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| /* 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_err(ks) ((ks)->end == -1) | ||
| #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_err(ks)) return -3; \ | ||
| 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;} \ | ||
| if (ks->end == -1) { ks->is_eof = 1; return -3;}\ | ||
| } \ | ||
| 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_err(ks)) return -3; \ | ||
| 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; } \ | ||
| if (ks->end == -1) { ks->is_eof = 1; return -3; } \ | ||
| } 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 | ||
| -3 error reading stream | ||
| */ | ||
| #define __KSEQ_READ(SCOPE) \ | ||
| SCOPE int kseq_read(kseq_t *seq) \ | ||
| { \ | ||
| int c,r; \ | ||
| kstream_t *ks = seq->f; \ | ||
| if (seq->last_char == 0) { /* then jump to the next header line */ \ | ||
| while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '@'); \ | ||
| if (c < 0) return c; /* end of file or error*/ \ | ||
| 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 ((r=ks_getuntil(ks, 0, &seq->name, &c)) < 0) return r; /* normal exit: EOF or error */ \ | ||
| 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)) >= 0 && 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)) >= 0 && c != '\n'); /* skip the rest of '+' line */ \ | ||
| if (c == -1) return -2; /* error: no quality string */ \ | ||
| while ((c = ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l)); \ | ||
| if (c == -3) return -3; /* stream error */ \ | ||
| 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 |
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