theplu::yat::omic::Pileup< Iterator >::Entry Class Reference

#include <yat/omic/Pileup.h>

Public Member Functions
	Entry (void)
	default constructor
	Entry (const BamRead &b)
const BamRead &	bam (void) const
uint8_t	cigar_op (void) const
uint32_t	cigar_oplen (void) const
unsigned short	qual (void) const
uint8_t	sequence (void) const
void	increment (void)
bool	is_del (void) const
size_t	qpos (void) const

Friends
class	Pileup

Detailed Description

template<typename Iterator>
class theplu::yat::omic::Pileup< Iterator >::Entry

Essentially a BamRead but with additional information regarding base we currently pointing to

Constructor & Destructor Documentation

Entry()

template<typename Iterator >

theplu::yat::omic::Pileup< Iterator >::Entry::Entry

(

const BamRead &

b

)

Create an Entry with read b. Entry is initialized to point to first aligned base (b.pos()).

Member Function Documentation

bam()

template<typename Iterator>

const BamRead& theplu::yat::omic::Pileup< Iterator >::Entry::bam ( void  ) const

inline

Returns

const reference to BamRead

cigar_op()

template<typename Iterator>

uint8_t theplu::yat::omic::Pileup< Iterator >::Entry::cigar_op ( void  ) const

inline

Returns

cigar operation at current position

cigar_oplen()

template<typename Iterator>

uint32_t theplu::yat::omic::Pileup< Iterator >::Entry::cigar_oplen ( void  ) const

inline

Returns

length of current cigar element

increment()

template<typename Iterator >

void theplu::yat::omic::Pileup< Iterator >::Entry::increment

(

void

)

Increment CIGAR. If current CIGAR element is consuming query (not deletion), increment to next base on query.

is_del()

template<typename Iterator>

bool theplu::yat::omic::Pileup< Iterator >::Entry::is_del ( void  ) const

inline

Returns

true if this position was deleted in this query

qpos()

template<typename Iterator>

size_t theplu::yat::omic::Pileup< Iterator >::Entry::qpos ( void  ) const

inline

Returns

index of base at this position

qual()

template<typename Iterator>

unsigned short theplu::yat::omic::Pileup< Iterator >::Entry::qual ( void  ) const

inline

Returns

base quality of current position

sequence()

template<typename Iterator >

uint8_t theplu::yat::omic::Pileup< Iterator >::Entry::sequence

(

void

)

const

Returned base is encoded in 4 bits and can be converted to char using nt16_str(uint8_t).

Returns

base of current position

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

• yat/omic/Pileup.h