C++ Class: SamFileHeader

SamFileHeader

This class allows a user to get/set the fields in a SAM/BAM Header.

This class is part of libbam.

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.

Proposed Accessors

• HD
  • getVersion - returns the VN field (will only be one)
• SQ
  • getRefSequenceCount - count of the number of SQ entries in the header
  • getRefSequenceName - gets the next reference sequence name.
  • getRefSequenceLength - gets the length associated with the specified reference sequence.
• RG
  • getSampleID - for a specified Read Group....???? but SampleID is the key...maybe passing in a record?
  • getReadGroup - pass in record, return a read group structure?
  • getLibrary - for a given read group
  • getSample - for a given read group
  • getTechnology - for a given read group
  • getPlatformUnit - for a given read group

NOTE: More Get Accessors will be coming. Let me know if you need a specific one, and I can add that first