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

Class holding a bam query. More...

#include </scratch/bob/jari/tmp/pristine/yat-0.10.x/yat/omic/BamRead.h>

List of all members.

Public Member Functions
	BamRead (void)
	default constructor
	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 bam1_core_t &	core (void) const
	access core data struct
bam1_core_t &	core (void)
	access core data struct
const uint32_t *	cigar (void) const
	access CIGAR array
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
uint8_t	qual (size_t i) const
const char *	name (void) const
int32_t	tid (void) const
	chromosome ID
int32_t	pos (void) const
	0-based laftmost coordinate
int32_t	end (void) const
	rightmost coordinate
int32_t	mtid (void) const
	Chromosome ID for mate.
int32_t	mpos (void) const
	leftmost position for mate
std::string	sequence (void) const
uint8_t	sequence (size_t index) const
uint32_t	sequence_length (void) const
uint16_t	flag (void) const
	bitwise flag
void	swap (BamRead &other)

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)

---

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

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.

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

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*

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

(

void

)

const

Returns:

query name

Length of array is described by core().l_qname

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

(

size_t

i

)

const

Returns:

Quality of base i

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

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

(

void

)

const

See also:

core().l_qseq

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

(

BamRead &

other

)

Exchanging this read with other.

---

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

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 pointers.

Since:

New in yat 0.10

---

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

• /scratch/bob/jari/tmp/pristine/yat-0.10.x/yat/omic/BamRead.h