Mercurial > repos > ryanmorin > nextgen_variant_identification
comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/kstring.h @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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-1:000000000000 | 0:74f5ea818cea |
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1 #ifndef KSTRING_H | |
2 #define KSTRING_H | |
3 | |
4 #include <stdlib.h> | |
5 #include <string.h> | |
6 #include <stdint.h> | |
7 | |
8 #ifndef kroundup32 | |
9 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) | |
10 #endif | |
11 | |
12 #ifndef KSTRING_T | |
13 #define KSTRING_T kstring_t | |
14 typedef struct __kstring_t { | |
15 size_t l, m; | |
16 char *s; | |
17 } kstring_t; | |
18 #endif | |
19 | |
20 int ksprintf(kstring_t *s, const char *fmt, ...); | |
21 int ksplit_core(char *s, int delimiter, int *_max, int **_offsets); | |
22 | |
23 // calculate the auxiliary array, allocated by calloc() | |
24 int *ksBM_prep(const uint8_t *pat, int m); | |
25 | |
26 /* Search pat in str and returned the list of matches. The size of the | |
27 * list is returned as n_matches. _prep is the array returned by | |
28 * ksBM_prep(). If it is a NULL pointer, ksBM_prep() will be called. */ | |
29 int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches); | |
30 | |
31 static inline int kputsn(const char *p, int l, kstring_t *s) | |
32 { | |
33 if (s->l + l + 1 >= s->m) { | |
34 s->m = s->l + l + 2; | |
35 kroundup32(s->m); | |
36 s->s = (char*)realloc(s->s, s->m); | |
37 } | |
38 strncpy(s->s + s->l, p, l); | |
39 s->l += l; | |
40 s->s[s->l] = 0; | |
41 return l; | |
42 } | |
43 | |
44 static inline int kputs(const char *p, kstring_t *s) | |
45 { | |
46 return kputsn(p, strlen(p), s); | |
47 } | |
48 | |
49 static inline int kputc(int c, kstring_t *s) | |
50 { | |
51 if (s->l + 1 >= s->m) { | |
52 s->m = s->l + 2; | |
53 kroundup32(s->m); | |
54 s->s = (char*)realloc(s->s, s->m); | |
55 } | |
56 s->s[s->l++] = c; | |
57 s->s[s->l] = 0; | |
58 return c; | |
59 } | |
60 | |
61 static inline int *ksplit(kstring_t *s, int delimiter, int *n) | |
62 { | |
63 int max = 0, *offsets = 0; | |
64 *n = ksplit_core(s->s, delimiter, &max, &offsets); | |
65 return offsets; | |
66 } | |
67 | |
68 #endif |