-
Notifications
You must be signed in to change notification settings - Fork 1
/
kseq.h
315 lines (291 loc) · 22.6 KB
/
kseq.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
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
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
/* The MIT License
Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
/* Last Modified: 05MAR2012 */
#ifndef AC_KSEQ_H
#define AC_KSEQ_H
#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
#define KS_SEP_TAB 1 // isspace() && !' '
#define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows)
#define KS_SEP_MAX 2
#define __KS_TYPE(type_t) \
typedef struct __kstream_t \
{ \
unsigned char *buf; \
int begin, end, is_eof; \
type_t f; \
} kstream_t;
#define ks_err(ks) ((ks)->end == -1)
#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
#define __KS_BASIC(type_t, __bufsize) \
static inline kstream_t *ks_init(type_t f) \
{ \
kstream_t *ks = (kstream_t *)calloc(1, sizeof(kstream_t)); \
ks->f = f; \
ks->buf = (unsigned char *)malloc(__bufsize); \
return ks; \
} \
static inline void ks_destroy(kstream_t *ks) \
{ \
if (ks) \
{ \
free(ks->buf); \
free(ks); \
} \
}
#define __KS_GETC(__read, __bufsize) \
static inline int ks_getc(kstream_t *ks) \
{ \
if (ks_err(ks)) \
return -3; \
if (ks->is_eof && ks->begin >= ks->end) \
return -1; \
if (ks->begin >= ks->end) \
{ \
ks->begin = 0; \
ks->end = __read(ks->f, ks->buf, __bufsize); \
if (ks->end == 0) \
{ \
ks->is_eof = 1; \
return -1; \
} \
if (ks->end == -1) \
{ \
ks->is_eof = 1; \
return -3; \
} \
} \
return (int)ks->buf[ks->begin++]; \
}
#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t
{
size_t l, m;
char *s;
} kstring_t;
#endif
#ifndef kroundup32
#define kroundup32(x) (--(x), (x) |= (x) >> 1, (x) |= (x) >> 2, (x) |= (x) >> 4, (x) |= (x) >> 8, (x) |= (x) >> 16, ++(x))
#endif
#define __KS_GETUNTIL(__read, __bufsize) \
static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
{ \
int gotany = 0; \
if (dret) \
*dret = 0; \
str->l = append ? str->l : 0; \
for (;;) \
{ \
int i; \
if (ks_err(ks)) \
return -3; \
if (ks->begin >= ks->end) \
{ \
if (!ks->is_eof) \
{ \
ks->begin = 0; \
ks->end = __read(ks->f, ks->buf, __bufsize); \
if (ks->end == 0) \
{ \
ks->is_eof = 1; \
break; \
} \
if (ks->end == -1) \
{ \
ks->is_eof = 1; \
return -3; \
} \
} \
else \
break; \
} \
if (delimiter == KS_SEP_LINE) \
{ \
for (i = ks->begin; i < ks->end; ++i) \
if (ks->buf[i] == '\n') \
break; \
} \
else if (delimiter > KS_SEP_MAX) \
{ \
for (i = ks->begin; i < ks->end; ++i) \
if (ks->buf[i] == delimiter) \
break; \
} \
else if (delimiter == KS_SEP_SPACE) \
{ \
for (i = ks->begin; i < ks->end; ++i) \
if (isspace(ks->buf[i])) \
break; \
} \
else if (delimiter == KS_SEP_TAB) \
{ \
for (i = ks->begin; i < ks->end; ++i) \
if (isspace(ks->buf[i]) && ks->buf[i] != ' ') \
break; \
} \
else \
i = 0; /* never come to here! */ \
if (str->m - str->l < (size_t)(i - ks->begin + 1)) \
{ \
str->m = str->l + (i - ks->begin) + 1; \
kroundup32(str->m); \
str->s = (char *)realloc(str->s, str->m); \
} \
gotany = 1; \
memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
str->l = str->l + (i - ks->begin); \
ks->begin = i + 1; \
if (i < ks->end) \
{ \
if (dret) \
*dret = ks->buf[i]; \
break; \
} \
} \
if (!gotany && ks_eof(ks)) \
return -1; \
if (str->s == 0) \
{ \
str->m = 1; \
str->s = (char *)calloc(1, 1); \
} \
else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l - 1] == '\r') \
