gamgee::SamPairIterator Class Reference

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

#include <sam_pair_iterator.h>

Public Member Functions
	SamPairIterator ()
	creates an empty iterator (used for the end() method) More...
	SamPairIterator (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...
	SamPairIterator (SamPairIterator &&other)
	a SamPairIterator move constructor guarantees all objects will have the same state. More...
bool	operator!= (const SamPairIterator &rhs)
	inequality operator (needed by for-each loop) More...
std::pair< Sam, Sam >	operator* ()
	dereference operator (needed by for-each loop) More...
std::pair< Sam, Sam >	operator++ ()
	pre-fetches the next record and tests for end of file More...

Detailed Description

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

Constructor & Destructor Documentation

gamgee::SamPairIterator::SamPairIterator

(

)

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

gamgee::SamPairIterator::SamPairIterator	(	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::SamPairIterator::SamPairIterator

(

SamPairIterator &&

other

)

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

Member Function Documentation

bool gamgee::SamPairIterator::operator!=

(

const SamPairIterator &

rhs

)

inequality operator (needed by for-each loop)

Parameters

rhs	the other SamPairIterator to compare to

Returns

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

pair< Sam, Sam > gamgee::SamPairIterator::operator*

(

)

dereference operator (needed by for-each loop)

Returns

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

pair< Sam, Sam > gamgee::SamPairIterator::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)

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

• gamgee/sam_pair_iterator.h
• gamgee/sam_pair_iterator.cpp