Public Types | |
| enum | RecordType { DEFAULT = 0, BASE_MAPPING, EVIDENCE, EVIDENCE_CACHE } |
| typedef std::vector< SamRecord * > | SamRecords |
|
typedef std::vector< const SamRecord * > | ConstSamRecords |
Public Member Functions | |
| SamRecord (const std::string &readName, bool isMapped, bool onNegativeStrand, bool isPrimary, uint8_t side, uint16_t chr, int32_t position, const std::string &extCigar, uint8_t mappingQuality, bool isConsistentMapQ, const std::string &fullReadSequence, const std::string &fullReadScores, UInt16Pair sequenceStartAndLength) | |
| bool | correctPosition (const reference::CrrFile &reference) |
| uint8_t | getMappingQuality () const |
| void | setMappingQuality (uint8_t value, bool isConsistent) |
| bool | isArtificialMateReported () const |
| void | setArtificialMateReported (bool isReported) |
| bool | isConsistent () const |
Public Attributes | |
| RecordType | typeId_ |
| std::string | readName_ |
| bool | isMapped_ |
| bool | onNegativeStrand_ |
| bool | isPrimary_ |
| bool | isGroupPrimary_ |
| uint8_t | side_ |
| uint16_t | chr_ |
| int32_t | position_ |
| std::string | extCigar_ |
| std::string | fullReadSequence_ |
| std::string | fullReadScores_ |
| bool | isSvCandidate_ |
| UInt16Pair | sequenceStartAndLength_ [2] |
| SamRecords | mates_ |
| SamRecords | alternatives_ |
Protected Attributes | |
| uint8_t | mappingQuality_ |
| bool | isConsistentMapQ_ |
| bool | isArtificialMateReported_ |
Friends | |
| std::ostream & | operator<< (std::ostream &ost, const SamRecord &r) |
1.6.2
