gamgee::ReadBases Class Reference

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)=default
ReadBases &	operator= (const ReadBases &other)
	creates a deep copy of a ReadBases object More...
ReadBases &	operator= (ReadBases &&other)=default
	~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...
void	set_base (const uint32_t index, const Base base)
	modify a base at a specific index More...
uint32_t	size () const
bool	operator== (const ReadBases &other) const
	number of base qualities in the container More...
bool	operator!= (const ReadBases &other) const
	check for inequality with another ReadBases object More...
std::string	to_string () const
	produce a string representation of the bases 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 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 )

default

gamgee::ReadBases::~ReadBases ( )

default

default destruction is sufficient, since our shared_ptr will handle deallocation

Member Function Documentation

bool gamgee::ReadBases::operator!=

(

const ReadBases &

other

)

const

check for inequality with another ReadBases object

check whether this object does not contain the same bases as another ReadBases object

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 )

default

bool gamgee::ReadBases::operator==

(

const ReadBases &

other

)

const

number of base qualities in the container

check whether this object contains the same bases as another ReadBases object

check for equality with another ReadBases object

Base gamgee::ReadBases::operator[]

(

const uint32_t

index

)

const

use freely as you would an array.

access an individual base by index

Note

currently implemented as read only

Returns

base at the specified index as an enumerated value

void gamgee::ReadBases::set_base	(	const uint32_t	index,
		const Base	base
	)

modify a base at a specific index

set an individual base at the given index to the specified value

Note

there's no way to implement this using non-const operator[], since we can't return a reference to a half-byte in memory

< zero out previous 4-bit base encoding

< insert new 4-bit base encoding

uint32_t gamgee::ReadBases::size ( ) const

inline

string gamgee::ReadBases::to_string

(

)

const

produce a string representation of the bases in this object

returns a string representation of the bases in this read

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/read_bases.h
• gamgee/sam/read_bases.cpp