cgatools::mapping::Map2SamConverter Class Reference

Inheritance diagram for cgatools::mapping::Map2SamConverter:

List of all members.

Public Types
typedef boost::shared_ptr < std::istream >	InStream
typedef boost::ptr_vector < SamRecord >	SamRecordArray
Public Member Functions
	Map2SamConverter (const Map2SamConfig &config, std::ostream &outSamFile)
virtual void	init ()
void	run ()
Static Public Attributes
static const size_t	MAX_SIDES = 2
Protected Member Functions
SamFileHeaderBlock	createHeader ()
virtual void	writeMappingRecord (const SamRecord &m) const
void	processDnbRecord (const ReadsRecord &readsRecord, const mapping::MappingsRecords &mappingsRecords) const
void	outputSamMappings (const mapping::ReadsRecord &readsRecord, SamRecordArray &samMappings) const
std::string	generateDnbId (const mapping::ReadsRecord &readsRecord) const
void	convertBaseMappingsIntoSamMappings (const mapping::ReadsRecord &readsRecord, SamRecordArray &samMappings, const mapping::MappingsRecords &baseMappingRecords) const
virtual bool	processMappings (const mapping::ReadsRecord &readsRecord, SamRecordArray &samMappings, const mapping::MappingsRecords &baseMappingRecords) const =0
	a template function allowing functionality extension by a derived class, such as merge additional mappings returns true if the processing has replaced the standard processing
reference::Range	getMappingRange (const SamRecord &mapping) const
size_t	getChunkNumber (const std::string &fileName, size_t formatVersion) const
	detect the chunk number for the older versions
Protected Attributes
size_t	batchNumber_
size_t	formatVersion_
std::string	slide_
std::string	lane_
std::string	laneId_
InStream	readsFileStream_
InStream	mappingsFileStream_
boost::shared_ptr < util::DelimitedFile >	readsFile_
boost::shared_ptr < util::DelimitedFile >	mappingsFile_
boost::shared_ptr< LibraryData >	library_
reference::CrrFile	reference_
std::ostream &	outSamFile_
const Map2SamConfig &	config_
boost::scoped_ptr < util::FastRangeSet >	exportRegions_
boost::scoped_ptr < mapping::SamRecordGenerator >	mappingSamRecordGenerator_

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

• Map2SamConverter.hpp