gamgee::BaseQuals Class Reference

Utility class to handle the memory management of the sam record object for a read base qualities. More...

#include <base_quals.h>

Public Member Functions
	BaseQuals (const std::shared_ptr< bam1_t > &sam_record)
	creates a BaseQuals object that points to htslib memory already allocated More...
	BaseQuals (const BaseQuals &other)
	creates a deep copy of a BaseQuals object More...
	BaseQuals (BaseQuals &&other) noexcept
	moves a BaseQuals object, transferring ownership of the underlying htslib memory More...
BaseQuals &	operator= (const BaseQuals &other)
	creates a deep copy of a BaseQuals object More...
BaseQuals &	operator= (BaseQuals &&other) noexcept
	moves a BaseQuals object, transferring ownership of the underlying htslib memory More...
	~BaseQuals ()=default
	Default destruction is sufficient, since our shared_ptr will handle deallocation. More...
uint8_t	operator[] (const uint32_t index) const
	use freely as you would an array. More...
uint32_t	size () const
	number of base qualities in the container More...

Detailed Description

Utility class to handle the memory management of the sam record object for a read base qualities.

Constructor & Destructor Documentation

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

explicit

creates a BaseQuals object that points to htslib memory already allocated

Note

the resulting BaseQuals object shares ownership of the pre-allocated memory via shared_ptr reference counting

gamgee::BaseQuals::BaseQuals

(

const BaseQuals &

other

)

creates a deep copy of a BaseQuals object

Note

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

gamgee::BaseQuals::BaseQuals ( BaseQuals &&  other )

noexcept

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

gamgee::BaseQuals::~BaseQuals ( )

default

Default destruction is sufficient, since our shared_ptr will handle deallocation.

Member Function Documentation

BaseQuals & gamgee::BaseQuals::operator=

(

const BaseQuals &

other

)

creates a deep copy of a BaseQuals 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

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

noexcept

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

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

uint8_t gamgee::BaseQuals::operator[]

(

const uint32_t

index

)

const

use freely as you would an array.

access an individual base quality by index

Note

currently implemented as read only

Returns

base quality at the specified index as an unsigned byte

uint32_t gamgee::BaseQuals::size ( ) const

inline

number of base qualities in the container

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

• gamgee/base_quals.h
• gamgee/base_quals.cpp