#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <ctype.h>
#include <zlib.h>
#include "htslib/sam.h"
#include "htslib/bgzf.h"
#include "cram/cram.h"
#include "htslib/hfile.h"
#include "htslib/khash.h"
#include "htslib/kseq.h"
#include "htslib/kstring.h"
#include <assert.h>

Classes
struct	hts_cram_idx_t

struct	cstate_t

struct	__linkbuf_t

struct	mempool_t

struct	__bam_mplp_t

Macros
#define	_read_token(_p) (_p); for (; (_p) && (_p) != '\t'; ++(_p)); if ((_p) != '\t') goto err_ret; (_p)++ = 0

#define	_read_token_aux(_p) (_p); for (; (_p) && (_p) != '\t'; ++(_p)); *(_p)++ = 0

#define	_get_mem(type_t, _x, _s, _l) ks_resize((_s), (_s)->l + (_l)); (_x) = (type_t)((_s)->s + (_s)->l); (_s)->l += (_l)

#define	_parse_err(cond, msg) do { if ((cond) && hts_verbose >= 1) { fprintf(stderr, "[E::%s] " msg "\n", __func__); goto err_ret; } } while (0)

#define	_parse_warn(cond, msg) if ((cond) && hts_verbose >= 2) fprintf(stderr, "[W::%s] " msg "\n", __func__)

#define	STRNCMP(a, b, n) (strncasecmp((a),(b),(n)) \|\| strlen(a)!=(n))

#define	_cop(c) ((c)&BAM_CIGAR_MASK)

#define	_cln(c) ((c)>>BAM_CIGAR_SHIFT)

Typedefs
typedef struct hts_cram_idx_t	hts_cram_idx_t

typedef struct __linkbuf_t	lbnode_t

Functions
typedef	khash_t (s2i)

void	bam_hdr_destroy (bam_hdr_t *h)

bam_hdr_t *	bam_hdr_dup (const bam_hdr_t *h0)

bam_hdr_t *	bam_hdr_read (BGZF *fp)

int	bam_hdr_write (BGZF fp, const bam_hdr_t h)

int	bam_name2id (bam_hdr_t h, const char ref)

bam1_t *	bam_init1 ()

void	bam_destroy1 (bam1_t *b)

bam1_t *	bam_copy1 (bam1_t bdst, const bam1_t bsrc)

bam1_t *	bam_dup1 (const bam1_t *bsrc)

int	bam_cigar2qlen (int n_cigar, const uint32_t *cigar)

int	bam_cigar2rlen (int n_cigar, const uint32_t *cigar)

int32_t	bam_endpos (const bam1_t *b)

int	bam_read1 (BGZF fp, bam1_t b)

int	bam_write1 (BGZF fp, const bam1_t b)

int	bam_index_build (const char *fn, int min_shift)

hts_idx_t *	sam_index_load (samFile fp, const char fn)

hts_itr_t *	sam_itr_queryi (const hts_idx_t *idx, int tid, int beg, int end)

hts_itr_t *	sam_itr_querys (const hts_idx_t idx, bam_hdr_t hdr, const char *region)

bam_hdr_t *	sam_hdr_parse (int l_text, const char *text)

bam_hdr_t *	sam_hdr_read (htsFile *fp)

int	sam_hdr_write (htsFile fp, const bam_hdr_t h)

int	sam_parse1 (kstring_t s, bam_hdr_t h, bam1_t *b)

int	sam_read1 (htsFile fp, bam_hdr_t h, bam1_t *b)

int	sam_format1 (const bam_hdr_t h, const bam1_t b, kstring_t *str)

int	sam_write1 (htsFile fp, const bam_hdr_t h, const bam1_t *b)

void	bam_aux_append (bam1_t b, const char tag[2], char type, int len, uint8_t data)

uint8_t *	bam_aux_get (const bam1_t *b, const char tag[2])

int	bam_aux_del (bam1_t b, uint8_t s)

int32_t	bam_aux2i (const uint8_t *s)

double	bam_aux2f (const uint8_t *s)

char	bam_aux2A (const uint8_t *s)

