kseq.h File Reference

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

Go to the source code of this file.

Classes
struct	__kstring_t

Macros
#define	KS_SEP_SPACE   0
#define	KS_SEP_TAB   1
#define	KS_SEP_LINE   2
#define	KS_SEP_MAX   2
#define	__KS_TYPE(type_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(SCOPE, type_t, __bufsize)
#define	__KS_INLINED(__read)
#define	KSTRING_T   kstring_t
#define	kroundup32(x)   (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#define	__KS_GETUNTIL(SCOPE, __read)
#define	KSTREAM_INIT2(SCOPE, type_t, __read, __bufsize)
#define	KSTREAM_INIT(type_t, __read, __bufsize)   KSTREAM_INIT2(static, type_t, __read, __bufsize)
#define	KSTREAM_DECLARE(type_t, __read)
#define	kseq_rewind(ks)   ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
#define	__KSEQ_BASIC(SCOPE, type_t)
#define	__KSEQ_READ(SCOPE)
#define	__KSEQ_TYPE(type_t)
#define	KSEQ_INIT2(SCOPE, type_t, __read)
#define	KSEQ_INIT(type_t, __read)   KSEQ_INIT2(static, type_t, __read)
#define	KSEQ_DECLARE(type_t)

Typedefs
typedef struct __kstring_t	kstring_t

Macro Definition Documentation

#define __KS_BASIC	(		SCOPE,
			type_t,
			__bufsize
	)

Value:

SCOPE kstream_t *ks_init(type_t f) \
  { \
    kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
    ks->f = f; ks->bufsize = __bufsize; \
    ks->buf = (unsigned char*)malloc(__bufsize); \
    return ks; \
  } \
  SCOPE void ks_destroy(kstream_t *ks) \
  { \
    if (!ks) return; \
    free(ks->buf); \
    free(ks); \
  }

#define __KS_GETUNTIL	(		SCOPE,
			__read
	)

#define __KS_INLINED

(

__read

)

Value:

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, ks->bufsize); \
      if (ks->end < ks->bufsize) ks->is_eof = 1; \
      if (ks->end == 0) return -1; \
    } \
        ks->seek_pos++; \
    return (int)ks->buf[ks->begin++]; \
  } \
  static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
  { return ks_getuntil2(ks, delimiter, str, dret, 0); }

#define __KS_TYPE

(

type_t

)

Value:

typedef struct __kstream_t { \
    int begin, end; \
    int is_eof:2, bufsize:30; \
        uint64_t seek_pos; \
    type_t f; \
    unsigned char *buf; \
  } kstream_t;

#define __KSEQ_BASIC	(		SCOPE,
			type_t
	)

Value:

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);                           \
  }

#define __KSEQ_READ

(

SCOPE

)

#define __KSEQ_TYPE

(

type_t

)

Value:

typedef struct {              \
		kstring_t name, comment, seq, qual;   \
    int last_char;              \
    kstream_t *f;             \
  } kseq_t;

#define kroundup32

(

x

)

(--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))

#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_SEP_LINE   2

#define KS_SEP_MAX   2

#define KS_SEP_SPACE   0

#define KS_SEP_TAB   1

#define KSEQ_DECLARE

(

type_t

)

Value:

__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);

#define KSEQ_INIT	(		type_t,
			__read
	)		KSEQ_INIT2(static, type_t, __read)

#define KSEQ_INIT2	(		SCOPE,
			type_t,
			__read
	)

Value:

KSTREAM_INIT(type_t, __read, 16384)     \
	__KSEQ_TYPE(type_t)              \
	__KSEQ_BASIC(SCOPE, type_t)          \
	__KSEQ_READ(SCOPE)

#define kseq_rewind

(

ks

)

((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)

#define KSTREAM_DECLARE	(		type_t,
			__read
	)

Value:

__KS_TYPE(type_t) \
  extern int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append); \
  extern kstream_t *ks_init(type_t f); \
  extern void ks_destroy(kstream_t *ks); \
	__KS_INLINED(__read)

#define KSTREAM_INIT	(		type_t,
			__read,
			__bufsize
	)		KSTREAM_INIT2(static, type_t, __read, __bufsize)

#define KSTREAM_INIT2	(		SCOPE,
			type_t,
			__read,
			__bufsize
	)

Value:

__KS_TYPE(type_t) \
	__KS_BASIC(SCOPE, type_t, __bufsize) \
	__KS_GETUNTIL(SCOPE, __read) \
	__KS_INLINED(__read)

#define KSTRING_T   kstring_t

Typedef Documentation

typedef struct __kstring_t kstring_t