iterator for VariantField objects. More...

#include <individual_field_iterator.h>

Inheritance diagram for gamgee::IndividualFieldIterator< TYPE >:

Public Member Functions
	IndividualFieldIterator (const std::shared_ptr< bcf1_t > &body, bcf_fmt_t *format_ptr, bool end_iterator=false)
	simple constructor used by VariantField to create an iterator More...

	IndividualFieldIterator (const IndividualFieldIterator &other)
	copy constructor is only meant for internal STL functions use. It makes a shallow copy of the underlying object which is sufficient for an iterator, but not exactly what a user would expect (user should expect copy constructors to make deep copies). But a deep copied iterator makes no sense. More...

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

IndividualFieldIterator &	operator= (const IndividualFieldIterator &other)
	copy constructor is only meant for internal STL functions use. It makes a shallow copy of the underlying object which is sufficient for an iterator, but not exactly what a user would expect (user should expect copy constructors to make deep copies). But a deep copied iterator makes no sense. More...

IndividualFieldIterator &	operator= (IndividualFieldIterator &&other) noexcept
	safely moves the data from one VariantField to a new one without making any copies More...

IndividualFieldIterator &	operator+= (const int n) noexcept
	simple compound assignment operation for random advances (back/forward) to the iterator More...

IndividualFieldIterator &	operator-= (const int n) noexcept
	simple compound assignment operation for random advances (back/forward) to the iterator More...

bool	operator== (const IndividualFieldIterator &other)
	two iterators are equal if they are in exactly the same state (pointing at the same location in memory More...

bool	operator!= (const IndividualFieldIterator &other)
	the oposite check of IndividualFieldIterator::operator==() More...

bool	operator< (const IndividualFieldIterator &other)
	an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the VariantField object. The order is determined by the Variant record. More...

bool	operator> (const IndividualFieldIterator &other)
	an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the VariantField object. The order is determined by the Variant record. More...

bool	operator<= (const IndividualFieldIterator &other)
	an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the VariantField object. The order is determined by the Variant record. More...

bool	operator>= (const IndividualFieldIterator &other)
	an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the VariantField object. The order is determined by the Variant record. More...

TYPE	operator* () const noexcept
	direct access to the value of the current sample More...

IndividualFieldIterator &	operator++ () noexcept
	Prefix increment. Advances to the next sample. More...

IndividualFieldIterator	operator++ (int) noexcept
	Postfix increment. Advances to the next sample. More...

IndividualFieldIterator &	operator-- () noexcept
	Prefix increment. Reverses to the previous sample. More...

IndividualFieldIterator	operator-- (int) noexcept
	Postfix decrement. Reverses to the previous sample. More...

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

int32_t	operator- (const IndividualFieldIterator< TYPE > &first) const
	Difference between two iterators as an integer. More...

Detailed Description

template<class TYPE>
class gamgee::IndividualFieldIterator< TYPE >

iterator for VariantField objects.

This iterator will walk through all the samples in a Variant record for a given VariantField object. For example if you want to iterate over all the GQ values of a Variant record you would do so through this iterator.

Note: implements a random access iterator which gives you full performance on STL algorithms that use iterators (mostly every one); this iterator never makes any copies of the underlying memory. It is implemented with pointer acrobatics behind the scenes for maximum performance while maintaining a friendly interface.

Constructor & Destructor Documentation

template<class TYPE>

gamgee::IndividualFieldIterator< TYPE >::IndividualFieldIterator	(	const std::shared_ptr< bcf1_t > &	body,
		bcf_fmt_t *	format_ptr,
		bool	end_iterator = `false`
	)

inline

simple constructor used by VariantField to create an iterator

Parameters

body	the Variant record used to access the data (shared ownership guarantees availability until iterator goes out of scope)
format_ptr	pointer to the raw byte array in body where all the values for this format field is encoded
end_iterator	whether or not this is being called by the VariantField::end() function.

Note: this constructor serves only the VariantField::begin() and VariantField::end() functions.

template<class TYPE>

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

inline

copy constructor is only meant for internal STL functions use. It makes a shallow copy of the underlying object which is sufficient for an iterator, but not exactly what a user would expect (user should expect copy constructors to make deep copies). But a deep copied iterator makes no sense.

