/usr/include/libGkArrays-2.1.0/kseq/kseq.h is in libgkarrays-dev 2.1.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | /* The MIT License
Copyright (c) 2008, by Heng Li <lh3@sanger.ac.uk>
2011, by Mikael Salson <mikael.salson@lifl.fr>
(added the ability to read raw files)
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.
*/
#ifndef AC_KSEQ_H
#define AC_KSEQ_H
#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#define __KS_TYPE(type_t) \
typedef struct __kstream_t { \
char *buf; \
int begin, end, is_eof; \
type_t f; \
char type; \
} kstream_t;
#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 = (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->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 < __bufsize) ks->is_eof = 1; \
if (ks->end == 0) return -1; \
} \
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_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
{ \
if (dret) *dret = 0; \
str->l = 0; \
if (ks->begin >= ks->end && ks->is_eof) return -1; \
for (;;) { \
int i; \
if (ks->begin >= ks->end) { \
if (!ks->is_eof) { \
ks->begin = 0; \
ks->end = __read(ks->f, ks->buf, __bufsize); \
if (ks->end < __bufsize) ks->is_eof = 1; \
if (ks->end == 0) break; \
} else break; \
} \
if (delimiter) { \
for (i = ks->begin; i < ks->end; ++i) \
if (ks->buf[i] == delimiter) break; \
} else { \
for (i = ks->begin; i < ks->end; ++i) \
if (isspace(ks->buf[i])) break; \
} \
if (((int) (str->m - str->l)) < i - ks->begin + 1) { \
str->m = str->l + (i - ks->begin) + 1; \
kroundup32(str->m); \
str->s = (char*)realloc(str->s, str->m); \
} \
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; \
} \
} \
str->s[str->l] = '\0'; \
return str->l; \
}
#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_BASIC(type_t) \
static inline kseq_t *kseq_init(type_t fd) \
{ \
kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
s->f = ks_init(fd); \
return s; \
} \
static inline void kseq_rewind(kseq_t *ks) \
{ \
ks->last_char = 0; \
ks->f->is_eof = ks->f->begin = ks->f->end = 0; \
} \
static inline 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
*/
#define __KSEQ_READ \
static void kseq_set_type(kstream_t *ks) { \
int c = ks_getc(ks); \
while (c != -1 && (c == '\r' || c == '\n' || c == ' ' || c == '\t')) \
c = ks_getc(ks); \
if ((c >= 'A' && c <= 'Z') || (c >= 'a' && c <= 'z')) { \
ks->type = 'r'; \
} else \
ks->type = 'f'; \
ks->begin--; \
} \
static int kseq_read(kseq_t *seq) \
{ \
int c; \
kstream_t *ks = seq->f; \
if (! ks->type) { \
kseq_set_type(ks); \
} \
if (seq->last_char == 0 && ks->type == 'f') { /* then jump to the next header line */ \
while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
if (c == -1) return -1; /* end of file */ \
seq->last_char = c; \
} /* the first header char has been read */ \
seq->comment.l = seq->seq.l = seq->qual.l = 0; \
if (ks->type == 'f') { \
if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \
if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \
} \
while ((c = ks_getc(ks)) != -1 \
&& ((ks->type == 'f' && c != '>' && c != '+' && c != '@') \
|| (ks->type == 'r' && c != '\n'))) { \
if (isgraph(c)) { /* printable non-space character */ \
if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
seq->seq.m = seq->seq.l + 2; \
kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
} \
seq->seq.s[seq->seq.l++] = (char)c; \
} \
} \
if (ks->type == 'r' && c==-1) return -1; \
if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
if (c != '+' || ks->type == 'r') return seq->seq.l; /* FASTA or raw */ \
if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \
seq->qual.m = seq->seq.m; \
seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
} \
while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
if (c == -1) return -2; /* we should not stop here */ \
while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \
if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \
seq->last_char = 0; /* we have not come to the next header line */ \
if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
return seq->seq.l; \
}
#define __KSEQ_TYPE(type_t) \
typedef struct { \
kstring_t name, comment, seq, qual; \
int last_char; \
kstream_t *f; \
} kseq_t;
#define KSEQ_INIT(type_t, __read) \
KSTREAM_INIT(type_t, __read, 4096) \
__KSEQ_TYPE(type_t) \
__KSEQ_BASIC(type_t) \
__KSEQ_READ
#endif
|