diff options
Diffstat (limited to 'debian/vendor-h2o/deps/klib/kseq.h')
| -rw-r--r-- | debian/vendor-h2o/deps/klib/kseq.h | 235 |
1 files changed, 0 insertions, 235 deletions
diff --git a/debian/vendor-h2o/deps/klib/kseq.h b/debian/vendor-h2o/deps/klib/kseq.h deleted file mode 100644 index b2238d1..0000000 --- a/debian/vendor-h2o/deps/klib/kseq.h +++ /dev/null @@ -1,235 +0,0 @@ -/* 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_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->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;} \ - } \ - 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->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; } \ - } 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_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 - */ -#define __KSEQ_READ(SCOPE) \ - SCOPE int kseq_read(kseq_t *seq) \ - { \ - int c; \ - kstream_t *ks = seq->f; \ - if (seq->last_char == 0) { /* 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; \ - } /* 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 (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \ - 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)) != -1 && 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)) != -1 && c != '\n'); /* skip the rest of '+' line */ \ - if (c == -1) return -2; /* error: no quality string */ \ - while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \ - 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_TYPE(type_t) \ - typedef struct { \ - kstring_t name, comment, seq, qual; \ - int last_char; \ - kstream_t *f; \ - } kseq_t; - -#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 |