35 #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r 36 #define KS_SEP_TAB 1 // isspace() && !' ' 37 #define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows) 40 #define __KS_TYPE(type_t) \ 41 typedef struct __kstream_t { \ 43 int begin, end, is_eof; \ 47 #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end) 48 #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0) 50 #define __KS_BASIC(type_t, __bufsize) \ 51 static inline kstream_t *ks_init(type_t f) \ 53 kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \ 55 ks->buf = (unsigned char*)malloc(__bufsize); \ 58 static inline void ks_destroy(kstream_t *ks) \ 66 #define __KS_GETC(__read, __bufsize) \ 67 static inline int ks_getc(kstream_t *ks) \ 69 if (ks->is_eof && ks->begin >= ks->end) return -1; \ 70 if (ks->begin >= ks->end) { \ 72 ks->end = __read(ks->f, ks->buf, __bufsize); \ 73 if (ks->end == 0) { ks->is_eof = 1; return -1;} \ 75 return (int)ks->buf[ks->begin++]; \ 79 #define KSTRING_T kstring_t 87 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) 90 #define __KS_GETUNTIL(__read, __bufsize) \ 91 static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \ 94 if (dret) *dret = 0; \ 95 str->l = append? str->l : 0; \ 98 if (ks->begin >= ks->end) { \ 101 ks->end = __read(ks->f, ks->buf, __bufsize); \ 102 if (ks->end == 0) { ks->is_eof = 1; break; } \ 105 if (delimiter == KS_SEP_LINE) { \ 106 for (i = ks->begin; i < ks->end; ++i) \ 107 if (ks->buf[i] == '\n') break; \ 108 } else 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; \ 118 if (str->m - str->l < (size_t)(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); \ 124 memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \ 125 str->l = str->l + (i - ks->begin); \ 128 if (dret) *dret = ks->buf[i]; \ 132 if (!gotany && ks_eof(ks)) return -1; \ 135 str->s = (char*)calloc(1, 1); \ 136 } else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \ 137 str->s[str->l] = '\0'; \ 140 static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ 141 { return ks_getuntil2(ks, delimiter, str, dret, 0); } 143 #define KSTREAM_INIT(type_t, __read, __bufsize) \ 145 __KS_BASIC(type_t, __bufsize) \ 146 __KS_GETC(__read, __bufsize) \ 147 __KS_GETUNTIL(__read, __bufsize) 149 #define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0) 151 #define __KSEQ_BASIC(SCOPE, type_t) \ 152 SCOPE kseq_t *kseq_init(type_t fd) \ 154 kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \ 155 s->f = ks_init(fd); \ 158 SCOPE void kseq_destroy(kseq_t *ks) \ 161 free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \ 171 #define __KSEQ_READ(SCOPE) \ 172 SCOPE int kseq_read(kseq_t *seq) \ 175 kstream_t *ks = seq->f; \ 176 if (seq->last_char == 0) { \ 177 while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \ 178 if (c == -1) return -1; \ 179 seq->last_char = c; \ 181 seq->comment.l = seq->seq.l = seq->qual.l = 0; \ 182 if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \ 183 if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); \ 184 if (seq->seq.s == 0) { \ 186 seq->seq.s = (char*)malloc(seq->seq.m); \ 188 while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \ 189 if (c == '\n') continue; \ 190 seq->seq.s[seq->seq.l++] = c; \ 191 ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); \ 193 if (c == '>' || c == '@') seq->last_char = c; \ 194 if (seq->seq.l + 1 >= seq->seq.m) { \ 195 seq->seq.m = seq->seq.l + 2; \ 196 kroundup32(seq->seq.m); \ 197 seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \ 199 seq->seq.s[seq->seq.l] = 0; \ 200 if (c != '+') return seq->seq.l; \ 201 if (seq->qual.m < seq->seq.m) { \ 202 seq->qual.m = seq->seq.m; \ 203 seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \ 205 while ((c = ks_getc(ks)) != -1 && c != '\n'); \ 206 if (c == -1) return -2; \ 207 while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \ 208 seq->last_char = 0; \ 209 if (seq->seq.l != seq->qual.l) return -2; \ 213 #define __KSEQ_TYPE(type_t) \ 215 kstring_t name, comment, seq, qual; \ 220 #define KSEQ_INIT2(SCOPE, type_t, __read) \ 221 KSTREAM_INIT(type_t, __read, 16384) \ 222 __KSEQ_TYPE(type_t) \ 223 __KSEQ_BASIC(SCOPE, type_t) \ 226 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 228 #define KSEQ_DECLARE(type_t) \ 230 __KSEQ_TYPE(type_t) \ 231 extern kseq_t *kseq_init(type_t fd); \ 232 void kseq_destroy(kseq_t *ks); \ 233 int kseq_read(kseq_t *seq);