3 Copyright (c) 2008 Genome Research Ltd (GRL).
5 Permission is hereby granted, free of charge, to any person obtaining
6 a copy of this software and associated documentation files (the
7 "Software"), to deal in the Software without restriction, including
8 without limitation the rights to use, copy, modify, merge, publish,
9 distribute, sublicense, and/or sell copies of the Software, and to
10 permit persons to whom the Software is furnished to do so, subject to
11 the following conditions:
13 The above copyright notice and this permission notice shall be
14 included in all copies or substantial portions of the Software.
16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
17 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
18 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
20 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
21 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
22 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
26 /* Contact: Heng Li <lh3@sanger.ac.uk> */
35 #define __KS_TYPE(type_t) \
36 typedef struct __kstream_t { \
38 int begin, end, is_eof; \
42 #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
43 #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
45 #define __KS_BASIC(type_t, __bufsize) \
46 static inline kstream_t *ks_init(type_t f) \
48 kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
50 ks->buf = (char*)malloc(__bufsize); \
53 static inline void ks_destroy(kstream_t *ks) \
61 #define __KS_GETC(__read, __bufsize) \
62 static inline int ks_getc(kstream_t *ks) \
64 if (ks->is_eof && ks->begin >= ks->end) return -1; \
65 if (ks->begin >= ks->end) { \
67 ks->end = __read(ks->f, ks->buf, __bufsize); \
68 if (ks->end < __bufsize) ks->is_eof = 1; \
69 if (ks->end == 0) return -1; \
71 return (int)ks->buf[ks->begin++]; \
74 typedef struct __kstring_t {
80 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
83 #define __KS_GETUNTIL(__read, __bufsize) \
84 static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
86 if (dret) *dret = 0; \
88 if (ks->begin >= ks->end && ks->is_eof) return -1; \
91 if (ks->begin >= ks->end) { \
94 ks->end = __read(ks->f, ks->buf, __bufsize); \
95 if (ks->end < __bufsize) ks->is_eof = 1; \
96 if (ks->end == 0) break; \
100 for (i = ks->begin; i < ks->end; ++i) \
101 if (ks->buf[i] == delimiter) break; \
103 for (i = ks->begin; i < ks->end; ++i) \
104 if (isspace(ks->buf[i])) break; \
106 if (str->m - str->l < i - ks->begin + 1) { \
107 str->m = str->l + (i - ks->begin) + 1; \
108 kroundup32(str->m); \
109 str->s = (char*)realloc(str->s, str->m); \
111 memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
112 str->l = str->l + (i - ks->begin); \
115 if (dret) *dret = ks->buf[i]; \
119 str->s[str->l] = '\0'; \
123 #define KSTREAM_INIT(type_t, __read, __bufsize) \
125 __KS_BASIC(type_t, __bufsize) \
126 __KS_GETC(__read, __bufsize) \
127 __KS_GETUNTIL(__read, __bufsize)
129 #define __KSEQ_BASIC(type_t) \
130 static inline kseq_t *kseq_init(type_t fd) \
132 kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
133 s->f = ks_init(fd); \
136 static inline void kseq_rewind(kseq_t *ks) \
139 ks->f->is_eof = ks->f->begin = ks->f->end = 0; \
141 static inline void kseq_destroy(kseq_t *ks) \
144 free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
150 >=0 length of the sequence (normal)
152 -2 truncated quality string
154 #define __KSEQ_READ \
155 static int kseq_read(kseq_t *seq) \
158 kstream_t *ks = seq->f; \
159 if (seq->last_char == 0) { /* then jump to the next header line */ \
160 while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
161 if (c == -1) return -1; /* end of file */ \
162 seq->last_char = c; \
163 } /* the first header char has been read */ \
164 seq->comment.l = seq->seq.l = seq->qual.l = 0; \
165 if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \
166 if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \
167 while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
168 if (isgraph(c)) { /* printable non-space character */ \
169 if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
170 seq->seq.m = seq->seq.l + 2; \
171 kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
172 seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
174 seq->seq.s[seq->seq.l++] = (char)c; \
177 if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
178 seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
179 if (c != '+') return seq->seq.l; /* FASTA */ \
180 if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \
181 seq->qual.m = seq->seq.m; \
182 seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
184 while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
185 if (c == -1) return -2; /* we should not stop here */ \
186 while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \
187 if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
188 seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \
189 seq->last_char = 0; /* we have not come to the next header line */ \
190 if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
194 #define __KSEQ_TYPE(type_t) \
196 kstring_t name, comment, seq, qual; \
201 #define KSEQ_INIT(type_t, __read) \
202 KSTREAM_INIT(type_t, __read, 4096) \
203 __KSEQ_TYPE(type_t) \
204 __KSEQ_BASIC(type_t) \