--str->l; \
str->s[str->l] = '\0'; \
return str->l; \
} \
static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
{ \
return ks_getuntil2(ks, delimiter, str, dret, 0); \
}
#define KSTREAM_INIT(type_t, __read, __bufsize) \
__KS_TYPE(type_t) \
__KS_BASIC(type_t, __bufsize) \
__KS_GETC(__read, __bufsize) \
__KS_GETUNTIL(__read, __bufsize)
#define __KSEQ_TYPE(type_t) \
typedef struct \
{ \
kstring_t name, comment, seq, qual; \
int last_char; \
kstream_t *f; \
} kseq_t;
#define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
#define __KSEQ_BASIC(SCOPE, type_t) \
SCOPE kseq_t *kseq_init(type_t fd) \
{ \
kseq_t *s = (kseq_t *)calloc(1, sizeof(kseq_t)); \
s->f = ks_init(fd); \
return s; \
} \
SCOPE void kseq_destroy(kseq_t *ks) \
{ \
if (!ks) \
return; \
free(ks->name.s); \
free(ks->comment.s); \
free(ks->seq.s); \
free(ks->qual.s); \
ks_destroy(ks->f); \
free(ks); \
}
/* Return value:
>=0 length of the sequence (normal)
-1 end-of-file
-2 truncated quality string
-3 error reading stream
*/
#define __KSEQ_READ(SCOPE) \
SCOPE int kseq_read(kseq_t *seq) \
{ \
int c, r; \
kstream_t *ks = seq->f; \
if (seq->last_char == 0) \
{ /* then jump to the next header line */ \
while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '@') \
; \
if (c < 0) \
return c; /* end of file or error*/ \
seq->last_char = c; \
} /* else: the first header char has been read in the previous call */ \
seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
if ((r = ks_getuntil(ks, 0, &seq->name, &c)) < 0) \
return r; /* normal exit: EOF or error */ \
if (c != '\n') \
ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
if (seq->seq.s == 0) \
{ /* we can do this in the loop below, but that is slower */ \
seq->seq.m = 256; \
seq->seq.s = (char *)malloc(seq->seq.m); \
} \
while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '+' && c != '@') \
{ \
if (c == '\n') \
continue; /* skip empty lines */ \
seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
} \
if (c == '>' || c == '@') \
seq->last_char = c; /* the first header char has been read */ \
if (seq->seq.l + 1 >= seq->seq.m) \
{ /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
seq->seq.m = seq->seq.l + 2; \
kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
seq->seq.s = (char *)realloc(seq->seq.s, seq->seq.m); \
} \
seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
if (c != '+') \
return seq->seq.l; /* FASTA */ \
if (seq->qual.m < seq->seq.m) \
{ /* allocate memory for qual in case insufficient */ \
seq->qual.m = seq->seq.m; \
seq->qual.s = (char *)realloc(seq->qual.s, seq->qual.m); \
} \
while ((c = ks_getc(ks)) >= 0 && c != '\n') \
; /* skip the rest of '+' line */ \
if (c == -1) \
return -2; /* error: no quality string */ \
while ((c = ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l)) \
; \
if (c == -3) \
return -3; /* stream error */ \
seq->last_char = 0; /* we have not come to the next header line */ \
if (seq->seq.l != seq->qual.l) \
return -2; /* error: qual string is of a different length */ \
return seq->seq.l; \
}
#define KSEQ_INIT2(SCOPE, type_t, __read) \
KSTREAM_INIT(type_t, __read, 16384) \
__KSEQ_TYPE(type_t) \
__KSEQ_BASIC(SCOPE, type_t) \
__KSEQ_READ(SCOPE)
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
#define KSEQ_DECLARE(type_t) \
__KS_TYPE(type_t) \
__KSEQ_TYPE(type_t) \
extern kseq_t *kseq_init(type_t fd); \
void kseq_destroy(kseq_t *ks); \
int kseq_read(kseq_t *seq);
#endif