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

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

	SamIterator (samFile *sam_file_ptr, const std::shared_ptr< bam_hdr_t > &sam_header_ptr)
	initializes a new iterator based on an input stream (e.g. sam/a file, stdin, ...) More...

	SamIterator (SamIterator &&)
	a SamIterator move constructor guarantees all objects will have the same state. More...

bool	operator!= (const SamIterator &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...

Detailed Description

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

Constructor & Destructor Documentation

gamgee::SamIterator::SamIterator ( )

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

gamgee::SamIterator::SamIterator	(	samFile *	sam_file_ptr,
		const std::shared_ptr< bam_hdr_t > &	sam_header_ptr
	)

initializes a new iterator based on an input stream (e.g. sam/a file, stdin, ...)

Parameters

sam_file_ptr	pointer to a sam file opened via the sam_open() macro from htslib
sam_header_ptr	pointer to a sam file header created with the sam_hdr_read() macro from htslib

gamgee::SamIterator::SamIterator ( SamIterator && original )

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

bool gamgee::SamIterator::operator!= ( const SamIterator & 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::SamIterator::operator* ( )

dereference operator (needed by for-each loop)

Returns: a persistent Sam object independent from the iterator (a copy of the iterator's object)

Sam & gamgee::SamIterator::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)

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