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); \
        }

Definition at line 52 of file kseq.h.

#define __KS_GETUNTIL	(		SCOPE,
			__read
	)

Definition at line 95 of file kseq.h.

#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); }

Definition at line 67 of file kseq.h.

#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;

Definition at line 40 of file kseq.h.

#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);                                                                                                               \
        }

Definition at line 169 of file kseq.h.

#define __KSEQ_READ

(

SCOPE)

Definition at line 189 of file kseq.h.

#define __KSEQ_TYPE

(

type_t)

Value:

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

Definition at line 231 of file kseq.h.

#define kroundup32

(

x)

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

Definition at line 92 of file kseq.h.

#define ks_eof

(

ks)

((ks)->is_eof && (ks)->begin >= (ks)->end)

Definition at line 49 of file kseq.h.

#define ks_rewind

(

ks)

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

Definition at line 50 of file kseq.h.

#define KS_SEP_LINE   2

Definition at line 37 of file kseq.h.

#define KS_SEP_MAX   2

Definition at line 38 of file kseq.h.

#define KS_SEP_SPACE   0

Definition at line 35 of file kseq.h.

#define KS_SEP_TAB   1

Definition at line 36 of file kseq.h.

#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);

Definition at line 246 of file kseq.h.

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

Definition at line 244 of file kseq.h.

#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)

Definition at line 238 of file kseq.h.

#define kseq_rewind

(

ks)

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

Definition at line 167 of file kseq.h.

#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)

Definition at line 156 of file kseq.h.

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

Definition at line 154 of file kseq.h.

#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)

Definition at line 148 of file kseq.h.

#define KSTRING_T   kstring_t

Definition at line 84 of file kseq.h.

Typedef Documentation

typedef struct __kstring_t kstring_t