A class template to hold the values a format field for a particular sample. More...

#include <individual_field_value.h>

Public Member Functions
	IndividualFieldValue (const std::shared_ptr< bcf1_t > &body, const bcf_fmt_t const format_ptr, uint8_t const data_ptr)
	creates a new IndividualFieldValue poiinting to the shared byte array inside the variant object More...

	IndividualFieldValue (const IndividualFieldValue &other)=delete
	copying of the IndividualFieldValue object is not allowed. More...

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

IndividualFieldValue &	operator= (const IndividualFieldValue &other)=delete

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

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

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

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

IndividualFieldValueIterator < VALUE_TYPE >	begin () const
	create a new begin iterator over the values for this sample More...

IndividualFieldValueIterator < VALUE_TYPE >	end () const
	create a new end iterator over the values for this sample More...

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

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

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

bool	missing () const
	returns true if all of the values are missing More...

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

Detailed Description

template<class VALUE_TYPE>
class gamgee::IndividualFieldValue< VALUE_TYPE >

A class template to hold the values a format field for a particular sample.

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 in a sample without making any copies and benefiting from data locality (all the data is stored contiguously in memory).

A typical use of the IndividualFieldValue can be exemplified by the phred likelihood accessor in Variant:

const auto all_pls = record.integer_individual_field("PL");
const auto my_pls = all_pls[2] // take the second sample
for_each(my_pls.begin(), my_pls.end(), [](const auto pl) { cout << pl << endl; });

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

for (const auto pl : my_pls)

cout << pl << endl;

While the IndividualFieldValue objects are not really intended to be created by the user, they are the returned by the IndividualField iterator for types that don't have a specialized object. 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 object type that holds the values for each sample. For example for GQ it's a uint8_t, some types like GT can have specialized classes like Genotype. For all other types it can be the IndividualFieldValue.

Constructor & Destructor Documentation

template<class VALUE_TYPE >

gamgee::IndividualFieldValue< VALUE_TYPE >::IndividualFieldValue	(	const std::shared_ptr< bcf1_t > &	body,
		const bcf_fmt_t *const	format_ptr,
		uint8_t *const	data_ptr
	)

inline

creates a new IndividualFieldValue poiinting to the shared byte array inside the variant object

Parameters

body	the full Variant object where all the values of the field are stored (shared ownership)
format_ptr	a structure with a pointer to the location in the raw byte array (m_body->indiv) where the format field starts and information about the values (size, type, number,...)

Note: this implementation doesn't make any copies, simply manages the access to the raw byte array in Variant giving iterator interfaces to the users

Parameters

body	the the bcf1_t structure to hold a shared pointer to
format_ptr	the format field pointer inside the body
data_ptr	the location in the specific value inside the format_ptr byte array

template<class VALUE_TYPE >

gamgee::IndividualFieldValue< VALUE_TYPE >::IndividualFieldValue ( const IndividualFieldValue< VALUE_TYPE > & other )

delete

copying of the IndividualFieldValue object is not allowed.

template<class VALUE_TYPE >

gamgee::IndividualFieldValue< VALUE_TYPE >::IndividualFieldValue ( IndividualFieldValue< VALUE_TYPE > && other )

inline

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

Parameters

other another IndividualFieldValue object

Member Function Documentation

template<class VALUE_TYPE >

VALUE_TYPE gamgee::IndividualFieldValue< VALUE_TYPE >::back ( ) const

inline

convenience function to access the last element

template<class VALUE_TYPE >

IndividualFieldValueIterator<VALUE_TYPE> gamgee::IndividualFieldValue< VALUE_TYPE >::begin ( ) const

inline

create a new begin iterator over the values for this sample

template<class VALUE_TYPE >

IndividualFieldValueIterator<VALUE_TYPE> gamgee::IndividualFieldValue< VALUE_TYPE >::end ( ) const

inline

create a new end iterator over the values for this sample

template<class VALUE_TYPE >

VALUE_TYPE gamgee::IndividualFieldValue< VALUE_TYPE >::front ( ) const

inline

convenience function to access the first element

template<class VALUE_TYPE >

bool gamgee::IndividualFieldValue< VALUE_TYPE >::missing ( ) const

inline

returns true if all of the values are missing

template<class VALUE_TYPE >

bool gamgee::IndividualFieldValue< VALUE_TYPE >::operator!= ( const IndividualFieldValue< VALUE_TYPE > & other ) const

inline

compares two IndividualFieldValue 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 VALUE_TYPE >

IndividualFieldValue& gamgee::IndividualFieldValue< VALUE_TYPE >::operator= ( const IndividualFieldValue< VALUE_TYPE > & other )

delete

template<class VALUE_TYPE >

IndividualFieldValue& gamgee::IndividualFieldValue< VALUE_TYPE >::operator= ( IndividualFieldValue< VALUE_TYPE > && other )

inline

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

Parameters

other another IndividualFieldValue object

template<class VALUE_TYPE >

bool gamgee::IndividualFieldValue< VALUE_TYPE >::operator== ( const IndividualFieldValue< VALUE_TYPE > & other ) const

inline

compares two IndividualFieldValue 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 VALUE_TYPE >

VALUE_TYPE gamgee::IndividualFieldValue< VALUE_TYPE >::operator[] ( const uint32_t index ) const

inline

random access to the value of a given sample for reading or writing

Parameters

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

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

Exceptions

std::out_of_range if sample is out of range

Returns: the value in that index

template<>

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

inline

template<class VALUE_TYPE >

uint32_t gamgee::IndividualFieldValue< VALUE_TYPE >::size ( ) const

inline

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

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

gamgee/variant/individual_field_value.h

Public Member Functions

Detailed Description

template<class VALUE_TYPE> class gamgee::IndividualFieldValue< VALUE_TYPE >

Constructor & Destructor Documentation

Member Function Documentation

template<class VALUE_TYPE>
class gamgee::IndividualFieldValue< VALUE_TYPE >