zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

keep the number of SW performed

This commit is contained in:
Heng Li 2013-02-16 11:03:27 -05:00
parent 8ee464478a
commit ea9fc7df48
2 changed files with 17 additions and 18 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
bwamem.c
View File

@ -664,7 +664,7 @@ static void *worker1(void *data)
static void *worker2(void *data)
{
extern void mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2]);
extern int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2]);
worker_t *w = (worker_t*)data;
int i;
if (!w->opt->is_pe) {
@ -673,10 +673,12 @@ static void *worker2(void *data)
free(w->regs[i].a);
}
} else {
int n = 0;
for (i = 0; i < w->n>>1; i += w->step) { // not implemented yet
mem_sam_pe(w->opt, w->bns, w->pac, w->pes, &w->seqs[i<<1], &w->regs[i<<1]);
n += mem_sam_pe(w->opt, w->bns, w->pac, w->pes, &w->seqs[i<<1], &w->regs[i<<1]);
free(w->regs[i<<1|0].a); free(w->regs[i<<1|1].a);
}
fprintf(stderr, "[M::%s@%d] performed mate-SW for %d reads\n", __func__, w->start, n);
}
return 0;
}

29
bwamem_pair.c
View File

@ -95,20 +95,18 @@ void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *
}
}
void mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_pestat_t pes[4], const mem_alnreg_t *a, int l_ms, const uint8_t *ms, mem_alnreg_v *ma)
int mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_pestat_t pes[4], const mem_alnreg_t *a, int l_ms, const uint8_t *ms, mem_alnreg_v *ma)
{
int i, r, skip[4];
int i, r, skip[4], n = 0;
for (r = 0; r < 4; ++r)
skip[r] = pes[r].failed? 1 : 0;
#if 0
for (i = 0; i < ma->n; ++i) { // check which orinentation has been found
int64_t dist;
r = mem_infer_dir(l_pac, a->rb, ma->a[i].rb, &dist);
if (dist >= pes[r].low && dist <= pes[r].high)
skip[r] = 1;
}
#endif
if (skip[0] + skip[1] + skip[2] + skip[3] == 4) return; // consistent pair exist; no need to perform SW
if (skip[0] + skip[1] + skip[2] + skip[3] == 4) return 0; // consistent pair exist; no need to perform SW
for (r = 0; r < 4; ++r) {
int is_rev, is_larger;
uint8_t *seq, *rev = 0, *ref;
@ -138,17 +136,12 @@ void mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const m
aln = ksw_align(l_ms, seq, len, ref, 5, opt->mat, opt->q, opt->r, xtra, 0);
memset(&b, 0, sizeof(mem_alnreg_t));
b.qb = aln.qb; b.qe = aln.qe + 1;
if (is_rev) {
b.rb = (l_pac<<1) - (rb + aln.te + 1);
b.re = (l_pac<<1) - (rb + aln.tb);
} else {
b.rb = rb + aln.tb;
b.re = rb + aln.te + 1;
}
b.rb = is_rev? (l_pac<<1) - (rb + aln.te + 1) : rb + aln.tb;
b.re = is_rev? (l_pac<<1) - (rb + aln.tb) : rb + aln.te + 1;
b.score = aln.score;
b.csub = aln.score2;
b.secondary = -1;
printf("*** %d, [%lld,%lld], %d:%d, (%lld,%lld), (%lld,%lld) == (%lld,%lld)\n", aln.score, rb, re, is_rev, is_larger, a->rb, a->re, ma->a[0].rb, ma->a[0].re, b.rb, b.re);
// printf("*** %d, [%lld,%lld], %d:%d, (%lld,%lld), (%lld,%lld) == (%lld,%lld)\n", aln.score, rb, re, is_rev, is_larger, a->rb, a->re, ma->a[0].rb, ma->a[0].re, b.rb, b.re);
kv_push(mem_alnreg_t, *ma, b); // make room for a new element
// move b s.t. ma is sorted
for (i = 0; i < ma->n - 1; ++i) // find the insertion point
@ -156,10 +149,12 @@ void mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const m
tmp = i;
for (i = ma->n - 1; i > tmp; --i) ma->a[i] = ma->a[i-1];
ma->a[i] = b;
++n;
}
if (rev == 0) free(rev);
free(ref);
}
return n;
}
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], bwahit_t h[2])
@ -217,8 +212,9 @@ int mem_pair(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_
return o.x == 0? -1 : 0;
}
void mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2])
int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2])
{
int n = 0;
kstring_t str;
bwahit_t h[2];
mem_alnreg_t a0[2];
@ -227,8 +223,8 @@ void mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, c
a0[0].score = a0[1].score = -1;
if (a[0].n) a0[0] = a[0].a[0];
if (a[1].n) a0[1] = a[1].a[0];
if (a0[0].score > 0) mem_matesw(opt, bns->l_pac, pac, pes, &a0[0], s[1].l_seq, (uint8_t*)s[1].seq, &a[1]);
if (a0[1].score > 0) mem_matesw(opt, bns->l_pac, pac, pes, &a0[1], s[0].l_seq, (uint8_t*)s[0].seq, &a[0]);
if (a0[0].score > 0) n += mem_matesw(opt, bns->l_pac, pac, pes, &a0[0], s[1].l_seq, (uint8_t*)s[1].seq, &a[1]);
if (a0[1].score > 0) n += mem_matesw(opt, bns->l_pac, pac, pes, &a0[1], s[0].l_seq, (uint8_t*)s[0].seq, &a[0]);
// pairing single-end hits
if (mem_pair(opt, bns->l_pac, pac, pes, s, a, h) == 0) { // successful pairing
bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, &s[0], &h[0], opt->is_hard);
@ -237,4 +233,5 @@ void mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, c
s[1].sam = str.s;
} else {
}
return n;
}