Public Types | |
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typedef boost::shared_ptr < std::istream > | InStream |
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typedef boost::ptr_vector < SamRecord > | SamRecordArray |
Public Member Functions | |
| Map2SamConverter (const Map2SamConfig &config, std::ostream &outSamFile) | |
| virtual void | init () |
| void | run () |
Static Public Attributes | |
| static const char | SAM_SEPARATOR = '\t' |
Protected Member Functions | |
| SamFileHeaderBlock | createHeader () |
| virtual void | filterMappingRecords (SamRecordArray &records) |
| virtual void | writeMappingRecord (const SamRecord &m) |
| void | processDnbRecord (const ReadsRecord &readsRecord, const mapping::MappingsRecords &mappingsRecords) |
| virtual bool | alternativeMappingProcessing (const mapping::ReadsRecord &readsRecord, SamRecordArray &records) |
| a template function allowing functionality extension by a derived class, such as merge additional mappings returns true if the processing has replaced the standard processing | |
| reference::Range | getMappingRange (const SamRecord &mapping) |
| size_t | detectPrimaryMapping (MappingsRecords &mappingsRecords, bool oneArmOnly) |
| size_t | getChunkNumber (const std::string &fileName, size_t formatVersion) |
| detect the chunk number for the older versions | |
Protected Attributes | |
| size_t | batchNumber_ |
| size_t | formatVersion_ |
| std::string | slide_ |
| std::string | lane_ |
| std::string | laneId_ |
| InStream | readsFileStream_ |
| InStream | mappingsFileStream_ |
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boost::shared_ptr < util::DelimitedFile > | readsFile_ |
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boost::shared_ptr < util::DelimitedFile > | mappingsFile_ |
| boost::shared_ptr< LibraryData > | library_ |
| reference::CrrFile | reference_ |
| std::ostream & | outSamFile_ |
| SamStatistics | statistics_ |
| const Map2SamConfig & | config_ |
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boost::scoped_ptr < util::FastRangeSet > | exportRegions_ |
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boost::scoped_ptr < mapping::SamRecordGenerator > | mappingSamRecordGenerator_ |
1.6.2
