, including all inherited members.
| addEvidenceRecords(const mapping::ReadsRecord &readsRecord, SamRecordArray &records) | cgatools::mapping::MergedMap2SamConverter | [protected] |
| alternativeMappingProcessing(const mapping::ReadsRecord &readsRecord, SamRecordArray &records) | cgatools::mapping::MergedMap2SamConverter | [protected, virtual] |
| batchNumber_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| computeMappingWeights(const SamRecordArray &records, const MappingIndicesBySide &mappings, MappingWeightsBySide &weights) const | cgatools::mapping::MergedMap2SamConverter | [protected] |
| computeTotalWeight(const DoubleMatrix &weightMatrix, MappingWeightsBySide &sumAllPairs) const (defined in cgatools::mapping::MergedMap2SamConverter) | cgatools::mapping::MergedMap2SamConverter | [protected] |
| computeWeightMatrix(const SamRecordArray &records, const MappingIndicesBySide &mappings, const MappingWeightsBySide &weights, DoubleMatrix &weightMatrix, DoubleMatrix &mateGaps) const (defined in cgatools::mapping::MergedMap2SamConverter) | cgatools::mapping::MergedMap2SamConverter | [protected] |
| config_ (defined in cgatools::mapping::MergedMap2SamConverter) | cgatools::mapping::MergedMap2SamConverter | [protected] |
| createHeader() (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| detectPrimaryMapping(MappingsRecords &mappingsRecords, bool oneArmOnly) (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| detectTheBestMappingAndMakeItPrimary(SamRecordArray &records) const | cgatools::mapping::MergedMap2SamConverter | [protected] |
| dumpBestLocalMatches(const mapping::ReadsRecord &readsRecord, const SamRecordArray &records, const MappingIndicesBySide &mappingsBySide, const MappingWeightsBySide &dnbArmWeights, const DoubleMatrix &weights, const DoubleMatrix &mateGaps, const MappingWeightsBySide &sumAllPairs, const MappingIndicesBySide &bestFullMappedArms, const MappingIndicesBySide &groups, const double &totalWeight) const | cgatools::mapping::MergedMap2SamConverter | [protected] |
| evidenceBatchRecords_ (defined in cgatools::mapping::MergedMap2SamConverter) | cgatools::mapping::MergedMap2SamConverter | [protected] |
| exportRegions_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| filterDuplicatedMappings(SamRecordArray &records) const | cgatools::mapping::MergedMap2SamConverter | [protected] |
| filterMappingRecords(SamRecordArray &records) | cgatools::mapping::MergedMap2SamConverter | [protected, virtual] |
| findBestCandidates(const DoubleMatrix &m, const DoubleMatrix &mateGaps, const MappingIndicesBySide &mappingsBySide, const MappingWeightsBySide &sumAllPairs, MappingIndicesBySide &bestGroupMappings, MappingIndicesBySide &groups) const (defined in cgatools::mapping::MergedMap2SamConverter) | cgatools::mapping::MergedMap2SamConverter | [protected] |
| formatVersion_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| getChunkNumber(const std::string &fileName, size_t formatVersion) | cgatools::mapping::Map2SamConverter | [protected] |
| getMappingRange(const SamRecord &mapping) (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| init() (defined in cgatools::mapping::MergedMap2SamConverter) | cgatools::mapping::MergedMap2SamConverter | [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] |
| leaveOneBestMapping(SamRecordArray &records) const | cgatools::mapping::MergedMap2SamConverter | [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 | |
| MappingIndicesBySide typedef (defined in cgatools::mapping::MergedMap2SamConverter) | cgatools::mapping::MergedMap2SamConverter | |
| 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] |
| MappingWeightsBySide typedef (defined in cgatools::mapping::MergedMap2SamConverter) | cgatools::mapping::MergedMap2SamConverter | |
| MergedMap2SamConverter(const MergedMap2SamConfig &config, std::ostream &outSamFile) (defined in cgatools::mapping::MergedMap2SamConverter) | cgatools::mapping::MergedMap2SamConverter | [inline] |
| outSamFile_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| printMatrix(const DoubleMatrix &m, std::ostream &ostr) const (defined in cgatools::mapping::MergedMap2SamConverter) | cgatools::mapping::MergedMap2SamConverter | [protected] |
| processDnbRecord(const ReadsRecord &readsRecord, const mapping::MappingsRecords &mappingsRecords) (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| 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] |
| regroupMappings(const mapping::ReadsRecord &readsRecord, SamRecordArray &records) | cgatools::mapping::MergedMap2SamConverter | [protected] |
| reweightDoubleArmMappings(SamRecordArray &records, const MappingIndicesBySide &mappingsBySide, const DoubleMatrix &weightMatrix, const DoubleMatrix &mateGapFrequency, const MappingWeightsBySide &sumAllPairs, const MappingIndicesBySide &bestFullMappedArms, const MappingIndicesBySide &groups, const double &totalWeight) const | cgatools::mapping::MergedMap2SamConverter | [protected] |
| reweightSingleMappings(SamRecordArray &records, const MappingIndicesBySide &mappingsBySide, const MappingWeightsBySide &dnbArmWeights, const MappingWeightsBySide &sumAllPairs) const | cgatools::mapping::MergedMap2SamConverter | [protected] |
| run() (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | |
| SAM_SEPARATOR (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [static] |
| SamRecordArray typedef (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | |
| slide_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [protected] |
| statistics_ (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [mutable, protected] |
| writeMappingRecord(const SamRecord &m) | cgatools::mapping::MergedMap2SamConverter | [protected, virtual] |
| ~Map2SamConverter() (defined in cgatools::mapping::Map2SamConverter) | cgatools::mapping::Map2SamConverter | [inline, virtual] |
1.6.2
