cgatools::mapping::SamRecordGenerator Member List

This is the complete list of members for cgatools::mapping::SamRecordGenerator, including all inherited members.

addMateSequenceAndScore_ (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
addMateSequenceAndScoreIfMateUnmapped_ (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
adjustedPosition(const SamRecord &record) const (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
flagAsSVCandidate()	cgatools::mapping::SamRecordGenerator	[protected]
header_ (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
mappingRecordToSam(const SamRecord &record) (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator
mateSvCandidates_ (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
outSamFile_ (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
printAlleleInfo_ (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
printAlleleInfoTag(const mapping::EvidenceSamRecord &evidenceRecord)	cgatools::mapping::SamRecordGenerator	[protected]
printMateSequence(const std::string &mateSeq, const std::string &mateScore)	cgatools::mapping::SamRecordGenerator	[protected]
printNegativeGapTag(const mapping::SamSequenceSplitter &splitter) (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
printReadGroup() (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
readGroup_ (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
reference_ (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[protected]
SAM_SEPARATOR (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[static]
SamRecordGenerator(std::ostream &outSamFile, const reference::CrrFile &reference, bool mateSvCandidates, bool addMateSequenceAndScore, bool addMateSequenceAndScoreIfMateUnmapped, bool printAlleleInfo) (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator	[inline]
setHeader(const SamFileHeaderBlock &header) (defined in cgatools::mapping::SamRecordGenerator)	cgatools::mapping::SamRecordGenerator