, including all inherited members.
| flagAsSVCandidate(OutputFileDescriptor &out) | cgatools::mapping::SamRecordGenerator | [protected] |
| getAdjustedSamPosition(const SamRecord &record) const (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| getOutputStream(const std::string &id) (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| getSamChr(uint16_t chr) const (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| header_ (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| isConsistent(const SamRecord &r) const (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| mappingRecordToSam(const SamRecord &record) (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | |
| OpenStreamPtr typedef (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| openStreams_ (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| outFiles_ (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| OutStreamMap typedef (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| OutStreams typedef (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| printAlleleInfoTag(OutputFileDescriptor &out, const mapping::EvidenceSamRecord &evidenceRecord) | cgatools::mapping::SamRecordGenerator | [protected] |
| printAlternatives(OutputFileDescriptor &out, const std::string &tag, const mapping::SamRecord::SamRecords &samRecords, size_t startFrom) | cgatools::mapping::SamRecordGenerator | [protected] |
| printMateSequence(OutputFileDescriptor &out, const std::string &mateSeq, const std::string &mateScore) | cgatools::mapping::SamRecordGenerator | [protected] |
| printNegativeGapTag(OutputFileDescriptor &out, const mapping::SamSequenceSplitter &splitter) (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| printReadGroup(OutputFileDescriptor &out) (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] |
| samGeneratorConfig_ (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | [protected] |
| SamRecordGenerator(std::ostream &outSamFile, const reference::CrrFile &reference, const SamGeneratorConfig &config, const std::vector< std::string > &outStreams) (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | |
| setHeader(const SamFileHeaderBlock &header) (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | |
| ~SamRecordGenerator() (defined in cgatools::mapping::SamRecordGenerator) | cgatools::mapping::SamRecordGenerator | |
1.6.2
