#include <zlib.h>
#include <ctype.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <fcntl.h>
#include <errno.h>
#include <sys/stat.h>
#include "htslib/bgzf.h"
#include "htslib/hts.h"
#include "cram/cram.h"
#include "htslib/hfile.h"
#include "version.h"
#include "htslib/kseq.h"
#include "htslib/khash.h"
#include "htslib/ksort.h"

Classes
struct	bins_t

struct	__hts_idx_t

Macros
#define	KS_BGZF 1

#define	HTS_MIN_MARKER_DIST 0x10000

#define	META_BIN(idx) ((idx)->n_bins + 1)

#define	pair64_lt(a, b) ((a).u < (b).u)

Functions
const char *	hts_version ()

int	hts_detect_format (hFILE hfile, htsFormat fmt)

const char *	hts_format_description (const htsFormat *format)

htsFile *	hts_open (const char fn, const char mode)

htsFile *	hts_hopen (struct hFILE hfile, const char fn, const char *mode)

int	hts_close (htsFile *fp)

const htsFormat *	hts_get_format (htsFile *fp)

int	hts_set_opt (htsFile *fp, enum cram_option opt,...)

int	hts_set_threads (htsFile *fp, int n)

int	hts_set_fai_filename (htsFile fp, const char fn_aux)

BGZF *	hts_get_bgzfp (htsFile *fp)

int	hts_useek (htsFile *fp, long uoffset, int where)

long	hts_utell (htsFile *fp)

int	hts_getline (htsFile fp, int delimiter, kstring_t str)

char **	hts_readlist (const char string, int is_file, int _n)

char **	hts_readlines (const char fn, int _n)

typedef	khash_t (bin)

hts_idx_t *	hts_idx_init (int n, int fmt, uint64_t offset0, int min_shift, int n_lvls)

void	hts_idx_finish (hts_idx_t *idx, uint64_t final_offset)

int	hts_idx_push (hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped)

void	hts_idx_destroy (hts_idx_t *idx)

void	hts_idx_save (const hts_idx_t idx, const char fn, int fmt)

hts_idx_t *	hts_idx_load_local (const char *fn, int fmt)

void	hts_idx_set_meta (hts_idx_t idx, int l_meta, uint8_t meta, int is_copy)

uint8_t *	hts_idx_get_meta (hts_idx_t idx, int l_meta)

const char **	hts_idx_seqnames (const hts_idx_t idx, int n, hts_id2name_f getid, void *hdr)

int	hts_idx_get_stat (const hts_idx_t idx, int tid, uint64_t mapped, uint64_t *unmapped)

uint64_t	hts_idx_get_n_no_coor (const hts_idx_t *idx)

hts_itr_t *	hts_itr_query (const hts_idx_t idx, int tid, int beg, int end, hts_readrec_func readrec)

void	hts_itr_destroy (hts_itr_t *iter)

const char *	hts_parse_reg (const char s, int beg, int *end)

hts_itr_t *	hts_itr_querys (const hts_idx_t idx, const char reg, hts_name2id_f getid, void hdr, hts_itr_query_func itr_query, hts_readrec_func *readrec)

int	hts_itr_next (BGZF fp, hts_itr_t iter, void r, void data)

char *	hts_idx_getfn (const char fn, const char ext)

hts_idx_t *	hts_idx_load (const char *fn, int fmt)

Variables
int	hts_verbose = 3

const unsigned char	seq_nt16_table [256]

const char	seq_nt16_str [] = "=ACMGRSVTWYHKDBN"

	lidx_t

Macro Definition Documentation

#define HTS_MIN_MARKER_DIST 0x10000

#define KS_BGZF 1

#define META_BIN ( idx ) ((idx)->n_bins + 1)

#define pair64_lt	(	a,
		b
	)	((a).u < (b).u)

Function Documentation

int hts_close ( htsFile * fp )

Close a file handle, flushing buffered data for output streams

Parameters

fp	The file handle to be closed

Returns: 0 for success, or negative if an error occurred.

int hts_detect_format	(	struct hFILE *	fp,
		htsFormat *	fmt
	)

Determine format by peeking at the start of a file

Parameters

fp	File opened for reading, positioned at the beginning
fmt	Format structure that will be filled out on return

Returns: 0 for success, or negative if an error occurred.

const char* hts_format_description ( const htsFormat * format )

Get a human-readable description of the file format

BGZF* hts_get_bgzfp ( htsFile * fp )

const htsFormat* hts_get_format ( htsFile * fp )

Returns the file's format information

Parameters

fp	The file handle

Returns: Read-only pointer to the file's htsFormat.

