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a bit refactoring for future changes

This commit is contained in:
Heng Li 2021-04-30 11:24:53 -04:00
parent ba52c79024
commit cdbd96be0c
2 changed files with 17 additions and 16 deletions
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25
map.c
View File

@ -80,21 +80,14 @@ static void collect_minimizers(void *km, const mm_mapopt_t *opt, const mm_idx_t
#define heap_lt(a, b) ((a).x > (b).x)
KSORT_INIT(heap, mm128_t, heap_lt)
typedef struct {
uint32_t n;
uint32_t q_pos, q_span;
uint32_t seg_id:31, is_tandem:1;
const uint64_t *cr;
} mm_match_t;
static mm_match_t *collect_matches(void *km, int *_n_m, int max_occ, const mm_idx_t *mi, const mm128_v *mv, int64_t *n_a, int *rep_len, int *n_mini_pos, uint64_t **mini_pos)
static mm_seed_t *collect_matches(void *km, int *_n_m, int max_occ, const mm_idx_t *mi, const mm128_v *mv, int64_t *n_a, int *rep_len, int *n_mini_pos, uint64_t **mini_pos)
{
int rep_st = 0, rep_en = 0, n_m;
size_t i;
mm_match_t *m;
mm_seed_t *m;
*n_mini_pos = 0;
*mini_pos = (uint64_t*)kmalloc(km, mv->n * sizeof(uint64_t));
m = (mm_match_t*)kmalloc(km, mv->n * sizeof(mm_match_t));
m = (mm_seed_t*)kmalloc(km, mv->n * sizeof(mm_seed_t));
for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < mv->n; ++i) {
const uint64_t *cr;
mm128_t *p = &mv->a[i];
@ -108,7 +101,7 @@ static mm_match_t *collect_matches(void *km, int *_n_m, int max_occ, const mm_id
rep_st = st, rep_en = en;
} else rep_en = en;
} else {
mm_match_t *q = &m[n_m++];
mm_seed_t *q = &m[n_m++];
q->q_pos = q_pos, q->q_span = q_span, q->cr = cr, q->n = t, q->seg_id = p->y >> 32;
q->is_tandem = 0;
if (i > 0 && p->x>>8 == mv->a[i - 1].x>>8) q->is_tandem = 1;
@ -122,7 +115,7 @@ static mm_match_t *collect_matches(void *km, int *_n_m, int max_occ, const mm_id
return m;
}
static inline int skip_seed(int flag, uint64_t r, const mm_match_t *q, const char *qname, int qlen, const mm_idx_t *mi, int *is_self)
static inline int skip_seed(int flag, uint64_t r, const mm_seed_t *q, const char *qname, int qlen, const mm_idx_t *mi, int *is_self)
{
*is_self = 0;
if (qname && (flag & (MM_F_NO_DIAG|MM_F_NO_DUAL))) {
@ -151,7 +144,7 @@ static mm128_t *collect_seed_hits_heap(void *km, const mm_mapopt_t *opt, int max
{
int i, n_m, heap_size = 0;
int64_t j, n_for = 0, n_rev = 0;
mm_match_t *m;
mm_seed_t *m;
mm128_t *a, *heap;
m = collect_matches(km, &n_m, max_occ, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
@ -168,7 +161,7 @@ static mm128_t *collect_seed_hits_heap(void *km, const mm_mapopt_t *opt, int max
}
ks_heapmake_heap(heap_size, heap);
while (heap_size > 0) {
mm_match_t *q = &m[heap->y>>32];
mm_seed_t *q = &m[heap->y>>32];
mm128_t *p;
uint64_t r = heap->x;
int32_t is_self, rpos = (uint32_t)r >> 1;
@ -216,12 +209,12 @@ static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ,
int *n_mini_pos, uint64_t **mini_pos)
{
int i, n_m;
mm_match_t *m;
mm_seed_t *m;
mm128_t *a;
m = collect_matches(km, &n_m, max_occ, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
a = (mm128_t*)kmalloc(km, *n_a * sizeof(mm128_t));
for (i = 0, *n_a = 0; i < n_m; ++i) {
mm_match_t *q = &m[i];
mm_seed_t *q = &m[i];
const uint64_t *r = q->cr;
uint32_t k;
for (k = 0; k < q->n; ++k) {

8
mmpriv.h
View File

@ -36,6 +36,14 @@
extern "C" {
#endif
typedef struct {
uint32_t n;
uint32_t q_pos;
uint32_t q_span:31, flt:1;
uint32_t seg_id:31, is_tandem:1;
const uint64_t *cr;
} mm_seed_t;
typedef struct {
int n_u, n_a;
uint64_t *u;