#include <genesis/population/stream/variant_parallel_input_stream.hpp>

Detailed Description

Iterator over loci of the input sources.

This is the class that does the actual work. Use the dereference operator*() and operator->() or the access functions variants() and variant_at() to get the set of variants at the current locus() of the iteration, or use joined_variant() to get one Variant that has all sample SampleCounts joined into it.

Definition at line 259 of file variant_parallel_input_stream.hpp.

Public Member Functions
	Iterator ()=default

	Iterator (self_type &&)=default

	Iterator (self_type const &)=default

	~Iterator ()=default

VariantInputStream const &	input_at (size_t index) const
	Get access to an input stream that has been added to this parallel stream. More...

std::vector< VariantInputStream > const &	inputs () const
	Get access to the input streams that have been added to this parallel stream. More...

Variant	joined_variant (JoinedVariantParams const &params=JoinedVariantParams{})
	Create a single Variant instance that combines all Variants from the input sources at the current locus. More...

GenomeLocus const &	locus () const
	Return the current locus where the iteration is at. More...

	operator bool () const

bool	operator!= (self_type const &it) const

std::vector< utils::Optional< Variant > > &	operator* ()

const std::vector< utils::Optional< Variant > > &	operator* () const

self_type &	operator++ ()

self_type	operator++ (int)

std::vector< utils::Optional< Variant > > *	operator-> ()

const std::vector< utils::Optional< Variant > > *	operator-> () const

Iterator &	operator= (self_type &&)=default

Iterator &	operator= (self_type const &)=default

bool	operator== (self_type const &it) const
	Compare two iterators for equality. More...

utils::Optional< Variant > &	variant_at (size_t index)
	Return the data of the input streams at the given `index` at the current locus. More...

utils::Optional< Variant > const &	variant_at (size_t index) const
	Return the data of the input streams at the given `index` at the current locus. More...

std::vector< utils::Optional< Variant > > &	variants ()
	Return the data of all input streams at the current locus. More...

std::vector< utils::Optional< Variant > > const &	variants () const
	Return the data of all input streams at the current locus. More...

Public Types
using	iterator_category = std::input_iterator_tag

using	pointer = value_type const *

using	reference = value_type const &

using	self_type = VariantParallelInputStream::Iterator

using	value_type = std::vector< utils::Optional< Variant > >

Public Attributes
friend	VariantParallelInputStream

Constructor & Destructor Documentation

◆ Iterator() [1/3]

Iterator ( )

default

◆ ~Iterator()

~Iterator ( )

default

◆ Iterator() [2/3]

Iterator ( self_type const & )

default

◆ Iterator() [3/3]

Iterator ( self_type && )

default

Member Function Documentation

◆ input_at()

VariantInputStream const& input_at ( size_t index ) const

inline

Get access to an input stream that has been added to this parallel stream.

This is just a concenience function that forwards the input_at() function of VariantParallelInputStream. See there for details.

Definition at line 357 of file variant_parallel_input_stream.hpp.

◆ inputs()

std::vector<VariantInputStream> const& inputs ( ) const

inline

Get access to the input streams that have been added to this parallel stream.

This is just a concenience function that forwards the inputs() function of VariantParallelInputStream. See there for details.

Definition at line 343 of file variant_parallel_input_stream.hpp.

◆ joined_variant()

Variant joined_variant ( JoinedVariantParams const & params = JoinedVariantParams{} )

Create a single Variant instance that combines all Variants from the input sources at the current locus.

This joins all SampleCounts of all Variants of the input sources at the current locus. For sources that have no data at the current position, as many empty SampleCounts (with all zero counts) are inserted as the iterator has samples; hence, the number of SampleCounts in the Variant::samples of the returned Variant (as indicated by Variant.samples.size()) is kept consistent at each locus.

Definition at line 142 of file variant_parallel_input_stream.cpp.

◆ locus()

GenomeLocus const& locus ( ) const

inline

Return the current locus where the iteration is at.

Definition at line 401 of file variant_parallel_input_stream.hpp.

◆ operator bool()

operator bool ( ) const

inline

Definition at line 423 of file variant_parallel_input_stream.hpp.

◆ operator!=()

bool operator!= ( self_type const & it ) const

inline

Definition at line 441 of file variant_parallel_input_stream.hpp.

◆ operator*() [1/2]

std::vector<utils::Optional<Variant> >& operator* ( )

inline

Definition at line 312 of file variant_parallel_input_stream.hpp.

◆ operator*() [2/2]

const std::vector<utils::Optional<Variant> >& operator* ( ) const

inline

Definition at line 307 of file variant_parallel_input_stream.hpp.

◆ operator++() [1/2]

self_type& operator++ ( )

inline

Definition at line 410 of file variant_parallel_input_stream.hpp.

◆ operator++() [2/2]

self_type operator++ ( int )

inline

Definition at line 416 of file variant_parallel_input_stream.hpp.

◆ operator->() [1/2]

std::vector<utils::Optional<Variant> >* operator-> ( )

inline

Definition at line 302 of file variant_parallel_input_stream.hpp.

◆ operator->() [2/2]

const std::vector<utils::Optional<Variant> >* operator-> ( ) const

inline

Definition at line 297 of file variant_parallel_input_stream.hpp.

◆ operator=() [1/2]

Iterator& operator= ( self_type && )

default

◆ operator=() [2/2]

Iterator& operator= ( self_type const & )

default

◆ operator==()

bool operator== ( self_type const & it ) const

inline

Compare two iterators for equality.

Any two iterators that are created by calling begin() on the same GenericInputStream instance will compare equal, as long as neither of them is past-the-end. A valid (not past-the-end) iterator and an end() iterator will not compare equal, no matter from which GenericInputStream they were created.

Definition at line 436 of file variant_parallel_input_stream.hpp.

◆ variant_at() [1/2]

utils::Optional<Variant>& variant_at ( size_t index )

inline

Return the data of the input streams at the given index at the current locus.

The indexing follows the order in which inputs have been added to the VariantParallelInputStream. See also VariantParallelInputStream::input_size() to get their count.

An input source that do not have data at the current locus() has an empty optional.

Definition at line 380 of file variant_parallel_input_stream.hpp.

◆ variant_at() [2/2]

utils::Optional<Variant> const& variant_at ( size_t index ) const

inline

Return the data of the input streams at the given index at the current locus.

The indexing follows the order in which inputs have been added to the VariantParallelInputStream. See also VariantParallelInputStream::input_size() to get their count.

An input source that do not have data at the current locus() has an empty optional.

Definition at line 371 of file variant_parallel_input_stream.hpp.