Skip to content

Commit

Permalink
drop the old SAM writer
Browse files Browse the repository at this point in the history
  • Loading branch information
@lh3
lh3 committed Mar 12, 2013
1 parent 0b0455c commit 26f4c70
Show file tree
Hide file tree
Showing 3 changed files with 0 additions and 156 deletions.
148 changes: 0 additions & 148 deletions bwamem.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -607,113 +607,6 @@ static inline int infer_bw(int l1, int l2, int score, int a, int q, int r)
return w;
}

void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, const bwahit_t *p_, int is_hard, const bwahit_t *m)
{
#define is_mapped(x) ((x)->rb >= 0 && (x)->rb < (x)->re && (x)->re <= bns->l_pac<<1)
int score, n_cigar, is_rev = 0, rid, mid, copy_mate = 0, NM = -1;
uint32_t *cigar = 0;
int64_t pos = -1;
bwahit_t ptmp, *p = &ptmp;

if (!p_) { // in this case, generate an unmapped alignment
memset(&ptmp, 0, sizeof(bwahit_t));
ptmp.rb = ptmp.re = -1;
} else ptmp = *p_;
p->flag |= m? 1 : 0; // is paired in sequencing
p->flag |= !is_mapped(p)? 4 : 0; // is mapped
p->flag |= m && !is_mapped(m)? 8 : 0; // is mate mapped
if (m && !is_mapped(p) && is_mapped(m)) {
p->rb = m->rb; p->re = m->re; p->qb = 0; p->qe = s->l_seq;
copy_mate = 1;
}
p->flag |= p->rb >= bns->l_pac? 0x10 : 0; // is reverse strand
p->flag |= m && m->rb >= bns->l_pac? 0x20 : 0; // is mate on reverse strand
if (is_mapped(p) && m && !is_mapped(m) && (p->flag&0x10)) p->flag |= 0x20; // if mate is unmapped, it takes the strand of the current read
kputs(s->name, str); kputc('\t', str);
if (is_mapped(p)) { // has a coordinate, no matter whether it is mapped or copied from the mate
int sam_flag = p->flag&0xff; // the flag that will be outputed to SAM; it is not always the same as p->flag
if (p->flag&0x10000) sam_flag |= 0x100;
if (!copy_mate) {
int w2;
w2 = infer_bw(p->qe - p->qb, p->re - p->rb, p->score, mat[0], q, r);
w2 = w2 < w? w2 : w;
cigar = bwa_gen_cigar(mat, q, r, w2, bns->l_pac, pac, p->qe - p->qb, (uint8_t*)&s->seq[p->qb], p->rb, p->re, &score, &n_cigar, &NM);
p->flag |= n_cigar == 0? 4 : 0; // FIXME: check why this may happen (this has already happened)
} else n_cigar = 0, cigar = 0;
pos = bns_depos(bns, p->rb < bns->l_pac? p->rb : p->re - 1, &is_rev);
bns_cnt_ambi(bns, pos, p->re - p->rb, &rid);
kputw(sam_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);
kputw(p->qual, str); kputc('\t', str);
if (n_cigar) {
int i, clip5, clip3;
clip5 = is_rev? s->l_seq - p->qe : p->qb;
clip3 = is_rev? p->qb : s->l_seq - p->qe;
if (clip5) { kputw(clip5, str); kputc("SH"[(is_hard!=0)], str); }
for (i = 0; i < n_cigar; ++i) {
kputw(cigar[i]>>4, str); kputc("MIDSH"[cigar[i]&0xf], str);
}
if (clip3) { kputw(clip3, str); kputc("SH"[(is_hard!=0)], str); }
} else kputc('*', str);
} else { // no coordinate
kputw(p->flag, str);
kputs("\t*\t0\t0\t*", str);
rid = -1;
}
if (m && is_mapped(m)) { // then print mate pos and isize
pos = bns_depos(bns, m->rb < bns->l_pac? m->rb : m->re - 1, &is_rev);
bns_cnt_ambi(bns, pos, m->re - m->rb, &mid);
kputc('\t', str);
if (mid == rid) kputc('=', str);
else kputs(bns->anns[mid].name, str);
kputc('\t', str); kputuw(pos - bns->anns[mid].offset + 1, str);
kputc('\t', str);
if (mid == rid) {
int64_t p0 = p->rb < bns->l_pac? p->rb : (bns->l_pac<<1) - 1 - p->rb;
int64_t p1 = m->rb < bns->l_pac? m->rb : (bns->l_pac<<1) - 1 - m->rb;
kputw(-(p0 - p1 + (p0 > p1? 1 : p0 < p1? -1 : 0)), str);
} else kputw(0, str);
kputc('\t', str);
} else if (m && is_mapped(p)) { // then copy the position
kputsn("\t=\t", 3, str);
kputuw(pos - bns->anns[rid].offset + 1, str);
kputsn("\t0\t", 3, str);
} else kputsn("\t*\t0\t0\t", 7, str);
if (p->flag&0x100) { // for secondary alignments, don't write SEQ and QUAL
kputsn("*\t*", 3, str);
} else if (!(p->flag&0x10)) { // print SEQ and QUAL, the forward strand
int i, qb = 0, qe = s->l_seq;
if (!(p->flag&4) && is_hard) qb = p->qb, qe = p->qe;
ks_resize(str, str->l + (qe - qb) + 1);
for (i = qb; i < qe; ++i) str->s[str->l++] = "ACGTN"[(int)s->seq[i]];
kputc('\t', str);
if (s->qual) { // printf qual
ks_resize(str, str->l + (qe - qb) + 1);
for (i = qb; i < qe; ++i) str->s[str->l++] = s->qual[i];
str->s[str->l] = 0;
} else kputc('*', str);
} else { // the reverse strand
int i, qb = 0, qe = s->l_seq;
if (!(p->flag&4) && is_hard) qb = p->qb, qe = p->qe;
ks_resize(str, str->l + (qe - qb) + 1);
for (i = qe-1; i >= qb; --i) str->s[str->l++] = "TGCAN"[(int)s->seq[i]];
kputc('\t', str);
if (s->qual) { // printf qual
ks_resize(str, str->l + (qe - qb) + 1);
for (i = qe-1; i >= qb; --i) str->s[str->l++] = s->qual[i];
str->s[str->l] = 0;
} else kputc('*', str);
}
if (NM >= 0) { kputsn("\tNM:i:", 6, str); kputw(NM, str); }
if (p->score >= 0) { kputsn("\tAS:i:", 6, str); kputw(p->score, str); }
if (p->sub >= 0) { kputsn("\tXS:i:", 6, str); kputw(p->sub, str); }
if (bwa_rg_id[0]) { kputsn("\tRG:Z:", 6, str); kputs(bwa_rg_id, str); }
if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
kputc('\n', str);
free(cigar);
#undef is_mapped
}

