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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/include/mash/kseq.h @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 /* The MIT License
2
3 Copyright (c) 2008 Genome Research Ltd (GRL).
4
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:
12
13 The above copyright notice and this permission notice shall be
14 included in all copies or substantial portions of the Software.
15
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
23 SOFTWARE.
24 */
25
26 /* Contact: Heng Li <lh3@sanger.ac.uk> */
27
28 /* Last Modified: 12APR2009 */
29
30 #ifndef AC_KSEQ_H
31 #define AC_KSEQ_H
32
33 #include <ctype.h>
34 #include <string.h>
35 #include <stdlib.h>
36
37 #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
38 #define KS_SEP_TAB 1 // isspace() && !' '
39 #define KS_SEP_MAX 1
40
41 #define __KS_TYPE(type_t) \
42 typedef struct __kstream_t { \
43 char *buf; \
44 int begin, end, is_eof; \
45 type_t f; \
46 } kstream_t;
47
48 #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
49 #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
50
51 #define __KS_BASIC(type_t, __bufsize) \
52 static inline kstream_t *ks_init(type_t f) \
53 { \
54 kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
55 ks->f = f; \
56 ks->buf = (char*)malloc(__bufsize); \
57 return ks; \
58 } \
59 static inline void ks_destroy(kstream_t *ks) \
60 { \
61 if (ks) { \
62 free(ks->buf); \
63 free(ks); \
64 } \
65 }
66
67 #define __KS_GETC(__read, __bufsize) \
68 static inline int ks_getc(kstream_t *ks) \
69 { \
70 if (ks->is_eof && ks->begin >= ks->end) return -1; \
71 if (ks->begin >= ks->end) { \
72 ks->begin = 0; \
73 ks->end = __read(ks->f, ks->buf, __bufsize); \
74 if (ks->end < __bufsize) ks->is_eof = 1; \
75 if (ks->end == 0) return -1; \
76 } \
77 return (int)ks->buf[ks->begin++]; \
78 }
79
80 #ifndef KSTRING_T
81 #define KSTRING_T kstring_t
82 typedef struct __kstring_t {
83 size_t l, m;
84 char *s;
85 } kstring_t;
86 #endif
87
88 #ifndef kroundup32
89 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
90 #endif
91
92 #define __KS_GETUNTIL(__read, __bufsize) \
93 static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
94 { \
95 if (dret) *dret = 0; \
96 str->l = 0; \
97 if (ks->begin >= ks->end && ks->is_eof) return -1; \
98 for (;;) { \
99 int i; \
100 if (ks->begin >= ks->end) { \
101 if (!ks->is_eof) { \
102 ks->begin = 0; \
103 ks->end = __read(ks->f, ks->buf, __bufsize); \
104 if (ks->end < __bufsize) ks->is_eof = 1; \
105 if (ks->end == 0) break; \
106 } else break; \
107 } \
108 if (delimiter > KS_SEP_MAX) { \
109 for (i = ks->begin; i < ks->end; ++i) \
110 if (ks->buf[i] == delimiter) break; \
111 } else if (delimiter == KS_SEP_SPACE) { \
112 for (i = ks->begin; i < ks->end; ++i) \
113 if (isspace(ks->buf[i])) break; \
114 } else if (delimiter == KS_SEP_TAB) { \
115 for (i = ks->begin; i < ks->end; ++i) \
116 if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
117 } else i = 0; /* never come to here! */ \
118 if (str->m - str->l < i - ks->begin + 1) { \
119 str->m = str->l + (i - ks->begin) + 1; \
120 kroundup32(str->m); \
121 str->s = (char*)realloc(str->s, str->m); \
122 } \
123 memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
124 str->l = str->l + (i - ks->begin); \
125 ks->begin = i + 1; \
126 if (i < ks->end) { \
127 if (dret) *dret = ks->buf[i]; \
128 break; \
129 } \
130 } \
131 if (str->l == 0) { \
132 str->m = 1; \
133 str->s = (char*)calloc(1, 1); \
134 } \
135 str->s[str->l] = '\0'; \
136 return str->l; \
137 }
138
139 #define KSTREAM_INIT(type_t, __read, __bufsize) \
140 __KS_TYPE(type_t) \
141 __KS_BASIC(type_t, __bufsize) \
142 __KS_GETC(__read, __bufsize) \
143 __KS_GETUNTIL(__read, __bufsize)
144
145 #define __KSEQ_BASIC(type_t) \
146 static inline kseq_t *kseq_init(type_t fd) \
147 { \
148 kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
149 s->f = ks_init(fd); \
150 return s; \
151 } \
152 static inline void kseq_rewind(kseq_t *ks) \
153 { \
154 ks->last_char = 0; \
155 ks->f->is_eof = ks->f->begin = ks->f->end = 0; \
156 } \
157 static inline void kseq_destroy(kseq_t *ks) \
158 { \
159 if (!ks) return; \
160 free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
161 ks_destroy(ks->f); \
162 free(ks); \
163 }
164
165 /* Return value:
166 >=0 length of the sequence (normal)
167 -1 end-of-file
168 -2 truncated quality string
169 */
170 #define __KSEQ_READ \
171 static int kseq_read(kseq_t *seq) \
172 { \
173 int c; \
174 kstream_t *ks = seq->f; \
175 if (seq->last_char == 0) { /* then jump to the next header line */ \
176 while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
177 if (c == -1) return -1; /* end of file */ \
178 seq->last_char = c; \
179 } /* the first header char has been read */ \
180 seq->comment.l = seq->seq.l = seq->qual.l = 0; \
181 if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \
182 if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \
183 while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
184 if (isgraph(c)) { /* printable non-space character */ \
185 if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
186 seq->seq.m = seq->seq.l + 2; \
187 kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
188 seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
189 } \
190 seq->seq.s[seq->seq.l++] = (char)c; \
191 } \
192 } \
193 if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
194 seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
195 if (c != '+') return seq->seq.l; /* FASTA */ \
196 if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \
197 seq->qual.m = seq->seq.m; \
198 seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
199 } \
200 while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
201 if (c == -1) return -2; /* we should not stop here */ \
202 while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \
203 if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
204 seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \
205 seq->last_char = 0; /* we have not come to the next header line */ \
206 if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
207 return seq->seq.l; \
208 }
209
210 #define __KSEQ_TYPE(type_t) \
211 typedef struct { \
212 kstring_t name, comment, seq, qual; \
213 int last_char; \
214 kstream_t *f; \
215 } kseq_t;
216
217 #define KSEQ_INIT(type_t, __read) \
218 KSTREAM_INIT(type_t, __read, 4096) \
219 __KSEQ_TYPE(type_t) \
220 __KSEQ_BASIC(type_t) \
221 __KSEQ_READ
222
223 #endif