cgatools::mapping::SamRecordGenerator Class Reference

Generates a SAM file record based on a given mapping record The final logic defining what goes into the output file is defined here. More...

#include <SamRecord.hpp>

List of all members.

Public Member Functions
	SamRecordGenerator (std::ostream &outSamFile, const reference::CrrFile &reference, bool mateSvCandidates, bool addMateSequenceAndScore, bool addMateSequenceAndScoreIfMateUnmapped, bool printAlleleInfo)
void	mappingRecordToSam (const SamRecord &record)
void	setHeader (const SamFileHeaderBlock &header)
Static Public Attributes
static const char	SAM_SEPARATOR = '\t'
Protected Member Functions
void	printMateSequence (const std::string &mateSeq, const std::string &mateScore)
	Generate additional tags: mate sequence.
void	printReadGroup ()
void	printNegativeGapTag (const mapping::SamSequenceSplitter &splitter)
void	flagAsSVCandidate ()
	Generate inconsistent mapping tag.
void	printAlleleInfoTag (const mapping::EvidenceSamRecord &evidenceRecord)
	print allele info for EvidenceRecords
uint32_t	adjustedPosition (const SamRecord &record) const
Protected Attributes
std::ostream &	outSamFile_
const reference::CrrFile &	reference_
bool	mateSvCandidates_
bool	addMateSequenceAndScore_
bool	addMateSequenceAndScoreIfMateUnmapped_
bool	printAlleleInfo_
SamFileHeaderBlock	header_
std::string	readGroup_

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Detailed Description

Generates a SAM file record based on a given mapping record The final logic defining what goes into the output file is defined here.

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

• SamRecord.hpp