Line 4: |
Line 4: |
| The '''SamFile''' class allows a user to easily read/write a SAM/BAM file. | | The '''SamFile''' class allows a user to easily read/write a SAM/BAM file. |
| The methods found in this class are: | | The methods found in this class are: |
− | {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" | + | {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
| |-style="background: #f2f2f2; text-align: center;" '''SamFile Class Methods''' | | |-style="background: #f2f2f2; text-align: center;" '''SamFile Class Methods''' |
| ! Method Name !! Description | | ! Method Name !! Description |
Line 16: |
Line 16: |
| Returns true if successfully opened reading, false if not. | | Returns true if successfully opened reading, false if not. |
| |- | | |- |
− | | <code>bool OpenForWrite(const char * filename)</code> | + | | <code>bool SamFile::OpenForWrite(const char * filename)</code> |
| | bool: true if successfully opened, false if not. | | | bool: true if successfully opened, false if not. |
| Opens as BAM file if the specified filename ends in .bam. Otherwise it is opened as a SAM file. | | Opens as BAM file if the specified filename ends in .bam. Otherwise it is opened as a SAM file. |
| Returns true if successfully opened for writing, false if not. | | Returns true if successfully opened for writing, false if not. |
| |- | | |- |
− | | void Close() | + | | <code>void SamFile::Close()</code> |
| | Close the file if there is one open. | | | Close the file if there is one open. |
| |- | | |- |
− | | bool ReadHeader(SamFileHeader& header) | + | | <code>bool SamFile::ReadHeader(SamFileHeader& header)</code> |
| | Reads the header section from the file and stores it in the passed in header. | | | Reads the header section from the file and stores it in the passed in header. |
| Returns true if successfully read, false if not. | | Returns true if successfully read, false if not. |
| |- | | |- |
− | | bool WriteHeader(const SamFileHeader& header) | + | | <code>bool SamFile::WriteHeader(const SamFileHeader& header)</code> |
| | Writes the specified header into the file. | | | Writes the specified header into the file. |
| Returns true if successfully written, false if not. | | Returns true if successfully written, false if not. |
| |- | | |- |
− | | bool ReadRecord(SamFileHeader& header, SamRecord& record) | + | | <code>bool SamFile::ReadRecord(SamFileHeader& header, SamRecord& record)</code> |
| | Reads the next record from the file and stores it in the passed in record. | | | Reads the next record from the file and stores it in the passed in record. |
| Returns true if successfully read, false if not. | | Returns true if successfully read, false if not. |
| |- | | |- |
− | | bool WriteRecord(SamFileHeader& header, SamRecord& record) | + | | <code>bool SamFile::WriteRecord(SamFileHeader& header, SamRecord& record)</code> |
| | Writes the specified record into the file. | | | Writes the specified record into the file. |
| Returns true if successfully written, false if not. | | Returns true if successfully written, false if not. |