theplu::yat::omic::BamRead Class Reference

Class holding a bam query. More...

#include <yat/omic/BamRead.h>

Public Member Functions
	BamRead (void)
	default constructor More...
	BamRead (const BamRead &other)
	Copy constructor.
virtual	~BamRead (void)
	Destructor.
const BamRead &	operator= (const BamRead &rhs)
	assignment operator
const uint8_t *	aux (void) const
const uint8_t *	aux (const char tag[2]) const
void	aux_append (const char tag[2], char type, int len, uint8_t *data)
	append a new tag to aux field More...
void	aux_del (const char tag[2])
	remove a tag in aux field More...
int	aux_size (void) const
const bam1_core_t &	core (void) const
	access core data struct More...
bam1_core_t &	core (void)
	access core data struct More...
const uint32_t *	cigar (void) const
	access CIGAR array More...
uint32_t	cigar (size_t i) const
uint32_t	cigar_op (size_t i) const
uint32_t	cigar_oplen (size_t i) const
std::string	cigar_str (void) const
void	cigar (const std::vector< uint32_t > &c)
	set CIGAR More...
void	cigar (const utility::Aligner::Cigar &cigar)
	set CIGAR More...
int32_t	end (void) const
	rightmost coordinate More...
uint16_t	flag (void) const
	bitwise flag More...
int32_t	mpos (void) const
	leftmost position for mate
int32_t	mtid (void) const
	Chromosome ID for mate.
const char *	name (void) const
void	name (const std::string &n)
	modify name More...
int32_t	pos (void) const
	0-based laftmost coordinate
uint8_t	qual (size_t i) const
void	qual (size_t i, uint8_t q)
	set quality of a base More...
std::string	sequence (void) const
uint8_t	sequence (size_t index) const
char	sequence_str (size_t index) const
void	sequence (size_t i, uint8_t x)
	modify a base in sequence More...
void	sequence (const std::string &seq, const std::vector< uint8_t > &qual)
	set sequence and quality More...
uint32_t	sequence_length (void) const
void	swap (BamRead &other)
int32_t	tid (void) const
	chromosome ID

Friends
class	InBamFile
class	OutBamFile
class	BamReadIterator

Related Functions
(Note that these are not member functions.)
void	swap (BamRead &lhs, BamRead &rhs)
bool	soft_clipped (const BamRead &bam)
uint32_t	left_soft_clipped (const BamRead &bam)
uint32_t	right_soft_clipped (const BamRead &bam)
bool	same_query_name (const BamRead &lhs, const BamRead &rhs)
bool	less_query_name (const BamRead &lhs, const BamRead &rhs)

Detailed Description

Class holding a bam query.

This is a wrapper around bam1_t and most of its information is held in the core struct. A BamRead is typically created from a InBamFile.

See Also

samtools

Since

New in yat 0.10

Constructor & Destructor Documentation

theplu::yat::omic::BamRead::BamRead

(

void

)

default constructor

Constructed object contains no data and most operations are not defined

Member Function Documentation

const uint8_t* theplu::yat::omic::BamRead::aux

(

void

)

const

Returns

pointer to auxiliary data

See Also

aux_size(void)

const uint8_t* theplu::yat::omic::BamRead::aux

(

const char

tag[2]

)

const

Use bam_aux2? functions (in samtools C api) to convert returned pointer to corresponding type.

Returns

pointer to field associated with tag, NULL if tag doesn't exist.

See Also

bam_aux_get

Since

New in yat 0.11

void theplu::yat::omic::BamRead::aux_append	(	const char	tag[2],
		char	type,
		int	len,
		uint8_t *	data
	)

append a new tag to aux field

Parameters

tag	two-charcter tag to append
type	describes which type and can be 'iIsScCdfAZH'
len	length of data
data	pointer to data

Since

New in yat 0.11

See Also

SAM specification

void theplu::yat::omic::BamRead::aux_del

(

const char

tag[2]

)

remove a tag in aux field

Exceptions

utility::runtime_error

if tag is not present in read

Since

New in yat 0.11

int theplu::yat::omic::BamRead::aux_size

(

void

)

const

Returns

length of aux field

Since

New in yat 0.11

const uint32_t* theplu::yat::omic::BamRead::cigar

(

void

)

const

access CIGAR array

In each element the lower 4 bits gives a CIGAR operation and the upper 28 bits keep the length.

