cgatools::variants::SuperlocusIterator Class Reference

A class to iterate through one or more variant files at a time, enabling access to a stream of Superlocus. More...

#include <SuperlocusIterator.hpp>

List of all members.

Public Member Functions
	SuperlocusIterator (uint32_t extend3Mers=4, uint32_t extendBases=0)
	Creates an empty SuperlocusIterator, with the given parameter values.
void	setVariantFile (VariantFileIterator &iter)
	Initialize the SuperlocusIterator to process one file.
void	setVariantFiles (VariantFileIterator &iterA, VariantFileIterator &iterB)
	Initialize the SuperlocusIterator to process two files.
void	setVariantFiles (const std::vector< VariantFileIterator * > iters)
	Initialize the SuperlocusIterator to process any number of files.
void	skipToVariant (const reference::Range &range, const std::string &alleleSeq)
	Skip to the next variant in a stream.
void	seekFirst ()
	Do the initial seek, in the case where you're iterating via ++.
bool	eof () const
	Returns true if this SuperlocusIterator is at end of file.
const Superlocus &	operator* () const
	Returns the Superlocus referred to by this iterator.
const Superlocus *	operator-> () const
	Returns the Superlocus referred to by this iterator.
reference::Location	getPrecedingRefStart () const
	Returns the beginning of pure reference call upstream of the current superlocus, or a location at or greater than the start of the current superlocus if the call upstream of the superlocus is not a pure reference.
SuperlocusIterator &	operator++ ()
	Moves to the next Superlocus.

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Detailed Description

A class to iterate through one or more variant files at a time, enabling access to a stream of Superlocus.

Example:

 VariantFileIterator locItA(crr), locItB(crr);
 locItA.open(variantFileNameA_);
 locItB.open(variantFileNameB_);
 SuperlocusIterator slIt;
 for(slIt.setVariantFiles(locItA, locItB); !slIt.eof(); ++slIt)
 {
     const Superlocus& sl = *slIt;
     Range range = sl.getRange();
 }

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Constructor & Destructor Documentation

cgatools::variants::SuperlocusIterator::SuperlocusIterator	(	uint32_t	extend3Mers = 4,
		uint32_t	extendBases = 0
	)

Creates an empty SuperlocusIterator, with the given parameter values.

Parameters:

	extend3Mers	Always extend superloci to the right and left by the given number of distinct reference 3-mers.
	extendBases	Always extend superloci to the right and left by at least the given number of bases.

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Member Function Documentation

reference::Location cgatools::variants::SuperlocusIterator::getPrecedingRefStart

(

)

const [inline]

Returns the beginning of pure reference call upstream of the current superlocus, or a location at or greater than the start of the current superlocus if the call upstream of the superlocus is not a pure reference.

void cgatools::variants::SuperlocusIterator::skipToVariant	(	const reference::Range &	range,
		const std::string &	alleleSeq
	)

Skip to the next variant in a stream.

The variants must stream in reference order.

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

• SuperlocusIterator.hpp