Public Types | |
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typedef boost::array < std::vector< size_t >, 2 > | MappingIndicesBySide |
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typedef boost::array < std::vector< double >, 2 > | MappingWeightsBySide |
Public Member Functions | |
| MergedMap2SamConverter (const MergedMap2SamConfig &config, std::ostream &outSamFile) | |
| virtual void | init () |
Protected Member Functions | |
| virtual bool | alternativeMappingProcessing (const mapping::ReadsRecord &readsRecord, SamRecordArray &records) |
| override the method to merge the evidence mappings | |
| virtual void | filterMappingRecords (SamRecordArray &records) |
| Prefilter mapping records. | |
| virtual void | writeMappingRecord (const SamRecord &m) |
| Export mapping record in SAM format. | |
| void | addEvidenceRecords (const mapping::ReadsRecord &readsRecord, SamRecordArray &records) |
| Merge evidence records into the base mappings. | |
| void | regroupMappings (const mapping::ReadsRecord &readsRecord, SamRecordArray &records) |
| Process merged mappings: recompute MAPQ, deduplicate, select best mapping pairs. | |
| void | computeMappingWeights (const SamRecordArray &records, const MappingIndicesBySide &mappings, MappingWeightsBySide &weights) const |
| computes P(DNBs) * P(gaps) | |
| void | filterDuplicatedMappings (SamRecordArray &records) const |
| filter the mappings that have equal position and alignment, leave Evidence mappings if equal to base | |
| void | computeWeightMatrix (const SamRecordArray &records, const MappingIndicesBySide &mappings, const MappingWeightsBySide &weights, DoubleMatrix &weightMatrix, DoubleMatrix &mateGaps) const |
| double | computeTotalWeight (const DoubleMatrix &weightMatrix, MappingWeightsBySide &sumAllPairs) const |
| void | findBestCandidates (const DoubleMatrix &m, const DoubleMatrix &mateGaps, const MappingIndicesBySide &mappingsBySide, const MappingWeightsBySide &sumAllPairs, MappingIndicesBySide &bestGroupMappings, MappingIndicesBySide &groups) const |
| void | reweightSingleMappings (SamRecordArray &records, const MappingIndicesBySide &mappingsBySide, const MappingWeightsBySide &dnbArmWeights, const MappingWeightsBySide &sumAllPairs) const |
| compute weights of double arm mappings and detect primary mappings for each group | |
| void | 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 |
| compute weights of single arm mappings | |
| void | detectTheBestMappingAndMakeItPrimary (SamRecordArray &records) const |
| the function selects the best mapping record based on MAPQ set by reweightDoubleArmMappings | |
| void | leaveOneBestMapping (SamRecordArray &records) const |
| the function filters mapping records based on primary flags set by reweightDoubleArmMappings | |
| void | 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 |
| output debug information to stdout | |
| void | printMatrix (const DoubleMatrix &m, std::ostream &ostr) const |
Protected Attributes | |
| const MergedMap2SamConfig & | config_ |
| mapping::BatchRecords | evidenceBatchRecords_ |
1.6.2
