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r181: limit the max number of chains

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Heng Li
2020-04-02 21:55:00 -04:00
parent 3838482851
commit 968b4caef9
9 changed files with 65 additions and 34 deletions
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38
anchor.cpp
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@@ -17,6 +17,9 @@ KRADIX_SORT_INIT(ha_an2, anchor1_t, an_key2, 4)
#define oreg_xs_lt(a, b) (((uint64_t)(a).x_pos_s<<32|(a).x_pos_e) < ((uint64_t)(b).x_pos_s<<32|(b).x_pos_e))
KSORT_INIT(or_xs, overlap_region, oreg_xs_lt)
#define oreg_ss_lt(a, b) ((a).shared_seed > (b).shared_seed) // in the decending order
KSORT_INIT(or_ss, overlap_region, oreg_ss_lt)
typedef struct {
int n;
const ha_idxpos_t *a;
@@ -40,7 +43,7 @@ void ha_abuf_destroy(ha_abuf_t *ab)
free(ab->seed); free(ab->a); free(ab->mz.a); free(ab);
}
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double band_width_threshold, int keep_whole_chain)
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain)
{
extern void *ha_flt_tab;
extern ha_pt_t *ha_idx;
@@ -106,9 +109,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
}
cl->length = ab->n_a;
calculate_overlap_region_by_chaining(cl, overlap_list, rid, ucr->length, &R_INF, band_width_threshold, keep_whole_chain);
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
calculate_overlap_region_by_chaining(cl, overlap_list, rid, ucr->length, &R_INF, bw_thres, keep_whole_chain);
#if 0
if (overlap_list->length > 2000) {
@@ -120,4 +121,33 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
}
}
#endif
if ((int)overlap_list->length > max_n_chain) {
uint32_t n[2], s[2];
n[0] = n[1] = 0, s[0] = s[1] = 0;
for (i = 0; i < (uint32_t)overlap_list->length; ++i) {
const overlap_region *r = &overlap_list->list[i];
int dir = r->x_pos_s == 0? 0 : 1;
++n[dir];
if ((int)n[dir] == max_n_chain) s[dir] = r->shared_seed;
}
if (s[0] > 0 || s[1] > 0) {
for (i = 0, k = 0; i < (uint32_t)overlap_list->length; ++i) {
overlap_region *r = &overlap_list->list[i];
int dir = r->x_pos_s == 0? 0 : 1;
if (r->shared_seed > s[dir]) {
if ((uint32_t)k != i) {
overlap_region t;
t = overlap_list->list[k];
overlap_list->list[k] = overlap_list->list[i];
overlap_list->list[i] = t;
}
++k;
}
}
overlap_list->length = k;
}
}
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}