Utility class to handle the memory management of the sam record object for read bases. More...

#include <read_bases.h>

Public Member Functions
	ReadBases (const std::shared_ptr< bam1_t > &sam_record)
	creates a ReadBases object that points to htslib memory already allocated More...

	ReadBases (const ReadBases &other)
	creates a deep copy of a ReadBases object More...

	ReadBases (ReadBases &&other) noexcept
	moves a ReadBases object, transferring ownership of the underlying htslib memory More...

ReadBases &	operator= (const ReadBases &other)
	creates a deep copy of a ReadBases object More...

ReadBases &	operator= (ReadBases &&other) noexcept
	moves a ReadBases object, transferring ownership of the underlying htslib memory More...

	~ReadBases ()=default
	default destruction is sufficient, since our shared_ptr will handle deallocation More...

Base	operator[] (const uint32_t index) const
	use freely as you would an array. More...

uint32_t	size () const

std::string	to_string () const
	number of base qualities in the container More...

Detailed Description

Utility class to handle the memory management of the sam record object for read bases.

This class uses Base to represent the bases A,C,G,T,N so we can get byte by byte correspondence with the underlying compressed memory model.

Note: Any functionality lost because of this should be made available by the ReadBases class.

Constructor & Destructor Documentation

gamgee::ReadBases::ReadBases ( const std::shared_ptr< bam1_t > & sam_record )

explicit

creates a ReadBases object that points to htslib memory already allocated

Parameters

sam_record a shared pointer to an htslib raw sam record pointer for this object to take shared ownership

Note: the resulting ReadBases object shares ownership of the pre-allocated memory via shared_ptr reference counting

gamgee::ReadBases::ReadBases ( const ReadBases & other )

creates a deep copy of a ReadBases object

Note: the copy will have exclusive ownership over the newly-allocated htslib memory

gamgee::ReadBases::ReadBases ( ReadBases && other )

noexcept

moves a ReadBases object, transferring ownership of the underlying htslib memory

gamgee::ReadBases::~ReadBases ( )

default

default destruction is sufficient, since our shared_ptr will handle deallocation

ReadBases & gamgee::ReadBases::operator= ( const ReadBases & other )

creates a deep copy of a ReadBases object

Note: the copy will have exclusive ownership over the newly-allocated htslib memory

< shared_ptr assignment will take care of deallocating old sam record if necessary

ReadBases & gamgee::ReadBases::operator= ( ReadBases && other )

noexcept

moves a ReadBases object, transferring ownership of the underlying htslib memory

< shared_ptr assignment will take care of deallocating old sam record if necessary

Base gamgee::ReadBases::operator[] ( const uint32_t index ) const

use freely as you would an array.

access an individual base by index

uint32_t gamgee::ReadBases::size ( ) const

inline

string gamgee::ReadBases::to_string ( ) const

number of base qualities in the container

returns a string representation of the bases in this read

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