-
Notifications
You must be signed in to change notification settings - Fork 7
/
pgpriv.h
118 lines (98 loc) · 3.58 KB
/
pgpriv.h
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
#ifndef PGPRIV_H
#define PGPRIV_H
#include <stddef.h>
#include <stdlib.h>
#include "pangene.h"
#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
size_t l, m;
char *s;
} kstring_t;
#endif
#define PG_MALLOC(type, cnt) ((type*)malloc((cnt) * sizeof(type)))
#define PG_CALLOC(type, cnt) ((type*)calloc((cnt), sizeof(type)))
#define PG_REALLOC(type, ptr, cnt) ((type*)realloc((ptr), (cnt) * sizeof(type)))
#define PG_GROW(type, ptr, __i, __m) do { \
if ((__i) >= (__m)) { \
(__m) = (__i) + 1; \
(__m) += ((__m)>>1) + 16; \
(ptr) = PG_REALLOC(type, ptr, (__m)); \
} \
} while (0)
#define PG_GROW0(type, ptr, __i, __m) do { \
if ((__i) >= (__m)) { \
size_t old_m = (__m); \
(__m) = (__i) + 1; \
(__m) += ((__m)>>1) + 16; \
(ptr) = PG_REALLOC(type, ptr, (__m)); \
memset((ptr) + old_m, 0, ((__m) - old_m) * sizeof(type)); \
} \
} while (0)
#ifndef kroundup64
#define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x))
#endif
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
void radix_sort_pg128x(pg128_t *st, pg128_t *en);
void radix_sort_pg64(uint64_t *st, uint64_t *en);
void *pg_dict_init(int32_t do_copy);
void pg_dict_destroy(void *h_);
int32_t pg_dict_size(const void *h_);
const char **pg_dict_put(void *d_, const char *s, int32_t v0, int32_t *v1, int32_t *absent_);
int32_t pg_dict_get(const void *d_, const char *s);
int32_t pg_dict_inc(void *h_, const char *s, int32_t v0);
void *pg_read_list_dict(const char *o);
char *pg_strndup(const char *src, size_t n);
void pg_sprintf_lite(kstring_t *s, const char *fmt, ...);
double pg_cputime(void);
long pg_peakrss(void);
double pg_realtime(void);
double pg_percent_cpu(void);
const char *pg_timestamp(void);
int64_t pg_hit_cal_cm(const pg_hit_t *a, const pg_exon_t *e);
void pg_hit_sort(pg_genome_t *g, int32_t by_cm);
uint64_t pg_hit_overlap(const pg_genome_t *g, const pg_hit_t *aa, const pg_hit_t *ab);
int32_t pg_flag_pseudo(const pg_prot_t *prot, pg_genome_t *g);
int32_t pg_flag_pseudo_joint(const pg_opt_t *opt, pg_data_t *d);
int32_t pg_flt_subopt_isoform(const pg_prot_t *prot, int32_t n_gene, pg_genome_t *g);
int32_t pg_flt_chain_shadow(const pg_prot_t *prot, int32_t n_prot, pg_genome_t *g);
void pg_flag_representative(pg_data_t *d);
void pg_cap_score_dom(pg_data_t *d);
void pg_gen_g2s(pg_graph_t *q);
void pg_graph_flag_vtx(pg_graph_t *q);
void pg_gen_vtx(const pg_opt_t *opt, pg_graph_t *q);
int32_t pg_mark_branch_flt_arc(const pg_opt_t *opt, pg_graph_t *q);
int32_t pg_mark_branch_flt_hit(const pg_opt_t *opt, pg_graph_t *q);
int32_t pg_flt_ov_isoform(const pg_opt_t *opt, pg_data_t *d, int32_t id, int32_t check_stand);
int32_t pg_shadow(const pg_opt_t *opt, pg_data_t *d, int32_t id, int32_t cal_dom_sc, int32_t check_strand);
char *pg_strdup(const char *src);
static inline uint32_t pg_hash_uint32(uint32_t key)
{
key += ~(key << 15);
key ^= (key >> 10);
key += (key << 3);
key ^= (key >> 6);
key += ~(key << 11);
key ^= (key >> 16);
return key;
}
static inline const pg_arc_t *pg_get_arc(const pg_graph_t *q, uint32_t v, uint32_t w)
{
int32_t i, n = (int32_t)q->idx[v];
const pg_arc_t *a = &q->arc[q->idx[v]>>32];
for (i = 0; i < n; ++i)
if ((uint32_t)a[i].x == w)
return &a[i];
return 0;
}
#define PG_SET_FILTER(__d, __field) do { \
int32_t j, i; \
for (j = 0; j < (__d)->n_genome; ++j) { \
pg_genome_t *g = &(__d)->genome[j]; \
for (i = 0; i < g->n_hit; ++i) \
if (g->hit[i].__field) g->hit[i].flt = 1; \
} \
} while (0)
#endif