, including all inherited members.
| BaseMap2SamConverter(const Map2SamConfig &config, std::ostream &outSamFile) (defined in cgatools::mapping::BaseMap2SamConverter) | cgatools::mapping::BaseMap2SamConverter | [inline] |
| batchNumber_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| config_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| convertBaseMappingsIntoSamMappings(const mapping::ReadsRecord &readsRecord, SamRecordArray &samMappings, const mapping::MappingsRecords &baseMappingRecords) const (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| createHeader() (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| detectPrimaryMapping(const MappingsRecords &mappingsRecords, bool oneArmOnly, SamRecordArray &samMappings) const (defined in cgatools::mapping::BaseMap2SamConverter) | cgatools::mapping::BaseMap2SamConverter | [protected] |
| exportRegions_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| formatVersion_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| generateDnbId(const mapping::ReadsRecord &readsRecord) const (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| getChunkNumber(const std::string &fileName, size_t formatVersion) const | cgatools::mapping::Map2SamConverter | [protected] |
| getMappingRange(const SamRecord &mapping) const (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| init() (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [virtual] |
| InStream typedef (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | |
| lane_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| laneId_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| library_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| Map2SamConverter(const Map2SamConfig &config, std::ostream &outSamFile) (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | |
| mappingSamRecordGenerator_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| mappingsFile_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| mappingsFileStream_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| MAX_SIDES (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [static] |
| outputSamMappings(const mapping::ReadsRecord &readsRecord, SamRecordArray &samMappings) const (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| outSamFile_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| processDnbRecord(const ReadsRecord &readsRecord, const mapping::MappingsRecords &mappingsRecords) const (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| processMappings(const mapping::ReadsRecord &readsRecord, SamRecordArray &samMappings, const mapping::MappingsRecords &baseMappingRecords) const | cgatools::mapping::BaseMap2SamConverter | [protected, virtual] |
| readsFile_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| readsFileStream_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| reference_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| run() (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | |
| SamRecordArray typedef (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | |
| slide_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| writeMappingRecord(const SamRecord &m) const (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected, virtual] |
| ~Map2SamConverter() (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [inline, virtual] |
1.6.2
