deletions
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26
format.c
View File

@ -54,7 +54,16 @@ static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
s->s[s->l] = 0;
}
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r)
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);
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\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->score, r->p->n_ambi);
}
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r)
{
s->l = 0;
mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
@ -63,12 +72,11 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r)
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);
mm_sprintf_lite(s, "\t%d\tcm:i:%d", r->mapq, r->cnt);
if (r->p) mm_sprintf_lite(s, "\ts1:i:%d", r->score);
if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
mm_sprintf_lite(s, "\t%d", r->mapq);
write_tags(s, r);
if (r->p) {
uint32_t k;
mm_sprintf_lite(s, "\tNM:i:%d\tAS:i:%d\tnn:i:%d\tcg:Z:", r->p->n_diff, r->p->score, r->p->n_ambi);
mm_sprintf_lite(s, "cg:Z:");
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]);
}
@ -98,7 +106,7 @@ static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
} else str_copy(s, seq, seq + l);
}
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r)
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r)
{
int flag = 0;
s->l = 0;
@ -115,8 +123,6 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r)
} else mm_sprintf_lite(s, "*");
mm_sprintf_lite(s, "\t*\t0\t0\t");
sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
mm_sprintf_lite(s, "\t*\tcm:i:%d", r->cnt);
if (r->p) mm_sprintf_lite(s, "\ts1:i:%d", r->score);
if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->score, r->p->n_ambi);
mm_sprintf_lite(s, "\t*");
write_tags(s, r);
}

2
hit.c
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@ -36,7 +36,7 @@ void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
r->cnt -= r2->cnt;
r->score -= r2->score;
mm_reg_set_coor(r, qlen, a);
r->split = r2->split = 1;
r->split |= 1, r2->split |= 2;
}
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r) // and compute mm_reg1_t::subsc

2
main.c
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@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r111-pre"
#define MM_VERSION "2.0-r112-pre"
void liftrlimit()
{

4
minimap.h
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@ -54,13 +54,13 @@ typedef struct {
typedef struct {
int32_t id;
uint32_t cnt:30, rev:1, split:1;
uint32_t cnt:31, rev:1;
uint32_t rid:31, rep:1;
int32_t score;
int32_t qs, qe, rs, re;
int32_t parent, subsc;
int32_t as;
uint32_t mapq:8, n_sub:24; // TODO: n_sub is not used for now
uint32_t mapq:8, split:2, n_sub:22; // TODO: n_sub is not used for now
mm_extra_t *p;
} mm_reg1_t;

4
mmpriv.h
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@ -31,8 +31,8 @@ void radix_sort_128x(mm128_t *beg, mm128_t *end);
void radix_sort_64(uint64_t *beg, uint64_t *end);
uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r);
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r);
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r);
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r);
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int64_t n, mm128_t *a, uint64_t **_u, void *km);
mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);