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.

Classes
class	OutputFileDescriptor
Public Member Functions
	SamRecordGenerator (std::ostream &outSamFile, const reference::CrrFile &reference, const SamGeneratorConfig &config, const std::vector< std::string > &outStreams)
void	mappingRecordToSam (const SamRecord &record)
void	setHeader (const SamFileHeaderBlock &header)
Static Public Attributes
static const char	SAM_SEPARATOR = '\t'
Protected Types
typedef std::map< std::string, boost::shared_ptr < OutputFileDescriptor > >	OutStreamMap
typedef boost::shared_ptr < std::ostream >	OpenStreamPtr
typedef std::vector < OpenStreamPtr >	OutStreams
Protected Member Functions
bool	isConsistent (const SamRecord &r) const
OutputFileDescriptor &	getOutputStream (const std::string &id)
void	printMateSequence (OutputFileDescriptor &out, const std::string &mateSeq, const std::string &mateScore)
	Generate additional tags: mate sequence.
void	printReadGroup (OutputFileDescriptor &out)
void	printNegativeGapTag (OutputFileDescriptor &out, const mapping::SamSequenceSplitter &splitter)
void	flagAsSVCandidate (OutputFileDescriptor &out)
	Generate inconsistent mapping tag.
void	printAlleleInfoTag (OutputFileDescriptor &out, const mapping::EvidenceSamRecord &evidenceRecord)
	print allele info for EvidenceRecords
void	printAlternatives (OutputFileDescriptor &out, const std::string &tag, const mapping::SamRecord::SamRecords &samRecords, size_t startFrom)
	print alternative mappings or mates
uint32_t	getAdjustedSamPosition (const SamRecord &record) const
std::string	getSamChr (uint16_t chr) const
Protected Attributes
OutStreamMap	outFiles_
OutStreams	openStreams_
const reference::CrrFile &	reference_
SamFileHeaderBlock	header_
std::string	readGroup_
const SamGeneratorConfig &	samGeneratorConfig_

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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