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r469: first step towards PE SAM

This commit is contained in:
Heng Li 2017-10-05 10:38:09 -04:00
parent 16e6e589a8
commit 7cc4f6f965
5 changed files with 83 additions and 37 deletions
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16
bseq.h
View File

@ -26,15 +26,19 @@ int mm_bseq_eof(mm_bseq_file_t *fp);
extern unsigned char seq_nt4_table[256];
extern unsigned char seq_comp_table[256];
static inline int mm_qname_len(const char *s)
{
int l;
l = strlen(s);
return l >= 3 && s[l-1] >= '0' && s[l-1] <= '9' && s[l-2] == '/'? l - 2 : l;
}
static inline int mm_qname_same(const char *s1, const char *s2)
{
int l1, l2;
l1 = strlen(s1);
l2 = strlen(s2);
if (l1 != l2 || l1 < 3) return 0;
if (!(s1[l1-1] >= '0' && s1[l1-1] <= '9' && s1[l1-2] == '/')) return 0;
if (!(s2[l2-1] >= '0' && s2[l2-1] <= '9' && s2[l2-2] == '/')) return 0;
return (strncmp(s1, s2, l1 - 2) == 0);
l1 = mm_qname_len(s1);
l2 = mm_qname_len(s2);
return (l1 == l2 && strncmp(s1, s2, l1) == 0);
}
static inline void mm_revcomp_bseq(mm_bseq1_t *s)

54
format.c
View File

@ -240,21 +240,30 @@ 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, int n_regs, const mm_reg1_t *regs)
void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regss, const mm_reg1_t *const* regss, void *km)
{
int flag = 0;
int flag = n_seg > 1? 0x1 : 0x0, n_regs = n_regss[seg_idx];
const mm_reg1_t *regs = regss[seg_idx];
const mm_reg1_t *r = n_regs > 0 && reg_idx < n_regs && reg_idx >= 0? &regs[reg_idx] : NULL;
// write QNAME
s->l = 0;
mm_sprintf_lite(s, "%s", t->name);
if (n_seg > 1) s->l = mm_qname_len(t->name); // trim the suffix like /1 or /2
// write up to CIGAR
if (r == 0) {
mm_sprintf_lite(s, "%s\t4\t*\t0\t0\t*\t*\t0\t0\t", t->name);
sam_write_sq(s, t->seq, t->l_seq, 0, 0);
mm_sprintf_lite(s, "\t");
if (t->qual) sam_write_sq(s, t->qual, t->l_seq, 0, 0);
else mm_sprintf_lite(s, "*");
mm_sprintf_lite(s, "\t4\t*\t0\t0\t*\t");
} else {
if (r->rev) flag |= 0x10;
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 (n_seg > 1) {
if (seg_idx == 0) flag |= 0x40;
else if (seg_idx == n_seg - 1) flag |= 0x80;
// TODO: set 0x2!!!
}
mm_sprintf_lite(s, "\t%d\t%s\t%d\t%d\t", flag, mi->seq[r->rid].name, r->rs+1, r->mapq);
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';
@ -264,7 +273,20 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
clip_len = r->rev? r->qs : t->l_seq - r->qe;
if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
} else mm_sprintf_lite(s, "*");
}
// write mate positions
if (n_seg > 1) {
mm_sprintf_lite(s, "\t*\t0\t0\t");
} else mm_sprintf_lite(s, "\t*\t0\t0\t");
// write SEQ and QUAL
if (r == 0) {
sam_write_sq(s, t->seq, t->l_seq, 0, 0);
mm_sprintf_lite(s, "\t");
if (t->qual) sam_write_sq(s, t->qual, t->l_seq, 0, 0);
else mm_sprintf_lite(s, "*");
} else {
if ((flag & 0x900) == 0) {
sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
mm_sprintf_lite(s, "\t");
@ -278,8 +300,13 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
if (t->qual) sam_write_sq(s, t->qual + r->qs, r->qe - r->qs, r->rev, 0);
else mm_sprintf_lite(s, "*");
}
}
// write tags
if (mm_rg_id[0]) mm_sprintf_lite(s, "\tRG:Z:%s", mm_rg_id);
if (n_seg > 2) mm_sprintf_lite(s, "\tFI:i:%d", seg_idx);
if (r) {
write_tags(s, r);
if (mm_rg_id[0]) mm_sprintf_lite(s, "\tRG:Z:%s", mm_rg_id);
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)
@ -306,5 +333,14 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
}
}
}
s->s[s->l] = 0; // we always have room for an extra byte (see str_enlarge)
}
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 i;
for (i = 0; i < n_regs; ++i)
if (r == &regs[i]) break;
mm_write_sam2(s, mi, t, 0, i, 1, &n_regs, &regs, NULL);
}

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r468-dirty"
#define MM_VERSION "2.2-r469-dirty"
#ifdef __linux__
#include <sys/resource.h>

47
map.c
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@ -410,7 +410,7 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
static void *worker_pipeline(void *shared, int step, void *in)
{
int i, j;
int i, j, k;
pipeline_t *p = (pipeline_t*)shared;
if (step == 0) { // step 0: read sequences
int with_qual = (!!(p->opt->flag & MM_F_OUT_SAM) && !(p->opt->flag & MM_F_NO_QUAL));
@ -448,29 +448,34 @@ static void *worker_pipeline(void *shared, int step, void *in)
for (i = 0; i < p->n_threads; ++i) mm_tbuf_destroy(s->buf[i]);
free(s->buf);
if ((p->opt->flag & MM_F_OUT_CS) && !(mm_dbg_flag & MM_DBG_NO_KALLOC)) km = km_init();
for (i = 0; i < s->n_seq; ++i) {
mm_bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
assert(!r->sam_pri || r->id == r->parent);
if ((p->opt->flag & MM_F_NO_PRINT_2ND) && r->id != r->parent)
continue;
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, km, p->opt->flag);
puts(p->str.s);
for (k = 0; k < s->n_frag; ++k) {
int seg_st = s->seg_off[k], seg_en = s->seg_off[k] + s->n_seg[k];
for (i = seg_st; i < seg_en; ++i) {
mm_bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
assert(!r->sam_pri || r->id == r->parent);
if ((p->opt->flag & MM_F_NO_PRINT_2ND) && r->id != r->parent)
continue;
if (p->opt->flag & MM_F_OUT_SAM)
mm_write_sam2(&p->str, mi, t, i - seg_st, j, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km);
else
mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
puts(p->str.s);
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km);
puts(p->str.s);
}
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
mm_write_sam(&p->str, 0, t, 0, 0, 0);
puts(p->str.s);
for (i = seg_st; i < seg_en; ++i) {
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);
}
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);
}
free(s->reg); free(s->n_reg); free(s->seq);
free(s->reg); free(s->n_reg); free(s->seq); // seg_off and n_seg were allocated with reg; no memory leak here
km_destroy(km);
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] mapped %d sequences\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), s->n_seq);

1
mmpriv.h
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@ -57,6 +57,7 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
void mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag);
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);
void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regs, const mm_reg1_t *const* regs, void *km);
void mm_idxopt_init(mm_idxopt_t *opt);
const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);