Utility class to enable for-each style iteration in the IndexedSamReader class. More...

Public Member Functions
	IndexedSamIterator ()
	creates an empty iterator (used for the end() method) More...

	IndexedSamIterator (const std::shared_ptr< htsFile > &sam_file_ptr, const std::shared_ptr< hts_idx_t > &sam_index_ptr, const std::shared_ptr< bam_hdr_t > &sam_header_ptr, const std::vector< std::string > &interval_list)
	initializes a new iterator based on an input file stream More...

	IndexedSamIterator (IndexedSamIterator &&other)=default
	iterators and readers can be moved More...

IndexedSamIterator &	operator= (IndexedSamIterator &&other)=default

	IndexedSamIterator (const IndexedSamIterator &other)=delete
	no copy construction/assignment allowed for iterators and readers More...

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

bool	operator!= (const IndexedSamIterator &rhs)
	inequality operator (needed by for-each loop) More...

Sam &	operator* ()
	dereference operator (needed by for-each loop) More...

Sam &	operator++ ()
	pre-fetches the next record and tests for end of file More...

const std::string &	current_interval () const

Detailed Description

Utility class to enable for-each style iteration in the IndexedSamReader class.

Constructor & Destructor Documentation

gamgee::IndexedSamIterator::IndexedSamIterator ( )

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

gamgee::IndexedSamIterator::IndexedSamIterator	(	const std::shared_ptr< htsFile > &	sam_file_ptr,
		const std::shared_ptr< hts_idx_t > &	sam_index_ptr,
		const std::shared_ptr< bam_hdr_t > &	sam_header_ptr,
		const std::vector< std::string > &	interval_list
	)

initializes a new iterator based on an input file stream

Parameters

sam_file_ptr	pointer to a bam/cram file opened via the sam_open() macro from htslib
sam_index_ptr	pointer to a bam/cram file opened via the sam_index_load() macro from htslib
sam_header_ptr	pointer to a bam/cram file header created with the sam_hdr_read() macro from htslib
interval_list	vector of intervals compatible with sam_itr_querys, hts_parse_reg, etc.

gamgee::IndexedSamIterator::IndexedSamIterator ( IndexedSamIterator && other )

default

iterators and readers can be moved

gamgee::IndexedSamIterator::IndexedSamIterator ( const IndexedSamIterator & other )

delete

no copy construction/assignment allowed for iterators and readers

const std::string & gamgee::IndexedSamIterator::current_interval ( ) const

bool gamgee::IndexedSamIterator::operator!= ( const IndexedSamIterator & rhs )

inequality operator (needed by for-each loop)

Parameters

rhs	the other SamIterator to compare to

Returns: whether or not the two iterators are the same (e.g. have the same input stream on the same status)

Sam & gamgee::IndexedSamIterator::operator* ( )

dereference operator (needed by for-each loop)

Returns: a Sam object by reference, valid until the next record is fetched (the iterator re-uses memory at each iteration)

Sam & gamgee::IndexedSamIterator::operator++ ( )

pre-fetches the next record and tests for end of file

Returns: a reference to the object (it can be const& because this return value should only be used by the for-each loop to check for the eof)

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

default

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

delete

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