C++ Class: SamFileHeader: Difference between revisions
Created page with '== SamFileHeader == This class allows a user to get/set the fields in a SAM/BAM Header. === Setting fields in the Header === The '''SamFileHeader''' class contains accessors to …' |
No edit summary |
||
| Line 9: | Line 9: | ||
! Method Name !! Description | ! Method Name !! Description | ||
|- | |- | ||
| <code>bool addHeaderLine(const char* type, const char* tag, int value)</code> | | <code>bool SamFileHeader::addHeaderLine(const char* type, const char* tag, int value)</code> | ||
| Adds the type, tag, and integer value to the header. | | Adds the type, tag, and integer value to the header. | ||
Returns true if successfully added, false if not. | Returns true if successfully added, false if not. | ||
NOTE: currently, this method will only do one tag per type on a line. If a type has multiple tags, then the whole line needs to be added at once. | NOTE: currently, this method will only do one tag per type on a line. If a type has multiple tags, then the whole line needs to be added at once. | ||
|- | |- | ||
| <code>bool addHeaderLine(const char* type, const char* tag, const char* value)</code> | | <code>bool SamFileHeader::addHeaderLine(const char* type, const char* tag, const char* value)</code> | ||
| Adds the type, tag, and const char* value to the header. | | Adds the type, tag, and const char* value to the header. | ||
Returns true if successfully added, false if not. | Returns true if successfully added, false if not. | ||
NOTE: currently, this method will only do one tag per type on a line. If a type has multiple tags, then the whole line needs to be added at once. | NOTE: currently, this method will only do one tag per type on a line. If a type has multiple tags, then the whole line needs to be added at once. | ||
|- | |- | ||
| <code>bool addHeaderLine(const char* headerLine)</code> | | <code>bool SamFileHeader::addHeaderLine(const char* headerLine)</code> | ||
| Adds the already setup/formatted headerLine to the header. It is assumed that the line does not contain a “\n”. | | Adds the already setup/formatted headerLine to the header. It is assumed that the line does not contain a “\n”. | ||
Returns true if successfully added, false if not. | Returns true if successfully added, false if not. | ||
| Line 32: | Line 32: | ||
! Method Name !! Description | ! Method Name !! Description | ||
|- | |- | ||
| <code>const char* getTagSO()</code> | | <code>const char* SamFileHeader::getTagSO()</code> | ||
| Return the value of the SO tag. If the field does not exist, "unsorted" is returned. | | Return the value of the SO tag. If the field does not exist, "unsorted" is returned. | ||
|} | |} | ||
'''NOTE: More Get Accessors will be coming. Let me know if you need a specific one, and I can add that first''' | '''NOTE: More Get Accessors will be coming. Let me know if you need a specific one, and I can add that first''' | ||
Revision as of 16:41, 6 April 2010
SamFileHeader
This class allows a user to get/set the fields in a SAM/BAM Header.
Setting fields in the Header
The SamFileHeader class contains accessors to set the header lines of a SAM/BAM header. By using these set methods to setup the header, they can be pulled back out using the get accessors or the header can be later written to a SAM/BAM file. The methods found in the SamFileHeader class for setting fields are:
| Method Name | Description |
|---|---|
bool SamFileHeader::addHeaderLine(const char* type, const char* tag, int value)
|
Adds the type, tag, and integer value to the header.
Returns true if successfully added, false if not. NOTE: currently, this method will only do one tag per type on a line. If a type has multiple tags, then the whole line needs to be added at once. |
bool SamFileHeader::addHeaderLine(const char* type, const char* tag, const char* value)
|
Adds the type, tag, and const char* value to the header.
Returns true if successfully added, false if not. NOTE: currently, this method will only do one tag per type on a line. If a type has multiple tags, then the whole line needs to be added at once. |
bool SamFileHeader::addHeaderLine(const char* headerLine)
|
Adds the already setup/formatted headerLine to the header. It is assumed that the line does not contain a “\n”.
Returns true if successfully added, false if not. |
Getting fields from the Header
| Method Name | Description |
|---|---|
const char* SamFileHeader::getTagSO()
|
Return the value of the SO tag. If the field does not exist, "unsorted" is returned. |
NOTE: More Get Accessors will be coming. Let me know if you need a specific one, and I can add that first
