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r221: output SA in the SAM output

This commit is contained in:
Heng Li 2017-07-28 23:08:39 -04:00
parent 84922cfe41
commit 2179e9e24b
4 changed files with 32 additions and 7 deletions
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29
format.c
View File

@ -105,7 +105,7 @@ 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, const mm_bseq1_t *t, const mm_reg1_t *r)
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs)
{
int flag = 0;
s->l = 0;
@ -120,7 +120,7 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
if (r->parent != r->id) flag |= 0x100;
else if (!r->sam_pri) flag |= 0x800;
mm_sprintf_lite(s, "%s\t%d\t%s\t%d\t%d\t", t->name, flag, mi->seq[r->rid].name, r->rs+1, r->mapq);
if (r->p) { // TODO: using hard clippings
if (r->p) { // actually this should always be true for SAM output
uint32_t k, clip_len = r->rev? t->l_seq - r->qe : r->qs;
int clip_char = (flag&0x800)? 'H' : 'S';
if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
@ -144,6 +144,31 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
else mm_sprintf_lite(s, "*");
}
write_tags(s, r);
if (r->parent == r->id && r->p && n_regs > 1 && regs && r >= regs && r - regs < n_regs) { // supplementary aln may exist
int i, n_sa = 0; // n_sa: number of SA fields
for (i = 0; i < n_regs; ++i)
if (i != r - regs && regs[i].parent == regs[i].id && regs[i].p)
++n_sa;
if (n_sa > 0) {
mm_sprintf_lite(s, "\tSA:Z:");
for (i = 0; i < n_regs; ++i) {
const mm_reg1_t *q = &regs[i];
int l_M, l_I = 0, l_D = 0, clip5 = 0, clip3 = 0;
if (r == q || q->parent != q->id || q->p == 0) continue;
if (q->qe - q->qs < q->re - q->rs) l_M = q->qe - q->qs, l_D = (q->re - q->rs) - l_M;
else l_M = q->re - q->rs, l_I = (q->qe - q->qs) - l_M;
clip5 = q->rev? t->l_seq - q->qe : q->qs;
clip3 = q->rev? q->qs : t->l_seq - q->qe;
mm_sprintf_lite(s, "%s,%d,%c,", mi->seq[q->rid].name, q->rs+1, "+-"[q->rev]);
if (clip5) mm_sprintf_lite(s, "%dS", clip5);
if (l_M) mm_sprintf_lite(s, "%dM", l_M);
if (l_I) mm_sprintf_lite(s, "%dI", l_I);
if (l_D) mm_sprintf_lite(s, "%dD", l_D);
if (clip3) mm_sprintf_lite(s, "%dS", clip3);
mm_sprintf_lite(s, ",%d,%d;", q->mapq, q->p->n_diff);
}
}
}
}
s->s[s->l] = 0; // we always have room for an extra byte (see str_enlarge)
}

2
main.c
View File

@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r219-dirty"
#define MM_VERSION "2.0-r221-dirty"
void liftrlimit()
{

6
map.c
View File

@ -346,15 +346,15 @@ static void *worker_pipeline(void *shared, int step, void *in)
mm_bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, r);
if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, r, s->n_reg[i], s->reg[i]);
else mm_write_paf(&p->str, mi, t, r);
puts(p->str.s);
free(r->p);
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
mm_write_sam(&p->str, 0, t, 0);
mm_write_sam(&p->str, 0, t, 0, 0, 0);
puts(p->str.s);
}
for (j = 0; j < s->n_reg[i]; ++j) free(s->reg[i][j].p);
free(s->reg[i]);
free(s->seq[i].seq); free(s->seq[i].name);
if (s->seq[i].qual) free(s->seq[i].qual);

2
mmpriv.h
View File

@ -40,7 +40,7 @@ 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, const mm_bseq1_t *t, const mm_reg1_t *r);
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r);
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);
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);