cgatools::reference::CrrFile Class Reference

Compact Randomly-accessible Reference file. More...

#include <CrrFile.hpp>

List of all members.

Public Member Functions
	CrrFile (const std::string &path)
void	open (const std::string &path)
const std::vector < CompactDnaSequence > &	listChromosomes () const
	Return the list of chromosomes (and their metadata).
std::vector< Range >	listContigs (uint32_t minGapLength=50) const
	Return the list of ranges that may be considered contigs, if you split contigs by stretches of reference N's that are at list minGapLength long.
std::string	getSequence (const Range &range) const
	Get the reference sequence for the given range.
char	getBase (const Location &loc) const
	Get the reference sequence for the given location.
uint16_t	getChromosomeId (const std::string &chromosomeName) const
	Get the chromosome id for the given chromosome name.
void	validate () const
	Validate the md5 checksums in the chromosome metadata.
Location	getLocation (const std::string &chromosomeName, boost::uint32_t offset) const
	Returns the internal location by chromosome name and the zero-based offset into that chromosome.
Static Public Member Functions
static uint32_t	currentVersion ()
	The expected .crr file version.

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Detailed Description

Compact Randomly-accessible Reference file.

It's a binary format.

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Member Function Documentation

Location cgatools::reference::CrrFile::getLocation	(	const std::string &	chromosomeName,
		boost::uint32_t	offset
	)			const [inline]

Returns the internal location by chromosome name and the zero-based offset into that chromosome.

std::vector<Range> cgatools::reference::CrrFile::listContigs

(

uint32_t

minGapLength = 50

)

const

Return the list of ranges that may be considered contigs, if you split contigs by stretches of reference N's that are at list minGapLength long.

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

• CrrFile.hpp