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)=default
BaseQuals &	operator= (const BaseQuals &other)
	creates a deep copy of a BaseQuals object More...
BaseQuals &	operator= (BaseQuals &&other)=default
	~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...
uint8_t &	operator[] (const uint32_t index)
	use freely as you would an array More...
uint32_t	size () const
	number of base qualities in the container More...
bool	operator== (const BaseQuals &other) const
	check for equality with another BaseQuals object More...
bool	operator!= (const BaseQuals &other) const
	check for inequality with another BaseQuals object More...
std::string	to_string () const
	produce a string representation of the base qualities in this object More...

Friends
class	SamBuilder
	builder needs access to the internals in order to build efficiently 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 )

default

gamgee::BaseQuals::~BaseQuals ( )

default

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

Member Function Documentation

bool gamgee::BaseQuals::operator!=

(

const BaseQuals &

other

)

const

check for inequality with another BaseQuals object

check whether this object does not contain the same base qualities as another BaseQuals object

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 )

default

bool gamgee::BaseQuals::operator==

(

const BaseQuals &

other

)

const

check for equality with another BaseQuals object

check whether this object contains the same base qualities as another BaseQuals object

uint8_t gamgee::BaseQuals::operator[]

(

const uint32_t

index

)

const

use freely as you would an array.

access an individual base quality by index

Returns

base quality at the specified index as an unsigned byte

uint8_t & gamgee::BaseQuals::operator[]

(

const uint32_t

index

)

use freely as you would an array

access and/or modify an individual base quality by index

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

std::string gamgee::BaseQuals::to_string

(

)

const

produce a string representation of the base qualities in this object

Friends And Related Function Documentation

friend class SamBuilder

friend

builder needs access to the internals in order to build efficiently

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

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