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Update kseq to latest
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@GuillaumeHolley
GuillaumeHolley authored Jun 30, 2023
1 parent 98dfaa7 commit d2ff315
Showing 1 changed file with 125 additions and 112 deletions.
237 changes: 125 additions & 112 deletions src/kseq.h
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Original file line number Diff line number Diff line change
Expand Up @@ -23,12 +23,13 @@
SOFTWARE.
*/

/* Last Modified: 05MAR2012 */
/* Last Modified: 2017-02-11 */

#ifndef AC_KSEQ_H
#define AC_KSEQ_H

#include <ctype.h>
#include <stdint.h>
#include <string.h>
#include <stdlib.h>

Expand All @@ -37,190 +38,202 @@
#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; \
#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 < 0)
#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_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++]; \
#define __KS_GETC(__read, __bufsize) \
static inline int ks_getc(kstream_t *ks) \
{ \
if (ks_err(ks)) return -3; \
if (ks_eof(ks)) 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; } \
else if (ks->end < 0) { 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;
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; \
} \
#ifndef kroundup64
#define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x))
#endif

#define __KS_GETUNTIL(__read, __bufsize) \
static int64_t 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) { \
unsigned char *sep = (unsigned char*)memchr(ks->buf + ks->begin, '\n', ks->end - ks->begin); \
i = sep != NULL ? sep - ks->buf : ks->end; \
} 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 (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; \
} 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; \
kroundup64(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); \
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; \
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_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; \
#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); \
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) \
SCOPE int64_t kseq_read(kseq_t *seq) \
{ \
int c; \
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)) != -1 && c != '>' && c != '@'); \
if (c == -1) return -1; /* end of file */ \
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 (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
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)) != -1 && c != '>' && c != '+' && c != '@') { \
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 (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 */ \
kroundup64(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 */ \
seq->is_fastq = (c == '+'); \
if (!seq->is_fastq) 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 */ \
while ((c = ks_getc(ks)) >= 0 && 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); \
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; \
#define __KSEQ_TYPE(type_t) \
typedef struct { \
kstring_t name, comment, seq, qual; \
int last_char, is_fastq; \
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) \
#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)
Expand All @@ -230,6 +243,6 @@ typedef struct __kstring_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);
int64_t kseq_read(kseq_t *seq);

#endif

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