int hts_getline	(	htsFile *	fp,
		int	delimiter,
		kstring_t *	str
	)

htsFile* hts_hopen	(	struct hFILE *	fp,
		const char *	fn,
		const char *	mode
	)

Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file

Parameters

fn	The already-open file handle
mode	Open mode, as per hts_open()

void hts_idx_destroy ( hts_idx_t * idx )

void hts_idx_finish	(	hts_idx_t *	idx,
		uint64_t	final_offset
	)

uint8_t* hts_idx_get_meta	(	hts_idx_t *	idx,
		int *	l_meta
	)

uint64_t hts_idx_get_n_no_coor ( const hts_idx_t * idx )

int hts_idx_get_stat	(	const hts_idx_t *	idx,
		int	tid,
		uint64_t *	mapped,
		uint64_t *	unmapped
	)

char* hts_idx_getfn	(	const char *	fn,
		const char *	ext
	)

hts_idx_t* hts_idx_init	(	int	n,
		int	fmt,
		uint64_t	offset0,
		int	min_shift,
		int	n_lvls
	)

hts_idx_t* hts_idx_load	(	const char *	fn,
		int	fmt
	)

hts_idx_t* hts_idx_load_local	(	const char *	fn,
		int	fmt
	)

int hts_idx_push	(	hts_idx_t *	idx,
		int	tid,
		int	beg,
		int	end,
		uint64_t	offset,
		int	is_mapped
	)

void hts_idx_save	(	const hts_idx_t *	idx,
		const char *	fn,
		int	fmt
	)

const char** hts_idx_seqnames	(	const hts_idx_t *	idx,
		int *	n,
		hts_id2name_f	getid,
		void *	hdr
	)

void hts_idx_set_meta	(	hts_idx_t *	idx,
		int	l_meta,
		uint8_t *	meta,
		int	is_copy
	)

void hts_itr_destroy ( hts_itr_t * iter )

int hts_itr_next	(	BGZF *	fp,
		hts_itr_t *	iter,
		void *	r,
		void *	data
	)

hts_itr_t* hts_itr_query	(	const hts_idx_t *	idx,
		int	tid,
		int	beg,
		int	end,
		hts_readrec_func *	readrec
	)

hts_itr_t* hts_itr_querys	(	const hts_idx_t *	idx,
		const char *	reg,
		hts_name2id_f	getid,
		void *	hdr,
		hts_itr_query_func *	itr_query,
		hts_readrec_func *	readrec
	)

htsFile* hts_open	(	const char *	fn,
		const char *	mode
	)

const char* hts_parse_reg	(	const char *	s,
		int *	beg,
		int *	end
	)

char** hts_readlines	(	const char *	fn,
		int *	_n
	)

char** hts_readlist	(	const char *	fn,
		int	is_file,
		int *	_n
	)

Parse comma-separated list or read list from a file

Parameters

list	File name or comma-separated list
is_file
_n	Size of the output array (number of items read)

Returns: NULL on failure or pointer to newly allocated array of strings

int hts_set_fai_filename	(	htsFile *	fp,
		const char *	fn_aux
	)

Set .fai filename for a file opened for reading

Returns: 0 for success, negative on failure Called before *_hdr_read(), this provides the name of a .fai file used to provide a reference list if the htsFile contains no headers.

int hts_set_opt	(	htsFile *	fp,
		enum cram_option	opt,
			...
	)

Sets a specified CRAM option on the open file handle.

Parameters

fp	The file handle open the open file.
opt	The CRAM_OPT_* option.
...	Optional arguments, dependent on the option used.

Returns: 0 for success, or negative if an error occurred.

int hts_set_threads	(	htsFile *	fp,
		int	n
	)

Create extra threads to aid compress/decompression for this file

Parameters

fp	The file handle
n	The number of worker threads to create

Returns: 0 for success, or negative if an error occurred. THIS THREADING API IS LIKELY TO CHANGE IN FUTURE.

int hts_useek	(	htsFile *	fp,
		long	uoffset,
		int	where
	)

long hts_utell ( htsFile * fp )

const char* hts_version ( void )

Get the htslib version number

Returns: For released versions, a string like "N.N[.N]"; or git describe output if using a library built within a Git repository.

typedef khash_t ( bin )

Variable Documentation

int hts_verbose = 3

lidx_t

const char seq_nt16_str[] = "=ACMGRSVTWYHKDBN"

Table for converting a 4-bit encoded nucleotide to a letter.

const unsigned char seq_nt16_table[256]

Initial value:

= {
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
     1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 ,15,15,
    15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
    15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
    15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
    15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
}

Table for converting a nucleotide character to the 4-bit encoding.

Classes

Macros

Functions

Variables

Macro Definition Documentation

Function Documentation

Variable Documentation