#include <stdint.h>
#include "hts.h"

Classes
struct	bam_hdr_t

struct	bam1_core_t

struct	bam1_t

struct	bam_pileup1_t

Macros
#define	BAM_CMATCH 0

#define	BAM_CINS 1

#define	BAM_CDEL 2

#define	BAM_CREF_SKIP 3

#define	BAM_CSOFT_CLIP 4

#define	BAM_CHARD_CLIP 5

#define	BAM_CPAD 6

#define	BAM_CEQUAL 7

#define	BAM_CDIFF 8

#define	BAM_CBACK 9

#define	BAM_CIGAR_STR "MIDNSHP=XB"

#define	BAM_CIGAR_SHIFT 4

#define	BAM_CIGAR_MASK 0xf

#define	BAM_CIGAR_TYPE 0x3C1A7

#define	bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)

#define	bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)

#define	bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])

#define	bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT\|(o))

#define	bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3)

#define	BAM_FPAIRED 1

#define	BAM_FPROPER_PAIR 2

#define	BAM_FUNMAP 4

#define	BAM_FMUNMAP 8

#define	BAM_FREVERSE 16

#define	BAM_FMREVERSE 32

#define	BAM_FREAD1 64

#define	BAM_FREAD2 128

#define	BAM_FSECONDARY 256

#define	BAM_FQCFAIL 512

#define	BAM_FDUP 1024

#define	BAM_FSUPPLEMENTARY 2048

#define	bam_is_rev(b) (((b)->core.flag&BAM_FREVERSE) != 0)

#define	bam_is_mrev(b) (((b)->core.flag&BAM_FMREVERSE) != 0)

#define	bam_get_qname(b) ((char*)(b)->data)

#define	bam_get_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))

#define	bam_get_seq(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname)

#define	bam_get_qual(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))

#define	bam_get_aux(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1) + (b)->core.l_qseq)

#define	bam_get_l_aux(b) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qseq - (((b)->core.l_qseq + 1)>>1))

#define	bam_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf)

#define	bam_itr_destroy(iter) hts_itr_destroy(iter)

#define	bam_itr_queryi(idx, tid, beg, end) sam_itr_queryi(idx, tid, beg, end)

#define	bam_itr_querys(idx, hdr, region) sam_itr_querys(idx, hdr, region)

#define	bam_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), 0)

#define	bam_index_load(fn) hts_idx_load((fn), HTS_FMT_BAI)

#define	sam_itr_destroy(iter) hts_itr_destroy(iter)

#define	sam_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), (htsfp))

#define	sam_open(fn, mode) (hts_open((fn), (mode)))

#define	sam_close(fp) hts_close(fp)

Typedefs
typedef htsFile	samFile

typedef int(*	bam_plp_auto_f )(void data, bam1_t b)

typedef struct __bam_plp_t *	bam_plp_t

typedef struct __bam_mplp_t *	bam_mplp_t

Functions
bam_hdr_t *	bam_hdr_init (void)

bam_hdr_t *	bam_hdr_read (BGZF *fp)

int	bam_hdr_write (BGZF fp, const bam_hdr_t h)

void	bam_hdr_destroy (bam_hdr_t *h)

int	bam_name2id (bam_hdr_t h, const char ref)

bam_hdr_t *	bam_hdr_dup (const bam_hdr_t *h0)

bam1_t *	bam_init1 (void)

void	bam_destroy1 (bam1_t *b)

int	bam_read1 (BGZF fp, bam1_t b)

int	bam_write1 (BGZF fp, const 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_str2flag (const char *str)

char *	bam_flag2str (int flag)

int	bam_index_build (const char *fn, int min_shift)

hts_idx_t *	sam_index_load (htsFile 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)

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

bam_hdr_t *	sam_hdr_read (samFile *fp)

int	sam_hdr_write (samFile fp, const bam_hdr_t h)

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

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

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

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

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

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)

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)

bam_plp_t	bam_plp_init (bam_plp_auto_f func, void *data)

void	bam_plp_destroy (bam_plp_t iter)

int	bam_plp_push (bam_plp_t iter, const bam1_t *b)

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

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

void	bam_plp_set_maxcnt (bam_plp_t iter, int maxcnt)

void	bam_plp_reset (bam_plp_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)

void	bam_mplp_destroy (bam_mplp_t iter)

void	bam_mplp_set_maxcnt (bam_mplp_t iter, int maxcnt)

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

Macro Definition Documentation

#define BAM_CBACK 9

#define BAM_CDEL 2

#define BAM_CDIFF 8

#define BAM_CEQUAL 7

#define BAM_CHARD_CLIP 5

#define bam_cigar_gen	(	l,
		o
	)	((l)<<BAM_CIGAR_SHIFT\|(o))

#define BAM_CIGAR_MASK 0xf

#define bam_cigar_op ( c ) ((c)&BAM_CIGAR_MASK)

#define bam_cigar_opchr ( c ) (BAM_CIGAR_STR[bam_cigar_op(c)])