char *	bam_aux2Z (const uint8_t *s)

int	sam_open_mode (char mode, const char fn, const char *format)

int	bam_str2flag (const char *str)

char *	bam_flag2str (int flag)

typedef	khash_t (olap_hash)

bam_plp_t	bam_plp_init (bam_plp_auto_f func, void *data)

void	bam_plp_init_overlaps (bam_plp_t iter)

void	bam_plp_destroy (bam_plp_t iter)

const bam_pileup1_t *	bam_plp_next (bam_plp_t iter, int _tid, int _pos, int *_n_plp)

int	bam_plp_push (bam_plp_t iter, const bam1_t *b)

const bam_pileup1_t *	bam_plp_auto (bam_plp_t iter, int _tid, int _pos, int *_n_plp)

void	bam_plp_reset (bam_plp_t iter)

void	bam_plp_set_maxcnt (bam_plp_t iter, int maxcnt)

bam_mplp_t	bam_mplp_init (int n, bam_plp_auto_f func, void **data)

void	bam_mplp_init_overlaps (bam_mplp_t iter)

void	bam_mplp_set_maxcnt (bam_mplp_t iter, int maxcnt)

void	bam_mplp_destroy (bam_mplp_t iter)

int	bam_mplp_auto (bam_mplp_t iter, int _tid, int _pos, int n_plp, const bam_pileup1_t *plp)

Macro Definition Documentation

#define _cln ( c ) ((c)>>BAM_CIGAR_SHIFT)

#define _cop ( c ) ((c)&BAM_CIGAR_MASK)

#define _get_mem	(	type_t,
		_x,
		_s,
		_l
	)	ks_resize((_s), (_s)->l + (_l)); (_x) = (type_t)((_s)->s + (_s)->l); (_s)->l += (_l)

#define _parse_err	(	cond,
		msg
	)	do { if ((cond) && hts_verbose >= 1) { fprintf(stderr, "[E::%s] " msg "\n", __func__); goto err_ret; } } while (0)

#define _parse_warn	(	cond,
		msg
	)	if ((cond) && hts_verbose >= 2) fprintf(stderr, "[W::%s] " msg "\n", __func__)

#define _read_token ( _p ) (_p); for (; *(_p) && *(_p) != '\t'; ++(_p)); if (*(_p) != '\t') goto err_ret; *(_p)++ = 0

#define _read_token_aux ( _p ) (_p); for (; *(_p) && *(_p) != '\t'; ++(_p)); *(_p)++ = 0

#define STRNCMP	(	a,
		b,
		n
	)	(strncasecmp((a),(b),(n)) \|\| strlen(a)!=(n))

Typedef Documentation

typedef struct hts_cram_idx_t hts_cram_idx_t

typedef struct __linkbuf_t lbnode_t

Function Documentation

char bam_aux2A ( const uint8_t * s )

double bam_aux2f ( const uint8_t * s )

int32_t bam_aux2i ( const uint8_t * s )

char* bam_aux2Z ( const uint8_t * s )

void bam_aux_append	(	bam1_t *	b,
		const char	tag[2],
		char	type,
		int	len,
		uint8_t *	data
	)

int bam_aux_del	(	bam1_t *	b,
		uint8_t *	s
	)

uint8_t* bam_aux_get	(	const bam1_t *	b,
		const char	tag[2]
	)

int bam_cigar2qlen	(	int	n_cigar,
		const uint32_t *	cigar
	)

int bam_cigar2rlen	(	int	n_cigar,
		const uint32_t *	cigar
	)

bam1_t* bam_copy1	(	bam1_t *	bdst,
		const bam1_t *	bsrc
	)

void bam_destroy1 ( bam1_t * b )

bam1_t* bam_dup1 ( const bam1_t * bsrc )

int32_t bam_endpos ( const bam1_t * b )

Calculate the rightmost base position of an alignment on the reference genome.

