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moved sorting to anchor.cpp for future changes

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Heng Li
2020-04-02 19:18:29 -04:00
parent 483ceb852c
commit 3838482851
2 changed files with 16 additions and 6 deletions
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16
anchor.cpp
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@@ -14,6 +14,9 @@ typedef struct { // this struct is not strictly necessary; we can use k_mer_pos
KRADIX_SORT_INIT(ha_an1, anchor1_t, an_key1, 8)
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)
typedef struct {
int n;
const ha_idxpos_t *a;
@@ -104,4 +107,17 @@ 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);
#if 0
if (overlap_list->length > 2000) {
fprintf(stderr, "B\t%ld\t%ld\t%ld\n", (long)rid, (long)overlap_list->length, (long)Get_READ_LENGTH(R_INF, rid));
for (int i = 0; i < (int)overlap_list->length; ++i) {
overlap_region *r = &overlap_list->list[i];
fprintf(stderr, "C\t%d\t%d\t%d\t%c\t%d\t%ld\t%d\t%d\t%c\t%d\n", (int)r->x_id, (int)r->x_pos_s, (int)r->x_pos_e, "+-"[r->x_pos_strand],
(int)r->y_id, (long)Get_READ_LENGTH(R_INF, r->y_id), (int)r->y_pos_s, (int)r->y_pos_e, "+-"[r->y_pos_strand], (int)r->shared_seed);
}
}
#endif
}