tbx.h File Reference

#include "hts.h"

Go to the source code of this file.

Classes
struct	tbx_conf_t
struct	tbx_t

Macros
#define	TBX_MAX_SHIFT   31
#define	TBX_GENERIC   0
#define	TBX_SAM   1
#define	TBX_VCF   2
#define	TBX_UCSC   0x10000
#define	tbx_itr_destroy(iter)   hts_itr_destroy(iter)
#define	tbx_itr_queryi(tbx, tid, beg, end)   hts_itr_query((tbx)->idx, (tid), (beg), (end), tbx_readrec)
#define	tbx_itr_querys(tbx, s)   hts_itr_querys((tbx)->idx, (s), (hts_name2id_f)(tbx_name2id), (tbx), hts_itr_query, tbx_readrec)
#define	tbx_itr_next(htsfp, tbx, itr, r)   hts_itr_next(hts_get_bgzfp(htsfp), (itr), (r), (tbx))
#define	tbx_bgzf_itr_next(bgzfp, tbx, itr, r)   hts_itr_next((bgzfp), (itr), (r), (tbx))

Functions
int	tbx_name2id (tbx_t *tbx, const char *ss)
BGZF *	hts_get_bgzfp (htsFile *fp)
int	tbx_readrec (BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end)
int	tbx_index_build (const char *fn, int min_shift, const tbx_conf_t *conf)
tbx_t *	tbx_index_load (const char *fn)
const char **	tbx_seqnames (tbx_t *tbx, int *n)
void	tbx_destroy (tbx_t *tbx)

Variables
tbx_conf_t	tbx_conf_gff
tbx_conf_t	tbx_conf_bed
tbx_conf_t	tbx_conf_psltbl
tbx_conf_t	tbx_conf_sam
tbx_conf_t	tbx_conf_vcf

Macro Definition Documentation

#define tbx_bgzf_itr_next	(		bgzfp,
			tbx,
			itr,
			r
	)		hts_itr_next((bgzfp), (itr), (r), (tbx))

Definition at line 35 of file tbx.h.

#define TBX_GENERIC   0

Definition at line 8 of file tbx.h.

#define tbx_itr_destroy

(

iter)

hts_itr_destroy(iter)

Definition at line 31 of file tbx.h.

#define tbx_itr_next	(		htsfp,
			tbx,
			itr,
			r
	)		hts_itr_next(hts_get_bgzfp(htsfp), (itr), (r), (tbx))

Definition at line 34 of file tbx.h.

#define tbx_itr_queryi	(		tbx,
			tid,
			beg,
			end
	)		hts_itr_query((tbx)->idx, (tid), (beg), (end), tbx_readrec)

Definition at line 32 of file tbx.h.

#define tbx_itr_querys	(		tbx,
			s
	)		hts_itr_querys((tbx)->idx, (s), (hts_name2id_f)(tbx_name2id), (tbx), hts_itr_query, tbx_readrec)

Definition at line 33 of file tbx.h.

#define TBX_MAX_SHIFT   31

Definition at line 6 of file tbx.h.

#define TBX_SAM   1

Definition at line 9 of file tbx.h.

#define TBX_UCSC   0x10000

Definition at line 11 of file tbx.h.

#define TBX_VCF   2

Definition at line 10 of file tbx.h.

Function Documentation

BGZF* hts_get_bgzfp

(

htsFile *

fp)

Definition at line 259 of file hts.c.

void tbx_destroy

(

tbx_t *

tbx)

Definition at line 214 of file tbx.c.

int tbx_index_build	(	const char *	fn,
		int	min_shift,
		const tbx_conf_t *	conf
	)

Definition at line 228 of file tbx.c.

tbx_t* tbx_index_load

(

const char *

fn)

Definition at line 243 of file tbx.c.

int tbx_name2id	(	tbx_t *	tbx,
		const char *	ss
	)

Definition at line 41 of file tbx.c.

int tbx_readrec	(	BGZF *	fp,
		void *	tbxv,
		void *	sv,
		int *	tid,
		int *	beg,
		int *	end
	)

Definition at line 129 of file tbx.c.

const char** tbx_seqnames	(	tbx_t *	tbx,
		int *	n
	)

Definition at line 266 of file tbx.c.

Variable Documentation

tbx_conf_t tbx_conf_bed

Definition at line 13 of file tbx.c.

tbx_conf_t tbx_conf_gff

Definition at line 12 of file tbx.c.

tbx_conf_t tbx_conf_psltbl

Definition at line 14 of file tbx.c.

tbx_conf_t tbx_conf_sam

Definition at line 15 of file tbx.c.

tbx_conf_t tbx_conf_vcf

Definition at line 16 of file tbx.c.