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keep track of the "parent" of a secondary

This commit is contained in:
Heng Li 2013-02-12 15:52:23 -05:00
parent 22b79b3475
commit cd0969332f
2 changed files with 7 additions and 5 deletions
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9
bwamem.c
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@ -351,7 +351,7 @@ void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a) // IMPORT
kvec_t(int) z; kvec_t(int) z;
if (n == 0) return; if (n == 0) return;
kv_init(z); kv_init(z);
for (i = 0; i < n; ++i) a[i].sub = a[i].is_primary = 0; for (i = 0; i < n; ++i) a[i].sub = 0, a[i].secondary = -1;
tmp = opt->a + opt->b > opt->q + opt->r? opt->a + opt->b : opt->q + opt->r; tmp = opt->a + opt->b > opt->q + opt->r? opt->a + opt->b : opt->q + opt->r;
kv_push(int, z, 0); kv_push(int, z, 0);
for (i = 1; i < n; ++i) { for (i = 1; i < n; ++i) {
@ -369,8 +369,8 @@ void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a) // IMPORT
} }
} }
if (k == z.n) kv_push(int, z, i); if (k == z.n) kv_push(int, z, i);
else a[i].secondary = z.a[k];
} }
for (k = 0; k < z.n; ++k) a[z.a[k]].is_primary = 1;
free(z.a); free(z.a);
} }
@ -597,7 +597,8 @@ 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->rb = a->rb; h->re = a->re; h->qb = a->qb; h->qe = a->qe;
h->score = a->score; h->score = a->score;
h->sub = a->sub > a->csub? a->sub : a->csub; h->sub = a->sub > a->csub? a->sub : a->csub;
h->qual = h->flag = 0; // these are unset h->qual = 0; // quality unset
h->flag = a->secondary? 0x100 : 0; // only the "secondary" bit is set
h->mb = h->me = -2; // mate positions are unset h->mb = h->me = -2; // mate positions are unset
} }
@ -610,7 +611,7 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
mem_mark_primary_se(opt, a->n, a->a); // NOTE: mem_sort_and_dedup() called in worker1() mem_mark_primary_se(opt, a->n, a->a); // NOTE: mem_sort_and_dedup() called in worker1()
for (k = 0; k < a->n; ++k) { for (k = 0; k < a->n; ++k) {
bwahit_t h; bwahit_t h;
if (!a->a[k].is_primary) continue; if (a->a[k].secondary >= 0) continue;
mem_alnreg2hit(&a->a[k], &h); mem_alnreg2hit(&a->a[k], &h);
h.qual = approx_mapq_se(opt, &a->a[k]); h.qual = approx_mapq_se(opt, &a->a[k]);
bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, &h, opt->is_hard); bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, &h, opt->is_hard);

3
bwamem.h
View File

@ -34,7 +34,8 @@ typedef struct {
typedef struct { typedef struct {
int64_t rb, re; int64_t rb, re;
int score, qb, qe, seedcov, sub, csub; // sub: suboptimal score; csub: suboptimal inside the chain int score, qb, qe, seedcov, sub, csub; // sub: suboptimal score; csub: suboptimal inside the chain
int sub_n, is_primary; int sub_n; // approximate number of suboptimal hits
int secondary; // non-negative if the hit is secondary
} mem_alnreg_t; } mem_alnreg_t;
typedef struct { typedef struct {