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== 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:
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-style="background: #f2f2f2; text-align: center;" '''SamFileHeader Class Methods'''
! Method Name !! Description
|-
| <code>bool addHeaderLine(const char* type, const char* tag, int value)</code>
| 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.
|-
| <code>bool addHeaderLine(const char* type, const char* tag, const char* value)</code>
| 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.
|-
| <code>bool 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”.
Returns true if successfully added, false if not.
|-
|}
=== Getting fields from the Header ===
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-style="background: #f2f2f2; text-align: center;" '''SamFileHeader Class Methods'''
! Method Name !! Description
|-
| <code>const char* getTagSO()</code>
| 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'''
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:
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-style="background: #f2f2f2; text-align: center;" '''SamFileHeader Class Methods'''
! Method Name !! Description
|-
| <code>bool addHeaderLine(const char* type, const char* tag, int value)</code>
| 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.
|-
| <code>bool addHeaderLine(const char* type, const char* tag, const char* value)</code>
| 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.
|-
| <code>bool 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”.
Returns true if successfully added, false if not.
|-
|}
=== Getting fields from the Header ===
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-style="background: #f2f2f2; text-align: center;" '''SamFileHeader Class Methods'''
! Method Name !! Description
|-
| <code>const char* getTagSO()</code>
| 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'''
