A class template to hold the values of a specific Variant's shared field. More...

#include <shared_field.h>

Public Member Functions
	SharedField ()
	default constructor of an empty SharedField More...

	SharedField (const std::shared_ptr< bcf1_t > &body, const bcf_info_t *const info_ptr)
	creates a new SharedField pointing to the shared byte array inside the variant object More...

	SharedField (const SharedField &other)=delete
	copying of the SharedField object is not allowed. Use move constructor instead. More...

SharedField &	operator= (const SharedField &other)=delete
	copying of the SharedField object is not allowed. Use move constructor instead. More...

	SharedField (SharedField &&other)=default
	safely moves the data from one SharedField to a new one without making any copies More...

SharedField &	operator= (SharedField &&other)=default
	safely moves the data from one SharedField to the other without making any copies More...

bool	operator== (const SharedField &other) const
	compares two SharedField objects in the following order: memory address, size and values. More...

bool	operator!= (const SharedField &other) const
	compares two SharedField objects in the following order: memory address, size and values. More...

TYPE	operator[] (const uint32_t index) const
	random access to a given value for reading or writing More...

SharedFieldIterator< TYPE >	begin () const
	create a new iterator pointing to the begining of the values of this field More...

SharedFieldIterator< TYPE >	end () const
	create a new iterator pointing to the end of the values of this field More...

uint32_t	size () const
	the number of values in this SharedField (values per sample) More...

bool	empty () const
	checks if the object is empty. More...

bool	missing () const
	simple overload of empty to work with gamgee's missing API More...

TYPE	front () const
	convenience function to access the first element More...

TYPE	back () const
	convenience function to access the last element More...

template<>
uint32_t	size () const

template<>
std::string	operator[] (const uint32_t index) const

Detailed Description

template<class TYPE>
class gamgee::SharedField< TYPE >

A class template to hold the values of a specific Variant's shared field.

The role of this class is to perform the pointer manipulations behind the scenes that permit the user to navigate the values of a field without making any copies and benefiting from data locality (all the data is stored contiguously in memory).

For example, the allele number shared field (AN) will hold one integer value. A ranksum test field for example could hold a vector of floats. The SharedField object will hold all these values for a shared field in a random access (and random access iterator compatible) way. The SharedField can be used in any algorithm of the STL that requires random access iterators.

A typical use of the SharedField can be exemplified by the following:

const auto an = variant_record.shared_integer_field("AN");

for_each(an.begin(), an.end(), [](const auto x) { cout << x[0] << endl; });

SharedField objects can also be used in for loops like so:

for (const auto q : variant_record.shared_string_field("CULPRIT"))

cout << q << endl;

Or directly like so:

const auto ab = variant_record.shared_float_field("AB");

cout << ab[0] << endl;

While the SharedField objects are not really intended to be created by the user, they are returned by many accessors in the Variant API like the Variant::shared_integer_field() example above. Utilizing them correctly can really simplify your work by leveraging the power of the STL functions.

Note: all methods are inlined on purpose because they are so simple

Template Parameters

TYPE	the output type desired for the given tag. For example for AN's typically you would request an int32_t. Conversions are allowed if possible.

Constructor & Destructor Documentation

template<class TYPE>

gamgee::SharedField< TYPE >::SharedField ( )

inline

default constructor of an empty SharedField

Warning: since private members are immutable, creating an empty SharedField like this means that it will stay empty forever (desired immutability effect)

Note: empty shared fields are created when the field requested is missing in the Variant record

template<class TYPE>

gamgee::SharedField< TYPE >::SharedField	(	const std::shared_ptr< bcf1_t > &	body,
		const bcf_info_t *const	info_ptr
	)

inlineexplicit

creates a new SharedField pointing to the shared byte array inside the variant object

Parameters

body	the the bcf1_t structure to hold a shared pointer to
info_ptr	the info field pointer inside the body

template<class TYPE>

gamgee::SharedField< TYPE >::SharedField ( const SharedField< TYPE > & other )

delete

copying of the SharedField object is not allowed. Use move constructor instead.

template<class TYPE>

gamgee::SharedField< TYPE >::SharedField ( SharedField< TYPE > && other )

default

safely moves the data from one SharedField to a new one without making any copies

Member Function Documentation

template<class TYPE>

TYPE gamgee::SharedField< TYPE >::back ( ) const

inline

convenience function to access the last element

template<class TYPE>

SharedFieldIterator<TYPE> gamgee::SharedField< TYPE >::begin ( ) const

inline

create a new iterator pointing to the begining of the values of this field

template<class TYPE>

bool gamgee::SharedField< TYPE >::empty ( ) const

inline

checks if the object is empty.

Note: empty objects are returned when the requested field is missing

template<class TYPE>

SharedFieldIterator<TYPE> gamgee::SharedField< TYPE >::end ( ) const

inline

create a new iterator pointing to the end of the values of this field

template<class TYPE>

TYPE gamgee::SharedField< TYPE >::front ( ) const

inline

convenience function to access the first element

template<class TYPE>

bool gamgee::SharedField< TYPE >::missing ( ) const

inline

simple overload of empty to work with gamgee's missing API

template<class TYPE>

bool gamgee::SharedField< TYPE >::operator!= ( const SharedField< TYPE > & other ) const

inline

compares two SharedField objects in the following order: memory address, size and values.

Parameters

other something to compare to

Returns: true if the objects are not the same (memory address-wise), or contain different number of values, or the values are not exactly the same. Value comparison is dictated by TYPE's operator== implementation

template<class TYPE>

SharedField& gamgee::SharedField< TYPE >::operator= ( const SharedField< TYPE > & other )

delete

copying of the SharedField object is not allowed. Use move constructor instead.

template<class TYPE>

SharedField& gamgee::SharedField< TYPE >::operator= ( SharedField< TYPE > && other )

default

safely moves the data from one SharedField to the other without making any copies

template<class TYPE>

bool gamgee::SharedField< TYPE >::operator== ( const SharedField< TYPE > & other ) const

inline

compares two SharedField objects in the following order: memory address, size and values.

Parameters

other something to compare to

Returns: true if the objects are the same (memory address-wise), or contain exactly the same values. Value comparison is dictated by TYPE's operator== implementation

template<class TYPE>

TYPE gamgee::SharedField< TYPE >::operator[] ( const uint32_t index ) const

inline

random access to a given value for reading or writing

Parameters

index must be between 0 and the number of values for this record

Note: implementation guarantees this operation to be O(1)

Exceptions

std::out_of_range if index is out of range or entire field is missing and trying to access invalid memory

Returns: the value in that index

template<>

std::string gamgee::SharedField< std::string >::operator[] ( const uint32_t index ) const

inline

template<class TYPE>

uint32_t gamgee::SharedField< TYPE >::size ( ) const

inline

the number of values in this SharedField (values per sample)

template<>

uint32_t gamgee::SharedField< std::string >::size ( ) const

inline

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

gamgee/variant/shared_field.h

Public Member Functions

Detailed Description

template<class TYPE> class gamgee::SharedField< TYPE >

Constructor & Destructor Documentation

Member Function Documentation

template<class TYPE>
class gamgee::SharedField< TYPE >