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Classes | Functions | Variables
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_ttbx_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_ttbx_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.