xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-01 06:48:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

moved sorting to anchor.cpp for future changes

Browse Source
This commit is contained in:
Heng Li
2020-04-02 19:18:29 -04:00
parent 483ceb852c
commit 3838482851
2 changed files with 16 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Hash_Table.cpp
-6
View File
@@ -12,9 +12,6 @@ pthread_mutex_t output_mutex;
#define overlap_region_key(a) ((a).y_id)
KRADIX_SORT_INIT(overlap_region_sort, overlap_region, overlap_region_key, member_size(overlap_region, y_id))
#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)
void overlap_region_sort_y_id(overlap_region *a, long long n)
{
radix_sort_overlap_region_sort(a, a + n);
@@ -648,13 +645,10 @@ void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_r
if (tmp_region.x_id != tmp_region.y_id)
{
append_inexact_overlap_region_alloc(overlap_list, &tmp_region, R_INF, add_beg_end);
///append_inexact_overlap_region_alloc_back(overlap_list, &tmp_region, R_INF);
}
}
destory_fake_cigar(&(tmp_region.f_cigar));
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
anchor.cpp
+16
View File
@@ -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
}