cgatools::cgdata::ReferenceSupportReader Class Reference

Sequential reader for CGI reference support files provided as a part of the genome data package. More...

#include <ReferenceSupportReader.hpp>

List of all members.

Classes
struct	DataItem
struct	File
Public Member Functions
	ReferenceSupportReader (const reference::CrrFile &crr, const GenomeMetadata &exp)
void	seek (const reference::Range &r)
	Buffer reference support data for the specified range of the genome.
int32_t	getMinScore (const reference::Range &r, int32_t noDataValue=std::numeric_limits< int32_t >::min()) const
	Returns the minimum reference score for the specified range.
int32_t	getMaxWeightedCoverage (const reference::Range &r, int32_t noDataValue=0) const
	Returns the maximum sum-of-weights coverage number over all bases of the specified range.

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Detailed Description

Sequential reader for CGI reference support files provided as a part of the genome data package.

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Member Function Documentation

int32_t cgatools::cgdata::ReferenceSupportReader::getMaxWeightedCoverage	(	const reference::Range &	r,
		int32_t	noDataValue = 0
	)			const

Returns the maximum sum-of-weights coverage number over all bases of the specified range.

int32_t cgatools::cgdata::ReferenceSupportReader::getMinScore	(	const reference::Range &	r,
		int32_t	noDataValue = std::numeric_limits< int32_t >::min()
	)			const

Returns the minimum reference score for the specified range.

The range must be within the currently buffered segment. If no data is in the file for the specified range, returns noDataValue.

void cgatools::cgdata::ReferenceSupportReader::seek

(

const reference::Range &

r

)

Buffer reference support data for the specified range of the genome.

Switching between chromosomes is expensive. Within chromosome, only forward movement is allowed: the file is always read sequentially. In other words, if the currently buffered range is OR, and the new range is NR, then (OR.begin_ <= NR.begin_ && OR.end_ <= NR.end_) must hold.

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

• ReferenceSupportReader.hpp