gamgee::ReferenceBlockSplittingVariantIterator Class Reference

Utility class to handle reference blocks while iterating over multiple variant files. More...

#include <reference_block_splitting_variant_iterator.h>

Inheritance diagram for gamgee::ReferenceBlockSplittingVariantIterator:

Public Member Functions
	ReferenceBlockSplittingVariantIterator ()=default
	creates an empty iterator (used for the end() method) More...
	ReferenceBlockSplittingVariantIterator (const std::vector< std::shared_ptr< htsFile >> &variant_files, const std::vector< std::shared_ptr< bcf_hdr_t >> &variant_headers)
	initializes a new iterator based on a vector of input files (vcf or bcf) More...
	ReferenceBlockSplittingVariantIterator (ReferenceBlockSplittingVariantIterator &&)=default
	a ReferenceBlockSplittingVariantIterator move constructor guarantees all objects will have the same state. More...
ReferenceBlockSplittingVariantIterator &	operator= (ReferenceBlockSplittingVariantIterator &&)=default
	ReferenceBlockSplittingVariantIterator (const ReferenceBlockSplittingVariantIterator &)=delete
	a ReferenceBlockSplittingVariantIterator cannot be copied. More...
ReferenceBlockSplittingVariantIterator &	operator= (const ReferenceBlockSplittingVariantIterator &)=delete
bool	operator!= (const ReferenceBlockSplittingVariantIterator &rhs)
	pseudo-inequality operator (needed by for-each loop) More...
std::vector< VariantIndexPair > &	operator* ()
	dereference operator (needed by for-each loop) More...
std::vector< VariantIndexPair > &	operator++ ()
	advances the iterator, fetching the next vector More...
Public Member Functions inherited from gamgee::MultipleVariantIterator
	MultipleVariantIterator ()=default
	creates an empty iterator (used for the end() method) More...
	MultipleVariantIterator (const std::vector< std::shared_ptr< htsFile >> &variant_files, const std::vector< std::shared_ptr< bcf_hdr_t >> &variant_headers)
	initializes a new iterator based on a vector of input files (vcf or bcf) More...
	MultipleVariantIterator (MultipleVariantIterator &&)=default
	a MultipleVariantIterator move constructor guarantees all objects will have the same state. More...
MultipleVariantIterator &	operator= (MultipleVariantIterator &&other)=default
	MultipleVariantIterator (const MultipleVariantIterator &)=delete
	a MultipleVariantIterator cannot be copied safely, as it is iterating over streams. More...
MultipleVariantIterator &	operator= (const MultipleVariantIterator &other)=delete
bool	operator!= (const MultipleVariantIterator &rhs)
	pseudo-inequality operator (needed by for-each loop) More...
std::vector< VariantIndexPair > &	operator* ()
	dereference operator (needed by for-each loop) More...
std::vector< VariantIndexPair > &	operator++ ()
	advances the iterator, fetching the next vector More...

Detailed Description

Utility class to handle reference blocks while iterating over multiple variant files.

This class is experimental/WIP

Constructor & Destructor Documentation

gamgee::ReferenceBlockSplittingVariantIterator::ReferenceBlockSplittingVariantIterator ( )

default

creates an empty iterator (used for the end() method)

gamgee::ReferenceBlockSplittingVariantIterator::ReferenceBlockSplittingVariantIterator	(	const std::vector< std::shared_ptr< htsFile >> &	variant_files,
		const std::vector< std::shared_ptr< bcf_hdr_t >> &	variant_headers
	)

initializes a new iterator based on a vector of input files (vcf or bcf)

Parameters

variant_files	vector of vcf/bcf files opened via the bcf_open() macro from htslib
variant_headers	vector of variant headers corresponding to these files

gamgee::ReferenceBlockSplittingVariantIterator::ReferenceBlockSplittingVariantIterator ( ReferenceBlockSplittingVariantIterator &&  )

default

a ReferenceBlockSplittingVariantIterator move constructor guarantees all objects will have the same state.

gamgee::ReferenceBlockSplittingVariantIterator::ReferenceBlockSplittingVariantIterator ( const ReferenceBlockSplittingVariantIterator &  )

delete

a ReferenceBlockSplittingVariantIterator cannot be copied.

Member Function Documentation

bool gamgee::ReferenceBlockSplittingVariantIterator::operator!=

(

const ReferenceBlockSplittingVariantIterator &

rhs

)

pseudo-inequality operator (needed by for-each loop)

Warning

this method does the minimal work necessary to determine that we have reached the end of iteration. it is NOT a valid general-purpose inequality method.

Parameters

rhs	the other ReferenceBlockSplittingVariantIterator to compare to

Returns

whether both iterators have entered their end states

std::vector< VariantIndexPair > & gamgee::ReferenceBlockSplittingVariantIterator::operator*

(

)

dereference operator (needed by for-each loop)

Returns

a reference to the iterator's Variant vector

std::vector< VariantIndexPair > & gamgee::ReferenceBlockSplittingVariantIterator::operator++

(

)

advances the iterator, fetching the next vector

Returns

a reference to the iterator's Variant vector

ReferenceBlockSplittingVariantIterator& gamgee::ReferenceBlockSplittingVariantIterator::operator= ( ReferenceBlockSplittingVariantIterator &&  )

default

ReferenceBlockSplittingVariantIterator& gamgee::ReferenceBlockSplittingVariantIterator::operator= ( const ReferenceBlockSplittingVariantIterator &  )

delete

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

• gamgee/variant/reference_block_splitting_variant_iterator.h
• gamgee/variant/reference_block_splitting_variant_iterator.cpp