Warning: does not deep copy the underlying data! (but the copied iterator will be able to navigate independentely).

template<class TYPE>

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

inlinenoexcept

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

Parameters

other another VariantField object

Member Function Documentation

template<class TYPE>

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

inline

the oposite check of IndividualFieldIterator::operator==()

template<class TYPE>

TYPE gamgee::IndividualFieldIterator< TYPE >::operator* ( ) const

inlinenoexcept

direct access to the value of the current sample

Returns: the value if it is a basic type (e.g. GQ, GL), or a specific object if it is a complex type (e.g. PL, AD,...)

template<class TYPE>

IndividualFieldIterator& gamgee::IndividualFieldIterator< TYPE >::operator++ ( )

inlinenoexcept

Prefix increment. Advances to the next sample.

Note: mainly designed for iterators

Warning: does not check for bounds exception, you should verify whether or not you've reached the end by comparing the result with end(). This is the STL way.

Returns: a reference to the start of the values of the next sample

template<class TYPE>

IndividualFieldIterator gamgee::IndividualFieldIterator< TYPE >::operator++ ( int )

inlinenoexcept

Postfix increment. Advances to the next sample.

Note: mainly designed for iterators

Warning: does not check for bounds exception, you should verify whether or not you've reached the end by comparing the result with end(). This is the STL way.

Returns: copy of the current position of the iterator (before the increment)

template<class TYPE>

IndividualFieldIterator& gamgee::IndividualFieldIterator< TYPE >::operator+= ( const int n )

inlinenoexcept

simple compound assignment operation for random advances (back/forward) to the iterator

Parameters

n	how much to advance (negative numbers to go the other direction)

Warning: there is no boundary check in this operator

template<class TYPE>

int32_t gamgee::IndividualFieldIterator< TYPE >::operator- ( const IndividualFieldIterator< TYPE > & first ) const

inline

Difference between two iterators as an integer.

Note: Useful as a substitute for size() when only begin() and end() are available.

Returns: the number of iterator steps between [first, last) where last is the current IndividualFieldIterator.

Parameters

first is the iterator the position of which is to be subtracted from the position of the current iterator.

template<class TYPE>

IndividualFieldIterator& gamgee::IndividualFieldIterator< TYPE >::operator-- ( )

inlinenoexcept

Prefix increment. Reverses to the previous sample.

Note: mainly designed for iterators

Warning: does not check for bounds exception, you should verify whether or not you've reached the beginning by comparing the result with begin(). This is the STL way.

Returns: a reference to the start of the values of the previous sample

template<class TYPE>

IndividualFieldIterator gamgee::IndividualFieldIterator< TYPE >::operator-- ( int )

inlinenoexcept

Postfix decrement. Reverses to the previous sample.

Note: mainly designed for iterators

Warning: does not check for bounds exception, you should verify whether or not you've reached the beginning by comparing the result with begin(). This is the STL way.

Returns: copy of the current position of the iterator (before the decrement)

template<class TYPE>

IndividualFieldIterator& gamgee::IndividualFieldIterator< TYPE >::operator-= ( const int n )

inlinenoexcept

simple compound assignment operation for random advances (back/forward) to the iterator

Parameters

n	how much to advance (negative numbers to go the other direction)

Warning: there is no boundary check in this operator

template<class TYPE>

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

inline

an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the VariantField object. The order is determined by the Variant record.

template<class TYPE>

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

inline

an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the VariantField object. The order is determined by the Variant record.

template<class TYPE>

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

inline

copy constructor is only meant for internal STL functions use. It makes a shallow copy of the underlying object which is sufficient for an iterator, but not exactly what a user would expect (user should expect copy constructors to make deep copies). But a deep copied iterator makes no sense.

Warning: does not deep copy the underlying data! (but the copied iterator will be able to navigate independentely).

template<class TYPE>

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

inlinenoexcept

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

Parameters

other another VariantField object

template<class TYPE>

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

inline

two iterators are equal if they are in exactly the same state (pointing at the same location in memory

template<class TYPE>

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

inline

an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the VariantField object. The order is determined by the Variant record.

template<class TYPE>

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

inline

an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the VariantField object. The order is determined by the Variant record.

template<class TYPE>

TYPE gamgee::IndividualFieldIterator< TYPE >::operator[] ( const uint32_t sample ) const

inline

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

Parameters

sample must be between 0 and the number of samples for this record

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

Exceptions

std::out_of_range if index is out of range

Returns: the value if it is a basic type (e.g. GQ, GL), or a specific object if it is a complex type (e.g. PL, AD,...)

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

gamgee/variant/individual_field_iterator.h

Public Member Functions

Detailed Description

template<class TYPE> class gamgee::IndividualFieldIterator< TYPE >

Constructor & Destructor Documentation

Member Function Documentation

template<class TYPE>
class gamgee::IndividualFieldIterator< TYPE >