tbx.c File Reference

#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <stdio.h>
#include <assert.h>
#include "htslib/tbx.h"
#include "htslib/bgzf.h"
#include "htslib/khash.h"

Go to the source code of this file.

Classes
struct	tbx_intv_t

Functions
int	tbx_name2id (tbx_t *tbx, const char *ss)
int	tbx_parse1 (const tbx_conf_t *conf, int len, char *line, tbx_intv_t *intv)
int	tbx_readrec (BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end)
void	tbx_set_meta (tbx_t *tbx)
tbx_t *	tbx_index (BGZF *fp, int min_shift, const tbx_conf_t *conf)
void	tbx_destroy (tbx_t *tbx)
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)

Variables
tbx_conf_t	tbx_conf_gff = { 0, 1, 4, 5, '#', 0 }
tbx_conf_t	tbx_conf_bed = { TBX_UCSC, 1, 2, 3, '#', 0 }
tbx_conf_t	tbx_conf_psltbl = { TBX_UCSC, 15, 17, 18, '#', 0 }
tbx_conf_t	tbx_conf_sam = { TBX_SAM, 3, 4, 0, '@', 0 }
tbx_conf_t	tbx_conf_vcf = { TBX_VCF, 1, 2, 0, '#', 0 }

Function Documentation

void tbx_destroy

(

tbx_t *

tbx)

Definition at line 214 of file tbx.c.

tbx_t* tbx_index	(	BGZF *	fp,
		int	min_shift,
		const tbx_conf_t *	conf
	)

Definition at line 173 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_parse1	(	const tbx_conf_t *	conf,
		int	len,
		char *	line,
		tbx_intv_t *	intv
	)

Definition at line 46 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.

void tbx_set_meta

(

tbx_t *

tbx)

Definition at line 142 of file tbx.c.

Variable Documentation

tbx_conf_t tbx_conf_bed = { TBX_UCSC, 1, 2, 3, '#', 0 }

Definition at line 13 of file tbx.c.

tbx_conf_t tbx_conf_gff = { 0, 1, 4, 5, '#', 0 }

Definition at line 12 of file tbx.c.

tbx_conf_t tbx_conf_psltbl = { TBX_UCSC, 15, 17, 18, '#', 0 }

Definition at line 14 of file tbx.c.

tbx_conf_t tbx_conf_sam = { TBX_SAM, 3, 4, 0, '@', 0 }

Definition at line 15 of file tbx.c.

tbx_conf_t tbx_conf_vcf = { TBX_VCF, 1, 2, 0, '#', 0 }

Definition at line 16 of file tbx.c.