yat  0.20.3pre
Public Member Functions | Friends | List of all members
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 BamReadbam (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

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

Generated on Sat Feb 18 2023 03:31:44 for yat by  doxygen 1.8.14