SequenceCoverageReader Class Reference

class for tracking BAM file sequence data that covers markers of interest. More...

#include <PileupReader.h>

Collaboration diagram for SequenceCoverageReader:

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List of all members.

Public Member Functions
	SequenceCoverageReader (SamFile &samFile)
void	useIndex (bool u=true)
bool	getBases (int32_t referenceID, uint32_t position, std::vector< ReadBase > &readBases, bool &basesInserted)
	getBases returns a pileup vector of the same length as the number of reads that overlaps the given chromosome and position
bool	getInsertedBases (int referenceID, uint32_t position, std::vector< ReadInsertion > &readInsertions)

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Detailed Description

class for tracking BAM file sequence data that covers markers of interest.

Given a sorted BAM file, allow us to scan over the file, either base by base or marker by marker in ascending order, and obtain a list of bases from the BAM file at the corresponding position.

In the event that an insertion is noticed after the marker of interest, signal that in getPileup, and allow the data to be returned by calling getInsertions().

Definition at line 142 of file PileupReader.h.

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Member Function Documentation

bool SequenceCoverageReader::getBases	(	int32_t	referenceID,
		uint32_t	position,
		std::vector< ReadBase > &	readBases,
		bool &	basesInserted
	)

getBases returns a pileup vector of the same length as the number of reads that overlaps the given chromosome and position

Parameters:

	referenceID	identifies the chromosome in which to retrieve bases from.
	position	indicates the 1-based offset of the base of interest on that chromosome. This number is relative to the genome reference that the BAM file was aligned against.
	readBases	a caller allocated vector of of readBase objects
	basesInserted	bool that indicates if getInsertions() will return a non-zero vector of bases that were inserted AFTER this position. Since reads may truncate this insertion, they may be different lengths.

Returns:

true if more data exists in the BAM file, false otherwise

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

• lib/bam/PileupReader.h
• lib/bam/PileupReader.cpp