Parameters

b	pointer to an alignment

Returns: the coordinate of the first base after the alignment, 0-based

For a mapped read, this is just b->core.pos + bam_cigar2rlen. For an unmapped read (either according to its flags or if it has no cigar string), we return b->core.pos + 1 by convention.

char* bam_flag2str ( int flag )

returns negative value on error

void bam_hdr_destroy ( bam_hdr_t * h )

bam_hdr_t* bam_hdr_dup ( const bam_hdr_t * h0 )

bam_hdr_t* bam_hdr_read ( BGZF * fp )

int bam_hdr_write	(	BGZF *	fp,
		const bam_hdr_t *	h
	)

int bam_index_build	(	const char *	fn,
		int	min_shift
	)

bam1_t* bam_init1 ( void )

int bam_mplp_auto	(	bam_mplp_t	iter,
		int *	_tid,
		int *	_pos,
		int *	n_plp,
		const bam_pileup1_t **	plp
	)

void bam_mplp_destroy ( bam_mplp_t iter )

bam_mplp_t bam_mplp_init	(	int	n,
		bam_plp_auto_f	func,
		void **	data
	)

void bam_mplp_init_overlaps ( bam_mplp_t iter )

bam_mplp_init_overlaps() - if called, mpileup will detect overlapping read pairs and for each base pair set the base quality of the lower-quality base to zero, thus effectively discarding it from calling. If the two bases are identical, the quality of the other base is increased to the sum of their qualities (capped at 200), otherwise it is multiplied by 0.8.

void bam_mplp_set_maxcnt	(	bam_mplp_t	iter,
		int	maxcnt
	)

int bam_name2id	(	bam_hdr_t *	h,
		const char *	ref
	)

const bam_pileup1_t* bam_plp_auto	(	bam_plp_t	iter,
		int *	_tid,
		int *	_pos,
		int *	_n_plp
	)

void bam_plp_destroy ( bam_plp_t iter )

bam_plp_t bam_plp_init	(	bam_plp_auto_f	func,
		void *	data
	)

bam_plp_init() - sets an iterator over multiple : see mplp_func in bam_plcmd.c in samtools for an example. Expected return status: 0 on success, -1 on end, < -1 on non-recoverable errors : user data to pass to

void bam_plp_init_overlaps ( bam_plp_t iter )

const bam_pileup1_t* bam_plp_next	(	bam_plp_t	iter,
		int *	_tid,
		int *	_pos,
		int *	_n_plp
	)

int bam_plp_push	(	bam_plp_t	iter,
		const bam1_t *	b
	)

void bam_plp_reset ( bam_plp_t iter )

void bam_plp_set_maxcnt	(	bam_plp_t	iter,
		int	maxcnt
	)

int bam_read1	(	BGZF *	fp,
		bam1_t *	b
	)

int bam_str2flag ( const char * str )

int bam_write1	(	BGZF *	fp,
		const bam1_t *	b
	)

typedef khash_t ( s2i )

typedef khash_t ( olap_hash )

int sam_format1	(	const bam_hdr_t *	h,
		const bam1_t *	b,
		kstring_t *	str
	)

bam_hdr_t* sam_hdr_parse	(	int	l_text,
		const char *	text
	)

bam_hdr_t* sam_hdr_read ( htsFile * fp )

int sam_hdr_write	(	htsFile *	fp,
		const bam_hdr_t *	h
	)

hts_idx_t* sam_index_load	(	samFile *	fp,
		const char *	fn
	)

hts_itr_t* sam_itr_queryi	(	const hts_idx_t *	idx,
		int	tid,
		int	beg,
		int	end
	)

hts_itr_t* sam_itr_querys	(	const hts_idx_t *	idx,
		bam_hdr_t *	hdr,
		const char *	region
	)

int sam_open_mode	(	char *	mode,
		const char *	fn,
		const char *	format
	)

int sam_parse1	(	kstring_t *	s,
		bam_hdr_t *	h,
		bam1_t *	b
	)

int sam_read1	(	htsFile *	fp,
		bam_hdr_t *	h,
		bam1_t *	b
	)

int sam_write1	(	htsFile *	fp,
		const bam_hdr_t *	h,
		const bam1_t *	b
	)

Classes

Macros

Typedefs

Functions

Macro Definition Documentation

Typedef Documentation

Function Documentation