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
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
|
#include <stdlib.h>
#include <stdint.h>
#include <string.h>
#include <stdio.h>
#include <zlib.h>
#ifdef _WIN32
#define drand48() ((double)rand() / RAND_MAX)
#endif
#include "ksort.h"
KSORT_INIT_GENERIC(uint64_t)
#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 8192)
typedef struct {
int n, m;
uint64_t *a;
int *idx;
} bed_reglist_t;
#include "khash.h"
KHASH_MAP_INIT_STR(reg, bed_reglist_t)
#define LIDX_SHIFT 13
typedef kh_reg_t reghash_t;
int *bed_index_core(int n, uint64_t *a, int *n_idx)
{
int i, j, m, *idx;
m = *n_idx = 0; idx = 0;
for (i = 0; i < n; ++i) {
int beg, end;
beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT;
if (m < end + 1) {
int oldm = m;
m = end + 1;
kroundup32(m);
idx = realloc(idx, m * sizeof(int));
for (j = oldm; j < m; ++j) idx[j] = -1;
}
if (beg == end) {
if (idx[beg] < 0) idx[beg] = i;
} else {
for (j = beg; j <= end; ++j)
if (idx[j] < 0) idx[j] = i;
}
*n_idx = end + 1;
}
return idx;
}
void bed_index(void *_h)
{
reghash_t *h = (reghash_t*)_h;
khint_t k;
for (k = 0; k < kh_end(h); ++k) {
if (kh_exist(h, k)) {
bed_reglist_t *p = &kh_val(h, k);
if (p->idx) free(p->idx);
ks_introsort(uint64_t, p->n, p->a);
p->idx = bed_index_core(p->n, p->a, &p->m);
}
}
}
int bed_overlap_core(const bed_reglist_t *p, int beg, int end)
{
int i, min_off;
if (p->n == 0) return 0;
min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT];
if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here
int n = beg>>LIDX_SHIFT;
if (n > p->n) n = p->n;
for (i = n - 1; i >= 0; --i)
if (p->idx[i] >= 0) break;
min_off = i >= 0? p->idx[i] : 0;
}
for (i = min_off; i < p->n; ++i) {
if ((int)(p->a[i]>>32) >= end) break; // out of range; no need to proceed
if ((int32_t)p->a[i] > beg && (int32_t)(p->a[i]>>32) < end)
return 1; // find the overlap; return
}
return 0;
}
int bed_overlap(const void *_h, const char *chr, int beg, int end)
{
const reghash_t *h = (const reghash_t*)_h;
khint_t k;
if (!h) return 0;
k = kh_get(reg, h, chr);
if (k == kh_end(h)) return 0;
return bed_overlap_core(&kh_val(h, k), beg, end);
}
void *bed_read(const char *fn)
{
reghash_t *h = kh_init(reg);
gzFile fp;
kstream_t *ks;
int dret;
kstring_t *str;
// read the list
fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) return 0;
str = calloc(1, sizeof(kstring_t));
ks = ks_init(fp);
while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name
int beg = -1, end = -1;
bed_reglist_t *p;
khint_t k = kh_get(reg, h, str->s);
if (k == kh_end(h)) { // absent from the hash table
int ret;
char *s = strdup(str->s);
k = kh_put(reg, h, s, &ret);
memset(&kh_val(h, k), 0, sizeof(bed_reglist_t));
}
p = &kh_val(h, k);
if (dret != '\n') { // if the lines has other characters
if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
beg = atoi(str->s); // begin
if (dret != '\n') {
if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
end = atoi(str->s); // end
if (end < beg) end = -1;
}
}
}
}
if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); // skip the rest of the line
if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column
if (beg >= 0 && end > beg) {
if (p->n == p->m) {
p->m = p->m? p->m<<1 : 4;
p->a = realloc(p->a, p->m * 8);
}
p->a[p->n++] = (uint64_t)beg<<32 | end;
}
}
ks_destroy(ks);
gzclose(fp);
free(str->s); free(str);
bed_index(h);
return h;
}
void bed_destroy(void *_h)
{
reghash_t *h = (reghash_t*)_h;
khint_t k;
for (k = 0; k < kh_end(h); ++k) {
if (kh_exist(h, k)) {
free(kh_val(h, k).a);
free(kh_val(h, k).idx);
free((char*)kh_key(h, k));
}
}
kh_destroy(reg, h);
}
|
