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moved array shrinking into chain_dp()

This commit is contained in:
Heng Li 2017-09-20 14:58:57 -04:00
parent 9943e5fdd0
commit 19d8eca3a1
3 changed files with 12 additions and 20 deletions
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10
chain.c
View File

@ -19,7 +19,7 @@ static inline int ilog2_32(uint32_t v)
return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
}
int mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int n_segs, int64_t n, mm128_t *a, uint64_t **_u, void *km)
mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
{ // TODO: make sure this works when n has more than 32 bits
int32_t st = 0, k, *f, *p, *t, *v, n_u, n_v;
int64_t i, j;
@ -148,6 +148,10 @@ int mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cn
k += n;
}
memcpy(u, u2, n_u * 8);
kfree(km, b); kfree(km, w); kfree(km, u2);
return n_u;
// write _a_ to _b_ and deallocate _a_ because _a_ is oversized, sometimes a lot
memcpy(b, a, n_v * sizeof(mm128_t));
*n_u_ = n_u;
kfree(km, a); kfree(km, w); kfree(km, u2);
return b;
}

20
map.c
View File

@ -252,7 +252,7 @@ static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *k
void mm_map_multi(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
int i, j, n_u, max_gap_ref, rep_len, qlen_sum, n_regs0;
int i, j, max_gap_ref, rep_len, qlen_sum, n_regs0;
int64_t n_a;
uint64_t *u;
mm128_t *a;
@ -275,23 +275,11 @@ void mm_map_multi(const mm_idx_t *mi, int n_segs, const int *qlens, const char *
}
max_gap_ref = opt->max_gap_ref >= 0? opt->max_gap_ref : opt->max_gap;
n_u = mm_chain_dp(max_gap_ref, opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, !!(opt->flag&MM_F_SPLICE), n_segs, n_a, a, &u, b->km);
if (n_u > 0) { // shrink _a_ because after chaining, the size of _a_ may be much reduced
int64_t n_a0 = n_a;
for (j = 0, n_a = 0; j < n_u; ++j)
n_a += (int32_t)u[j];
if (n_a < n_a0>>1) {
mm128_t *a0 = a;
a = (mm128_t*)kmalloc(b->km, n_a * sizeof(mm128_t));
memcpy(a, a0, n_a * sizeof(mm128_t)); // anything beyond n_a is not used
kfree(b->km, a0);
}
}
regs0 = mm_gen_regs(b->km, qlen_sum, n_u, u, a);
n_regs0 = n_u;
a = mm_chain_dp(max_gap_ref, opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, !!(opt->flag&MM_F_SPLICE), n_segs, n_a, a, &n_regs0, &u, b->km);
regs0 = mm_gen_regs(b->km, qlen_sum, n_regs0, u, a);
if (mm_dbg_flag & MM_DBG_PRINT_SEED)
for (j = 0; j < n_u; ++j)
for (j = 0; j < n_regs0; ++j)
for (i = regs0[j].as; i < regs0[j].as + regs0[j].cnt; ++i)
fprintf(stderr, "CN\t%d\t%s\t%d\t%c\t%d\t%d\t%d\n", j, mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),
i == regs0[j].as? 0 : ((int32_t)a[i].y - (int32_t)a[i-1].y) - ((int32_t)a[i].x - (int32_t)a[i-1].x));

2
mmpriv.h
View File

@ -63,7 +63,7 @@ void mm_idxopt_init(mm_idxopt_t *opt);
const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f);
int mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int n_segs, int64_t n, mm128_t *a, uint64_t **_u, void *km);
mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, 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);
mm_reg1_t *mm_gen_regs(void *km, int qlen, int n_u, uint64_t *u, mm128_t *a);