SamRecord Class Reference
Collaboration diagram for SamRecord:
Public Member Functions | |
| SamRecord () | |
| Default Constructor. | |
| SamRecord (ErrorHandler::HandlingType errorHandlingType) | |
| Constructor that sets the error handling type. | |
| void | resetRecord () |
| void | resetTagIter () |
| bool | isValid (SamFileHeader &header) |
| bool | setReadName (const char *readName) |
| bool | setFlag (uint16_t flag) |
| bool | setReferenceName (SamFileHeader &header, const char *referenceName) |
| bool | set1BasedPosition (int32_t position) |
| bool | set0BasedPosition (int32_t position) |
| bool | setMapQuality (uint8_t mapQuality) |
| bool | setCigar (const char *cigar) |
| bool | setCigar (const Cigar &cigar) |
| bool | setMateReferenceName (SamFileHeader &header, const char *mateReferenceName) |
| bool | set1BasedMatePosition (int32_t matePosition) |
| bool | set0BasedMatePosition (int32_t matePosition) |
| bool | setInsertSize (int32_t insertSize) |
| bool | setSequence (const char *seq) |
| bool | setQuality (const char *quality) |
| SamStatus::Status | setBufferFromFile (IFILE filePtr, SamFileHeader &header) |
| SamStatus::Status | setBuffer (const char *fromBuffer, uint32_t fromBufferSize, SamFileHeader &header) |
| bool | addTag (const char *tag, char vtype, const char *value) |
| const void * | getRecordBuffer () |
| SamStatus::Status | writeRecordBuffer (IFILE filePtr) |
| int32_t | getBlockSize () |
| const char * | getReferenceName () |
| int32_t | getReferenceID () |
| int32_t | get1BasedPosition () |
| int32_t | get0BasedPosition () |
| uint8_t | getReadNameLength () |
| uint8_t | getMapQuality () |
| uint16_t | getBin () |
| uint16_t | getCigarLength () |
| uint16_t | getFlag () |
| int32_t | getReadLength () |
| const char * | getMateReferenceName () |
| const char * | getMateReferenceNameOrEqual () |
| int32_t | getMateReferenceID () |
| int32_t | get1BasedMatePosition () |
| int32_t | get0BasedMatePosition () |
| int32_t | getInsertSize () |
| int32_t | get0BasedAlignmentEnd () |
| int32_t | get1BasedAlignmentEnd () |
| int32_t | getAlignmentLength () |
| int32_t | get0BasedUnclippedStart () |
| int32_t | get1BasedUnclippedStart () |
| int32_t | get0BasedUnclippedEnd () |
| int32_t | get1BasedUnclippedEnd () |
| const char * | getReadName () |
| const char * | getCigar () |
| const char * | getSequence () |
| const char * | getQuality () |
| char | getSequence (int index) |
| char | getQuality (int index) |
| Cigar * | getCigarInfo () |
| uint32_t | getTagLength () |
| bool | getNextSamTag (char *tag, char &vtype, void **value) |
| bool | getFields (bamRecordStruct &recStruct, String &readName, String &cigar, String &sequence, String &quality) |
| bool | isIntegerType (char vtype) const |
| bool | isDoubleType (char vtype) const |
| bool | isCharType (char vtype) const |
| bool | isStringType (char vtype) const |
| void | clearTags () |
| const SamStatus & | getStatus () |
| String & | getString (const char *tag) |
| int & | getInteger (const char *tag) |
| double & | getDouble (const char *tag) |
| bool | checkString (const char *tag) |
| bool | checkInteger (const char *tag) |
| bool | checkDouble (const char *tag) |
| bool | checkTag (const char *tag, char type) |
| uint32_t | getNumOverlaps (int32_t start, int32_t end) |
Detailed Description
Definition at line 46 of file SamRecord.h.
Constructor & Destructor Documentation
| SamRecord::SamRecord | ( | ErrorHandler::HandlingType | errorHandlingType | ) |
Constructor that sets the error handling type.
- Parameters:
-
errorHandlingType how to handle errors.
Definition at line 51 of file SamRecord.cpp.
00052 : myStatus(errorHandlingType) 00053 { 00054 int32_t defaultAllocSize = DEFAULT_BLOCK_SIZE + sizeof(int32_t); 00055 00056 myRecordPtr = 00057 (bamRecordStruct *) malloc(defaultAllocSize); 00058 00059 myCigarTempBuffer = NULL; 00060 myCigarTempBufferAllocatedSize = 0; 00061 00062 allocatedSize = defaultAllocSize; 00063 00064 resetRecord(); 00065 }
The documentation for this class was generated from the following files:
- lib/bam/SamRecord.h
- lib/bam/SamRecord.cpp