The size of CIGAR array is accessed via core().n_cigar.

uint32_t theplu::yat::omic::BamRead::cigar

(

size_t

i

)

const

Returns

i th element of CIGAR array

void theplu::yat::omic::BamRead::cigar

(

const std::vector< uint32_t > &

c

)

set CIGAR

Parameters

c

new cigar

Deprecated:

Provided for backward compatibility with 0.11 API. Use cigar(const utility::Aligner::Cigar&) instead.

void theplu::yat::omic::BamRead::cigar

(

const utility::Aligner::Cigar &

cigar

)

set CIGAR

Parameters

cigar

new cigar

Since

new in yat 0.12

uint32_t theplu::yat::omic::BamRead::cigar_op

(

size_t

i

)

const

Returns

i th CIGAR operation

uint32_t theplu::yat::omic::BamRead::cigar_oplen

(

size_t

i

)

const

Returns

length of i th CIGAR element

std::string theplu::yat::omic::BamRead::cigar_str

(

void

)

const

Translate CIGAR array to a string such as '72M3S'

const bam1_core_t& theplu::yat::omic::BamRead::core

(

void

)

const

access core data struct

See Also

samtools C api documentaion

bam1_core_t& theplu::yat::omic::BamRead::core

(

void

)

access core data struct

See Also

samtools C api documentaion

int32_t theplu::yat::omic::BamRead::end

(

void

)

const

rightmost coordinate

Coordinate is 0-based, i.e., the end is one passed the last matching position.

See Also

bam_calend

uint16_t theplu::yat::omic::BamRead::flag

(

void

)

const

bitwise flag

See Also

Preprocessor defines BAM_F*

Since

implemented since yat 0.12

const char* theplu::yat::omic::BamRead::name

(

void

)

const

Returns

query name

Length of array is described by core().l_qname

void theplu::yat::omic::BamRead::name

(

const std::string &

n

)

modify name

Since

New in yat 0.11

uint8_t theplu::yat::omic::BamRead::qual

(

size_t

i

)

const

Returns

Quality of base i

void theplu::yat::omic::BamRead::qual	(	size_t	i,
		uint8_t	q
	)

set quality of a base

Parameters

i	base to modify
q	new quality

Since

New in yat 0.11

std::string theplu::yat::omic::BamRead::sequence

(

void

)

const

Each character in returned sequence is either A, C, G, T, or N.

Returns

sequence

uint8_t theplu::yat::omic::BamRead::sequence

(

size_t

index

)

const

4-bit integer describing base index

See Also

bam_nt16_rev_table

void theplu::yat::omic::BamRead::sequence	(	size_t	i,
		uint8_t	x
	)

modify a base in sequence

Set i-th base in sequence to x, where seq is a 4-bit integer.

See Also

bam_nt16_table

Since

New in yat 0.11

void theplu::yat::omic::BamRead::sequence	(	const std::string &	seq,
		const std::vector< uint8_t > &	qual
	)

set sequence and quality

Since

New in yat 0.11

uint32_t theplu::yat::omic::BamRead::sequence_length

(

void

)

const

See Also

core().l_qseq

char theplu::yat::omic::BamRead::sequence_str

(

size_t

index

)

const

Returns

A, C, G, T, or N.

Since

New in yat 0.13

void theplu::yat::omic::BamRead::swap

(

BamRead &

other

)

Exchanging this read with other.

See Also

swap(BamRead&, BamRead&)

Friends And Related Function Documentation

uint32_t left_soft_clipped ( const BamRead &  bam )

related

If read is soft clipped on left side, return how many bases are clipped, otherwise return 0.

Since

New in yat 0.10

bool less_query_name ( const BamRead &  lhs, const BamRead &  rhs  )

related

return true if lhs query name is less than rhs query name

See Also

BamRead::name()

Since

New in yat 0.13

uint32_t right_soft_clipped ( const BamRead &  bam )

related

If read is soft clipped on right side, return how many bases are clipped, otherwise return 0.

Since

New in yat 0.10

bool same_query_name ( const BamRead &  lhs, const BamRead &  rhs  )

related

return true if query names are equal

See Also

BamRead::name()

Since

New in yat 0.10

bool soft_clipped ( const BamRead &  bam )

related

Returns

true if read is soft clipped, either left_soft_clipped or right_soft_clipped.

Since

New in yat 0.10

void swap ( BamRead &  lhs, BamRead &  rhs  )

related

Swap specialization for BamRead that is faster than generic std::swap as it just swap a pair of pointers.

Since

New in yat 0.10

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The documentation for this class was generated from the following file:

• yat/omic/BamRead.h