BamTools::SamReadGroup Struct Reference

Represents a SAM read group entry. More...

#include <SamReadGroup.h>

List of all members.

Public Member Functions
	SamReadGroup (void)
	default constructor
	SamReadGroup (const std::string &id)
	constructs read group with id
	SamReadGroup (const SamReadGroup &other)
	copy constructor
	~SamReadGroup (void)
	destructor
void	Clear (void)
	Clears all data fields.
bool	HasDescription (void) const
	Returns true if read group contains @RG DS:<Description>
bool	HasFlowOrder (void) const
	Returns true if read group contains @RG FO:<FlowOrder>
bool	HasID (void) const
	Returns true if read group contains @RG: ID:<ID>
bool	HasKeySequence (void) const
	Returns true if read group contains @RG KS:<KeySequence>
bool	HasLibrary (void) const
	Returns true if read group contains @RG LB:<Library>
bool	HasPlatformUnit (void) const
	Returns true if read group contains @RG PU:<PlatformUnit>
bool	HasPredictedInsertSize (void) const
	Returns true if read group contains @RG PI:<PredictedInsertSize>
bool	HasProductionDate (void) const
	Returns true if read group contains @RG DT:<ProductionDate>
bool	HasProgram (void) const
	Returns true if read group contains @RG PG:<Program>
bool	HasSample (void) const
	Returns true if read group contains @RG SM:<Sample>
bool	HasSequencingCenter (void) const
	Returns true if read group contains @RG CN:<SequencingCenter>
bool	HasSequencingTechnology (void) const
	Returns true if read group contains @RG PL:<SequencingTechnology>
Public Attributes
std::string	Description
	corresponds to @RG DS:<Description>
std::string	FlowOrder
	corresponds to @RG FO:<FlowOrder>
std::string	ID
	corresponds to @RG ID:<ID>
std::string	KeySequence
	corresponds to @RG KS:<KeySequence>
std::string	Library
	corresponds to @RG LB:<Library>
std::string	PlatformUnit
	corresponds to @RG PU:<PlatformUnit>
std::string	PredictedInsertSize
	corresponds to @RG PI:<PredictedInsertSize>
std::string	ProductionDate
	corresponds to @RG DT:<ProductionDate>
std::string	Program
	corresponds to @RG PG:<Program>
std::string	Sample
	corresponds to @RG SM:<Sample>
std::string	SequencingCenter
	corresponds to @RG CN:<SequencingCenter>
std::string	SequencingTechnology
	corresponds to @RG PL:<SequencingTechnology>

---

Detailed Description

Represents a SAM read group entry.

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

See also:

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

---

Constructor & Destructor Documentation

SamReadGroup::SamReadGroup

(

void

)

default constructor

SamReadGroup::SamReadGroup

(

const std::string &

id

)

constructs read group with id

Parameters:

id

desired read group ID

SamReadGroup::SamReadGroup

(

const SamReadGroup &

other

)

copy constructor

SamReadGroup::~SamReadGroup

(

void

)

destructor

---

Member Function Documentation

void SamReadGroup::Clear

(

void

)

Clears all data fields.

bool SamReadGroup::HasDescription

(

void

)

const

Returns true if read group contains @RG DS:<Description>

bool SamReadGroup::HasFlowOrder

(

void

)

const

Returns true if read group contains @RG FO:<FlowOrder>

bool SamReadGroup::HasID

(

void

)

const

Returns true if read group contains @RG: ID:<ID>

bool SamReadGroup::HasKeySequence

(

void

)

const

Returns true if read group contains @RG KS:<KeySequence>

bool SamReadGroup::HasLibrary

(

void

)

const

Returns true if read group contains @RG LB:<Library>

bool SamReadGroup::HasPlatformUnit

(

void

)

const

Returns true if read group contains @RG PU:<PlatformUnit>

bool SamReadGroup::HasPredictedInsertSize

(

void

)

const

Returns true if read group contains @RG PI:<PredictedInsertSize>

bool SamReadGroup::HasProductionDate

(

void

)

const

Returns true if read group contains @RG DT:<ProductionDate>

bool SamReadGroup::HasProgram

(

void

)

const

Returns true if read group contains @RG PG:<Program>

bool SamReadGroup::HasSample

(

void

)

const

Returns true if read group contains @RG SM:<Sample>

bool SamReadGroup::HasSequencingCenter

(

void

)

const

Returns true if read group contains @RG CN:<SequencingCenter>

bool SamReadGroup::HasSequencingTechnology

(

void

)

const

Returns true if read group contains @RG PL:<SequencingTechnology>

---

Member Data Documentation

SamReadGroup::Description

corresponds to @RG DS:<Description>

SamReadGroup::FlowOrder

corresponds to @RG FO:<FlowOrder>

SamReadGroup::ID

corresponds to @RG ID:<ID>

Required for valid SAM header.

SamReadGroup::KeySequence

corresponds to @RG KS:<KeySequence>

SamReadGroup::Library

corresponds to @RG LB:<Library>

SamReadGroup::PlatformUnit

corresponds to @RG PU:<PlatformUnit>

SamReadGroup::PredictedInsertSize

corresponds to @RG PI:<PredictedInsertSize>

SamReadGroup::ProductionDate

corresponds to @RG DT:<ProductionDate>

SamReadGroup::Program

corresponds to @RG PG:<Program>

SamReadGroup::Sample

corresponds to @RG SM:<Sample>

SamReadGroup::SequencingCenter

corresponds to @RG CN:<SequencingCenter>

SamReadGroup::SequencingTechnology

corresponds to @RG PL:<SequencingTechnology>

---

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

• SamReadGroup.h
• SamReadGroup.cpp