static inline int get_rlen(int n_cigar, const uint32_t *cigar)
{
int k, l;
Expand Down Expand Up @@ -834,46 +727,6 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
return mapq;
}

void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h)
{
h->rb = a->rb; h->re = a->re; h->qb = a->qb; h->qe = a->qe;
h->score = a->score;
h->sub = a->secondary >= 0? -1 : a->sub > a->csub? a->sub : a->csub;
h->qual = 0; // quality unset
h->flag = a->secondary >= 0? 0x100 : 0; // only the "secondary" bit is set
}

void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const bwahit_t *m)
{
int k;
kstring_t str;
str.l = str.m = 0; str.s = 0;
if (a->n > 0 && a->a[0].score >= opt->T) {
int mapq0 = -1;
for (k = 0; k < a->n; ++k) {
bwahit_t h;
mem_alnreg_t *p = &a->a[k];
if (p->score < opt->T) continue;
if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
if (p->secondary >= 0 && p->score < a->a[p->secondary].score * .5) continue;
mem_alnreg2hit(p, &h);
bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)s->seq, &h.qb, &h.qe, &h.rb, &h.re);
h.flag |= extra_flag;
if ((opt->flag&MEM_F_NO_MULTI) && k && p->secondary < 0) h.flag |= 0x10000; // print the sequence, but flag as secondary (for Picard)
h.qual = p->secondary >= 0? 0 : mem_approx_mapq_se(opt, p);
if (k == 0) mapq0 = h.qual;
else if (h.qual > mapq0) h.qual = mapq0;
bwa_hit2sam(&str, opt->mat, opt->q, opt->r, p->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP, m);
}
} else {
bwahit_t h;
memset(&h, 0, sizeof(bwahit_t));
h.rb = h.re = -1; h.flag = extra_flag;
bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP, m);
}
s->sam = str.s;
}

void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m)
{
kstring_t str;
Expand Down Expand Up @@ -1024,7 +877,6 @@ static void *worker2(void *data)
if (!(w->opt->flag&MEM_F_PE)) {
for (i = w->start; i < w->n; i += w->step) {
mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a);
//mem_sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
mem_reg2sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
free(w->regs[i].a);
}
Expand Down
7 changes: 0 additions & 7 deletions bwamem.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -59,13 +59,6 @@ typedef struct {
double avg, std;
} mem_pestat_t;

typedef struct { // TODO: This is an intermediate struct only. Better get rid of it.
int64_t rb, re;
int qb, qe, flag, qual;
// optional info
int score, sub;
} bwahit_t;

typedef struct { // This struct is only used for the convenience of API.
int64_t pos; // forward strand 5'-end mapping position
int rid; // reference sequence index in bntseq_t; <0 for unmapped
Expand Down
1 change: 0 additions & 1 deletion bwamem_pair.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,6 @@ int mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const me

int mem_pair(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2], int id, int *sub, int *n_sub, int z[2])
{
extern void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h);
pair64_v v, u;
int r, i, k, y[4], ret; // y[] keeps the last hit
kv_init(v); kv_init(u);
Expand Down

0 comments on commit 26f4c70

Please sign in to comment.