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- Committer: Bazaar Package Importer
- Author(s): Charles Plessy
- Date: 2009-09-03 19:29:40 UTC
- Revision ID: james.westby@ubuntu.com-20090903192940-o9gv6ubu11aztg8b
Tags: upstream-0.1.5c
Import upstream version 0.1.5c
- files added:
- examples
- misc
added
removed
kseq.h
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/* The MIT License
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Copyright (c) 2008 Genome Research Ltd (GRL).
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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*/
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/* Contact: Heng Li <lh3@sanger.ac.uk> */
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/* Last Modified: 12APR2009 */
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#ifndef AC_KSEQ_H
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#define AC_KSEQ_H
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#include <ctype.h>
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#include <string.h>
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#include <stdlib.h>
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#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
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#define KS_SEP_TAB 1 // isspace() && !' '
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#define KS_SEP_MAX 1
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#define __KS_TYPE(type_t) \
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typedef struct __kstream_t { \
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char *buf; \
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int begin, end, is_eof; \
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type_t f; \
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} kstream_t;
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#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
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#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
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#define __KS_BASIC(type_t, __bufsize) \
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static inline kstream_t *ks_init(type_t f) \
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{ \
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kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
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ks->f = f; \
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ks->buf = (char*)malloc(__bufsize); \
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return ks; \
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} \
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static inline void ks_destroy(kstream_t *ks) \
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{ \
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if (ks) { \
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free(ks->buf); \
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free(ks); \
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} \
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}
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#define __KS_GETC(__read, __bufsize) \
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static inline int ks_getc(kstream_t *ks) \
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{ \
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if (ks->is_eof && ks->begin >= ks->end) return -1; \
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if (ks->begin >= ks->end) { \
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ks->begin = 0; \
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ks->end = __read(ks->f, ks->buf, __bufsize); \
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if (ks->end < __bufsize) ks->is_eof = 1; \
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if (ks->end == 0) return -1; \
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} \
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return (int)ks->buf[ks->begin++]; \
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}
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#ifndef KSTRING_T
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#define KSTRING_T kstring_t
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typedef struct __kstring_t {
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size_t l, m;
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char *s;
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} kstring_t;
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#endif
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#ifndef kroundup32
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#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
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#endif
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#define __KS_GETUNTIL(__read, __bufsize) \
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static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
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{ \
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if (dret) *dret = 0; \
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str->l = 0; \
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if (ks->begin >= ks->end && ks->is_eof) return -1; \
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for (;;) { \
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int i; \
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if (ks->begin >= ks->end) { \
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if (!ks->is_eof) { \
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ks->begin = 0; \
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ks->end = __read(ks->f, ks->buf, __bufsize); \
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if (ks->end < __bufsize) ks->is_eof = 1; \
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if (ks->end == 0) break; \
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} else break; \
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} \
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if (delimiter > KS_SEP_MAX) { \
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for (i = ks->begin; i < ks->end; ++i) \
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if (ks->buf[i] == delimiter) break; \
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} else if (delimiter == KS_SEP_SPACE) { \
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for (i = ks->begin; i < ks->end; ++i) \
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if (isspace(ks->buf[i])) break; \
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} else if (delimiter == KS_SEP_TAB) { \
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for (i = ks->begin; i < ks->end; ++i) \
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if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
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} else i = 0; /* never come to here! */ \
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if (str->m - str->l < i - ks->begin + 1) { \
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str->m = str->l + (i - ks->begin) + 1; \
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kroundup32(str->m); \
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str->s = (char*)realloc(str->s, str->m); \
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} \
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memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
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str->l = str->l + (i - ks->begin); \
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ks->begin = i + 1; \
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if (i < ks->end) { \
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if (dret) *dret = ks->buf[i]; \
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break; \
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} \
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} \
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if (str->l == 0) { \
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str->m = 1; \
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str->s = (char*)calloc(1, 1); \
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} \
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str->s[str->l] = '\0'; \
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return str->l; \
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}
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#define KSTREAM_INIT(type_t, __read, __bufsize) \
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__KS_TYPE(type_t) \
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__KS_BASIC(type_t, __bufsize) \
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__KS_GETC(__read, __bufsize) \
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__KS_GETUNTIL(__read, __bufsize)
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#define __KSEQ_BASIC(type_t) \
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static inline kseq_t *kseq_init(type_t fd) \
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{ \
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kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
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s->f = ks_init(fd); \
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return s; \
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} \
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static inline void kseq_rewind(kseq_t *ks) \
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{ \
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ks->last_char = 0; \
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ks->f->is_eof = ks->f->begin = ks->f->end = 0; \
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} \
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static inline void kseq_destroy(kseq_t *ks) \
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{ \
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if (!ks) return; \
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free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
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ks_destroy(ks->f); \
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free(ks); \
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}
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/* Return value:
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>=0 length of the sequence (normal)
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-1 end-of-file
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-2 truncated quality string
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*/
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#define __KSEQ_READ \
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static int kseq_read(kseq_t *seq) \
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{ \
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int c; \
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kstream_t *ks = seq->f; \
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if (seq->last_char == 0) { /* then jump to the next header line */ \
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while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
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if (c == -1) return -1; /* end of file */ \
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seq->last_char = c; \
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} /* the first header char has been read */ \
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seq->comment.l = seq->seq.l = seq->qual.l = 0; \
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if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \
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if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \
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while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
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if (isgraph(c)) { /* printable non-space character */ \
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if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
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seq->seq.m = seq->seq.l + 2; \
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kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
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seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
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} \
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seq->seq.s[seq->seq.l++] = (char)c; \
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} \
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} \
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if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
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seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
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if (c != '+') return seq->seq.l; /* FASTA */ \
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if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \
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seq->qual.m = seq->seq.m; \
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seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
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} \
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while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
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if (c == -1) return -2; /* we should not stop here */ \
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while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \
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if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
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seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \
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seq->last_char = 0; /* we have not come to the next header line */ \
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if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
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return seq->seq.l; \
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}
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#define __KSEQ_TYPE(type_t) \
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typedef struct { \
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kstring_t name, comment, seq, qual; \
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int last_char; \
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kstream_t *f; \
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} kseq_t;
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#define KSEQ_INIT(type_t, __read) \
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KSTREAM_INIT(type_t, __read, 4096) \
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__KSEQ_TYPE(type_t) \
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__KSEQ_BASIC(type_t) \
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__KSEQ_READ
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#endif
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