BamTools::SamHeader Struct Reference

Represents the SAM-formatted text header that is part of the BAM file header. More...

#include <SamHeader.h>

List of all members.

Public Member Functions
	SamHeader (const std::string &headerText="")
	constructor
	SamHeader (const SamHeader &other)
	copy constructor
	~SamHeader (void)
	destructor
void	Clear (void)
	Clears all header contents.
std::string	GetErrorString (void) const
	Returns a human-readable description of the last error that occurred.
bool	HasError (void) const
	Returns true if header encountered an error.
bool	IsValid (bool verbose=false) const
	Checks header contents for required data and proper formatting.
void	SetHeaderText (const std::string &headerText)
	Replaces header contents with headerText.
std::string	ToString (void) const
	Converts data fields to SAM-formatted text.
bool	HasVersion (void) const
	Returns true if header contains @HD ID:<Version>
bool	HasSortOrder (void) const
	Returns true if header contains @HD SO:<SortOrder>
bool	HasGroupOrder (void) const
	Returns true if header contains @HD GO:<GroupOrder>
bool	HasSequences (void) const
	Returns true if header contains any @SQ entries.
bool	HasReadGroups (void) const
	Returns true if header contains any @RG entries.
bool	HasPrograms (void) const
	Returns true if header contains any @PG entries.
bool	HasComments (void) const
	Returns true if header contains any @CO entries.
Public Attributes
std::string	Version
	corresponds to @HD VN:<Version>
std::string	SortOrder
	corresponds to @HD SO:<SortOrder>
std::string	GroupOrder
	corresponds to @HD GO:<GroupOrder>
SamSequenceDictionary	Sequences
	corresponds to @SQ entries
SamReadGroupDictionary	ReadGroups
	corresponds to @RG entries
SamProgramChain	Programs
	corresponds to @PG entries
std::vector< std::string >	Comments
	corresponds to @CO entries

---

Detailed Description

Represents the SAM-formatted text header that is part of the BAM file header.

Provides direct read/write access to the SAM header data fields.

See also:

http://samtools.sourceforge.net/SAM1.pdf

---

Constructor & Destructor Documentation

SamHeader::SamHeader

(

const std::string &

headerText = ""

)

constructor

SamHeader::SamHeader

(

const SamHeader &

other

)

copy constructor

SamHeader::~SamHeader

(

void

)

destructor

---

Member Function Documentation

void SamHeader::Clear

(

void

)

Clears all header contents.

std::string SamHeader::GetErrorString

(

void

)

const

Returns a human-readable description of the last error that occurred.

This method allows elimination of STDERR pollution. Developers of client code may choose how the messages are displayed to the user, if at all.

Returns:

error description

bool SamHeader::HasComments

(

void

)

const

Returns true if header contains any @CO entries.

bool SamHeader::HasError

(

void

)

const

Returns true if header encountered an error.

bool SamHeader::HasGroupOrder

(

void

)

const

Returns true if header contains @HD GO:<GroupOrder>

bool SamHeader::HasPrograms

(

void

)

const

Returns true if header contains any @PG entries.

bool SamHeader::HasReadGroups

(

void

)

const

Returns true if header contains any @RG entries.

bool SamHeader::HasSequences

(

void

)

const

Returns true if header contains any @SQ entries.

bool SamHeader::HasSortOrder

(

void

)

const

Returns true if header contains @HD SO:<SortOrder>

bool SamHeader::HasVersion

(

void

)

const

Returns true if header contains @HD ID:<Version>

bool SamHeader::IsValid

(

bool

verbose = false

)

const

Checks header contents for required data and proper formatting.

Parameters:

[in]

verbose

If set to true, validation errors & warnings will be printed to stderr. Otherwise, messages are available through SamHeader::GetErrorString().

Returns:

true if SAM header is well-formed

void SamHeader::SetHeaderText

(

const std::string &

headerText

)

Replaces header contents with headerText.

Parameters:

[in]

headerText

SAM formatted-text that will be parsed into data fields

string SamHeader::ToString

(

void

)

const

Converts data fields to SAM-formatted text.

Applies any local modifications made since creating this object or calling SetHeaderText().

Returns:

SAM-formatted header text

---

Member Data Documentation

SamHeader::Comments

corresponds to @CO entries

SamHeader::GroupOrder

corresponds to @HD GO:<GroupOrder>

SamHeader::Programs

corresponds to @PG entries

See also:

SamProgram, SamProgramChain

SamHeader::ReadGroups

corresponds to @RG entries

See also:

SamReadGroup, SamReadGroupDictionary

SamHeader::Sequences

corresponds to @SQ entries

See also:

SamSequence, SamSequenceDictionary

SamHeader::SortOrder

corresponds to @HD SO:<SortOrder>

SamHeader::Version

corresponds to @HD VN:<Version>

Required for valid SAM header, if @HD record is present.

---

The documentation for this struct was generated from the following files:

• SamHeader.h
• SamHeader.cpp