-
Notifications
You must be signed in to change notification settings - Fork 18
/
bedcov-itree.cpp
131 lines (119 loc) · 2.78 KB
/
bedcov-itree.cpp
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
#include <zlib.h>
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include "IntervalTree.h"
#include "khash.h"
#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 0x10000)
typedef IntervalTree<int32_t, int32_t> ITree;
typedef struct {
ITree::interval_vector *a;
ITree *tree;
} range_index_t;
KHASH_MAP_INIT_STR(idx, range_index_t)
char *parse_bed(char *s, int32_t *st_, int32_t *en_)
{
char *p, *q, *ctg = 0;
int32_t i, st = -1, en = -1;
for (i = 0, p = q = s;; ++q) {
if (*q == '\t' || *q == '\0') {
int c = *q;
*q = 0;
if (i == 0) ctg = p;
else if (i == 1) st = atol(p);
else if (i == 2) en = atol(p);
++i, p = q + 1;
if (c == '\0') break;
}
}
*st_ = st, *en_ = en;
return i >= 3? ctg : 0;
}
khash_t(idx) *read_bed(const char *fn)
{
gzFile fp;
kstream_t *ks;
kstring_t str = {0,0,0};
khash_t(idx) *h;
if ((fp = gzopen(fn, "r")) == 0)
return 0;
ks = ks_init(fp);
h = kh_init(idx);
while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
char *ctg;
int32_t st, en;
ctg = parse_bed(str.s, &st, &en);
if (ctg) {
khint_t k;
int absent;
k = kh_put(idx, h, ctg, &absent);
if (absent) {
kh_key(h, k) = strdup(ctg);
kh_val(h, k).a = new ITree::interval_vector;
kh_val(h, k).tree = 0;
}
kh_val(h, k).a->push_back(ITree::interval(st + 1, en, kh_val(h, k).a->size()));
}
}
free(str.s);
ks_destroy(ks);
gzclose(fp);
for (khint_t k = 0; k < kh_end(h); ++k) {
if (!kh_exist(h, k)) continue;
range_index_t *p = &kh_val(h, k);
p->tree = new ITree(std::move(*p->a));
delete p->a;
p->a = 0;
}
return h;
}
int main(int argc, char *argv[])
{
gzFile fp;
kstream_t *ks;
kstring_t str = {0,0,0};
if (argc < 3) {
printf("Usage: bedcov <loaded.bed> <streamed.bed>\n");
return 0;
}
auto h = read_bed(argv[1]);
fp = gzopen(argv[2], "r");
assert(fp);
ks = ks_init(fp);
while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
int32_t st1, en1;
char *ctg;
ctg = parse_bed(str.s, &st1, &en1);
if (ctg == 0) continue;
auto k = kh_get(idx, h, ctg);
if (k == kh_end(h)) {
printf("%s\t%d\t%d\t0\t0\n", ctg, st1, en1);
continue;
}
auto a = kh_val(h, k).tree->findOverlapping(st1 + 1, en1, true);
int32_t cnt = 0, cov = 0, cov_st = 0, cov_en = 0;
for (size_t j = 0; j < a.size(); ++j) {
int32_t st0 = a[j].start - 1, en0 = a[j].stop;
if (st0 < st1) st0 = st1;
if (en0 > en1) en0 = en1;
if (st0 > cov_en) {
cov += cov_en - cov_st;
cov_st = st0, cov_en = en0;
} else cov_en = cov_en > en0? cov_en : en0;
++cnt;
}
cov += cov_en - cov_st;
printf("%s\t%d\t%d\t%d\t%d\n", ctg, st1, en1, cnt, cov);
}
free(str.s);
ks_destroy(ks);
gzclose(fp);
for (khint_t k = 0; k < kh_end(h); ++k)
if (kh_exist(h, k)) {
delete kh_val(h, k).tree;
free((void*)kh_key(h, k));
}
kh_destroy(idx, h);
return 0;
}