SamFileHeader Class Reference
Collaboration diagram for SamFileHeader:
Public Member Functions | |
| SamFileHeader (const SamFileHeader &header) | |
| SamFileHeader & | operator= (const SamFileHeader &header) |
| bool | copy (const SamFileHeader &header) |
| void | resetHeader () |
| bool | getHeaderString (std::string &header) const |
| int | getReferenceID (const String &referenceName) |
| int | getReferenceID (const char *referenceName) |
| const String & | getReferenceLabel (int id) const |
| const SamReferenceInfo * | getReferenceInfo () const |
| void | addReferenceInfo (const char *referenceSequenceName, int32_t referenceSequenceLength) |
| bool | addHeaderLine (const char *type, const char *tag, const char *value) |
| bool | addHeaderLine (const char *headerLine) |
| bool | setHDTag (const char *tag, const char *value) |
| bool | setSQTag (const char *tag, const char *value, const char *name) |
| bool | setRGTag (const char *tag, const char *value, const char *id) |
| bool | setPGTag (const char *tag, const char *value, const char *id) |
| bool | addHD (SamHeaderHD *hd) |
| bool | addSQ (SamHeaderSQ *sq) |
| bool | addRG (SamHeaderRG *rg) |
| bool | addPG (SamHeaderPG *pg) |
| bool | removeHD () |
| bool | removeSQ (const char *name) |
| bool | removeRG (const char *id) |
| bool | removePG (const char *id) |
| SamStatus::Status | setHeaderFromBamFile (IFILE filePtr) |
| const char * | getHDTagValue (const char *tag) |
| const char * | getSQTagValue (const char *tag, const char *name) |
| const char * | getRGTagValue (const char *tag, const char *id) |
| const char * | getPGTagValue (const char *tag, const char *id) |
| int | getNumSQs () |
| int | getNumRGs () |
| int | getNumPGs () |
| SamHeaderHD * | getHD () |
| SamHeaderSQ * | getSQ (const char *name) |
| SamHeaderRG * | getRG (const char *id) |
| SamHeaderPG * | getPG (const char *id) |
| const char * | getSortOrder () |
| const char * | getTagSO () |
| SamHeaderRecord * | getNextSQRecord () |
| SamHeaderRecord * | getNextRGRecord () |
| SamHeaderRecord * | getNextPGRecord () |
| void | resetSQRecordIter () |
| void | resetRGRecordIter () |
| void | resetPGRecordIter () |
| SamHeaderRecord * | getNextHeaderRecord (uint32_t &index, SamHeaderRecord::SamHeaderRecordType headerType) |
| SamHeaderRecord * | getNextHeaderRecord () |
| bool | getNextHeaderLine (std::string &headerLine) |
| void | resetHeaderRecordIter () |
| const char * | getNextComment () |
| void | resetCommentIter () |
| bool | addComment (const char *comment) |
| void | generateReferenceInfo () |
Detailed Description
Definition at line 31 of file SamFileHeader.h.
The documentation for this class was generated from the following files:
- lib/bam/SamFileHeader.h
- lib/bam/SamFileHeader.cpp