#define bam_cigar_oplen ( c ) ((c)>>BAM_CIGAR_SHIFT)

#define BAM_CIGAR_SHIFT 4

#define BAM_CIGAR_STR "MIDNSHP=XB"

#define BAM_CIGAR_TYPE 0x3C1A7

#define bam_cigar_type ( o ) (BAM_CIGAR_TYPE>>((o)<<1)&3)

#define BAM_CINS 1

#define BAM_CMATCH 0

#define BAM_CPAD 6

#define BAM_CREF_SKIP 3

#define BAM_CSOFT_CLIP 4

#define BAM_FDUP 1024

optical or PCR duplicate

#define BAM_FMREVERSE 32

the mate is mapped to the reverse strand

#define BAM_FMUNMAP 8

the mate is unmapped

#define BAM_FPAIRED 1

the read is paired in sequencing, no matter whether it is mapped in a pair

#define BAM_FPROPER_PAIR 2

the read is mapped in a proper pair

#define BAM_FQCFAIL 512

QC failure

#define BAM_FREAD1 64

this is read1

#define BAM_FREAD2 128

this is read2

#define BAM_FREVERSE 16

the read is mapped to the reverse strand

#define BAM_FSECONDARY 256

not primary alignment

#define BAM_FSUPPLEMENTARY 2048

supplementary alignment

#define BAM_FUNMAP 4

the read itself is unmapped; conflictive with BAM_FPROPER_PAIR

#define bam_get_aux ( b ) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1) + (b)->core.l_qseq)

Get auxiliary data

Parameters

b	pointer to an alignment

Returns: pointer to the concatenated auxiliary data

#define bam_get_cigar ( b ) ((uint32_t*)((b)->data + (b)->core.l_qname))

Get the CIGAR array

Parameters

b	pointer to an alignment

Returns: pointer to the CIGAR array

In the CIGAR array, each element is a 32-bit integer. The lower 4 bits gives a CIGAR operation and the higher 28 bits keep the length of a CIGAR.

#define bam_get_l_aux ( b ) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qseq - (((b)->core.l_qseq + 1)>>1))

Get length of auxiliary data

Parameters

b	pointer to an alignment

Returns: length of the concatenated auxiliary data

#define bam_get_qname ( b ) ((char*)(b)->data)

Get the name of the query

Parameters

b	pointer to an alignment

Returns: pointer to the name string, null terminated

#define bam_get_qual ( b ) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))

Get query quality

Parameters

b	pointer to an alignment

Returns: pointer to quality string

#define bam_get_seq ( b ) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname)

Get query sequence

Parameters

b	pointer to an alignment

Returns: pointer to sequence

Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G, 8 for T and 15 for N. Two bases are packed in one byte with the base at the higher 4 bits having smaller coordinate on the read. It is recommended to use bam_seqi() macro to get the base.

#define bam_index_load ( fn ) hts_idx_load((fn), HTS_FMT_BAI)

#define bam_is_mrev ( b ) (((b)->core.flag&BAM_FMREVERSE) != 0)

Get whether the query's mate is on the reverse strand

Parameters

b	pointer to an alignment

Returns: boolean true if query's mate on the reverse strand

#define bam_is_rev ( b ) (((b)->core.flag&BAM_FREVERSE) != 0)

Get whether the query is on the reverse strand

Parameters

b	pointer to an alignment

Returns: boolean true if query is on the reverse strand

#define bam_itr_destroy ( iter ) hts_itr_destroy(iter)

The string must be freed by the user

#define bam_itr_next	(	htsfp,
		itr,
		r
	)	hts_itr_next((htsfp)->fp.bgzf, (itr), (r), 0)

#define bam_itr_queryi	(	idx,
		tid,
		beg,
		end
	)	sam_itr_queryi(idx, tid, beg, end)

#define bam_itr_querys	(	idx,
		hdr,
		region
	)	sam_itr_querys(idx, hdr, region)

#define bam_seqi	(	s,
		i
	)	((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf)

Get a base on read

Parameters

s	Query sequence returned by bam1_seq()
i	The i-th position, 0-based

Returns: 4-bit integer representing the base.

#define sam_close ( fp ) hts_close(fp)

#define sam_itr_destroy ( iter ) hts_itr_destroy(iter)

#define sam_itr_next	(	htsfp,
		itr,
		r
	)	hts_itr_next((htsfp)->fp.bgzf, (itr), (r), (htsfp))

#define sam_open	(	fn,
		mode
	)	(hts_open((fn), (mode)))

Typedef Documentation

typedef struct __bam_mplp_t* bam_mplp_t

typedef int(* bam_plp_auto_f)(void *data, bam1_t *b)

typedef struct __bam_plp_t* bam_plp_t

typedef htsFile samFile

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_init ( void )

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

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
	)

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 ( samFile * fp )

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

hts_idx_t* sam_index_load	(	htsFile *	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	(	samFile *	fp,
		bam_hdr_t *	h,
		bam1_t *	b
	)

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

Classes

Macros

Typedefs

Functions

Macro Definition Documentation

Typedef Documentation

Function Documentation