gamgee::IndexedVariantIterator Class Reference

#include <indexed_variant_iterator.h>

Inheritance diagram for gamgee::IndexedVariantIterator:

Public Member Functions
	IndexedVariantIterator ()
	creates an empty iterator (used for the end() method) More...
	IndexedVariantIterator (const std::shared_ptr< htsFile > &file_ptr, const std::shared_ptr< hts_idx_t > &index_ptr, const std::shared_ptr< bcf_hdr_t > &header_ptr, const std::vector< std::string > &interval_list=all_intervals)
	initializes a new iterator based on a file, an index, a header, and a vector of intervals More...
	IndexedVariantIterator (const IndexedVariantIterator &other)=delete
	an IndexedVariantIterator cannot be copied safely, as it is iterating over a stream. More...
IndexedVariantIterator &	operator= (const IndexedVariantIterator &other)=delete
	IndexedVariantIterator (IndexedVariantIterator &&other)=default
	an IndexedVariantIterator can be moved More...
IndexedVariantIterator &	operator= (IndexedVariantIterator &&other)=default
bool	operator!= (const IndexedVariantIterator &rhs)
	inequality operator (needed by for-each loop) More...
Public Member Functions inherited from gamgee::VariantIterator
	VariantIterator ()=default
	creates an empty iterator (used for the end() method) More...
	VariantIterator (const std::shared_ptr< htsFile > &variant_file_ptr, const std::shared_ptr< bcf_hdr_t > &variant_header_ptr)
	initializes a new iterator based on an input stream (e.g. a vcf/bcf file, stdin, ...) More...
	VariantIterator (VariantIterator &&)=default
	a VariantIterator move constructor guarantees all objects will have the same state. More...
VariantIterator &	operator= (VariantIterator &&)=default
	a VariantIterator move assignment operator guarantees all objects will have the same state. More...
	VariantIterator (const VariantIterator &)=delete
	a VariantIterator cannot be copy-constructed. More...
VariantIterator &	operator= (const VariantIterator &)=delete
	a VariantIterator cannot be copied. More...
bool	operator!= (const VariantIterator &rhs) const
	inequality operator (needed by for-each loop) More...
Variant &	operator* ()
	dereference operator (needed by for-each loop) More...
Variant &	operator++ ()
	pre-fetches the next record and tests for end of file More...
bool	empty () const
	returns whether the iterator has no additional records More...

Static Public Attributes
static const std::vector < std::string >	all_intervals = {"."}

Protected Member Functions
void	fetch_next_record () override
	fetches next Variant record into existing htslib memory without making a copy More...

Additional Inherited Members
Protected Attributes inherited from gamgee::VariantIterator
std::shared_ptr< htsFile >	m_variant_file_ptr
	pointer to the vcf/bcf file More...
std::shared_ptr< bcf_hdr_t >	m_variant_header_ptr
	pointer to the variant header More...
std::shared_ptr< bcf1_t >	m_variant_record_ptr
	pointer to the internal structure of the variant record. Useful to only allocate it once. More...
Variant	m_variant_record
	temporary record to hold between fetch (operator++) and serve (operator*) More...

Constructor & Destructor Documentation

gamgee::IndexedVariantIterator::IndexedVariantIterator

(

)

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

gamgee::IndexedVariantIterator::IndexedVariantIterator	(	const std::shared_ptr< htsFile > &	file_ptr,
		const std::shared_ptr< hts_idx_t > &	index_ptr,
		const std::shared_ptr< bcf_hdr_t > &	header_ptr,
		const std::vector< std::string > &	interval_list = all_intervals
	)

initializes a new iterator based on a file, an index, a header, and a vector of intervals

Parameters

file_ptr	shared pointer to a BCF file opened via the bcf_open() macro from htslib
index_ptr	shared pointer to a BCF file index (CSI) created with the bcf_index_load() macro from htslib
header_ptr	shared pointer to a BCF file header created with the bcf_hdr_read() macro from htslib
interval_list	vector of intervals represented by strings

gamgee::IndexedVariantIterator::IndexedVariantIterator ( const IndexedVariantIterator &  other )

delete

an IndexedVariantIterator cannot be copied safely, as it is iterating over a stream.

gamgee::IndexedVariantIterator::IndexedVariantIterator ( IndexedVariantIterator &&  other )

default

an IndexedVariantIterator can be moved

Member Function Documentation

void gamgee::IndexedVariantIterator::fetch_next_record ( )

overrideprotectedvirtual

fetches next Variant record into existing htslib memory without making a copy

pre-fetches the next variant record

Warning

we're reusing the existing htslib memory, so users should be aware that all objects from the previous iteration are now stale unless a deep copy has been performed

Reimplemented from gamgee::VariantIterator.

bool gamgee::IndexedVariantIterator::operator!=

(

const IndexedVariantIterator &

rhs

)

inequality operator (needed by for-each loop)

Parameters

rhs	the other IndexedVariantIterator to compare to

Returns

whether or not the two iterators are the same (e.g. have the same input file on the same status and the same intervals)

IndexedVariantIterator& gamgee::IndexedVariantIterator::operator= ( const IndexedVariantIterator &  other )

delete

IndexedVariantIterator& gamgee::IndexedVariantIterator::operator= ( IndexedVariantIterator &&  other )

default

Member Data Documentation

const std::vector< std::string > gamgee::IndexedVariantIterator::all_intervals = {"."}

static

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

• gamgee/variant/indexed_variant_iterator.h
• gamgee/variant/indexed_variant_iterator.cpp