Represents a SAM read group entry. More...

#include <SamReadGroup.h>

Public Member Functions
	SamReadGroup ()
	default constructor More...

	SamReadGroup (const std::string &id)
	constructs read group with id More...

void	Clear ()
	Clears all data fields. More...

bool	HasDescription () const
	Returns `true` if read group contains @RG DS:<Description> More...

bool	HasFlowOrder () const
	Returns `true` if read group contains @RG FO:<FlowOrder> More...

bool	HasID () const
	Returns `true` if read group contains @RG: ID:<ID> More...

bool	HasKeySequence () const
	Returns `true` if read group contains @RG KS:<KeySequence> More...

bool	HasLibrary () const
	Returns `true` if read group contains @RG LB:<Library> More...

bool	HasPlatformUnit () const
	Returns `true` if read group contains @RG PU:<PlatformUnit> More...

bool	HasPredictedInsertSize () const
	Returns `true` if read group contains @RG PI:<PredictedInsertSize> More...

bool	HasProductionDate () const
	Returns `true` if read group contains @RG DT:<ProductionDate> More...

bool	HasProgram () const
	Returns `true` if read group contains @RG PG:<Program> More...

bool	HasSample () const
	Returns `true` if read group contains @RG SM:<Sample> More...

bool	HasSequencingCenter () const
	Returns `true` if read group contains @RG CN:<SequencingCenter> More...

bool	HasSequencingTechnology () const
	Returns `true` if read group contains @RG PL:<SequencingTechnology> More...

Public Attributes
std::string	Description
	corresponds to @RG DS:<Description> More...

std::string	FlowOrder
	corresponds to @RG FO:<FlowOrder> More...

std::string	ID
	corresponds to @RG ID:<ID> More...

std::string	KeySequence
	corresponds to @RG KS:<KeySequence> More...

std::string	Library
	corresponds to @RG LB:<Library> More...

std::string	PlatformUnit
	corresponds to @RG PU:<PlatformUnit> More...

std::string	PredictedInsertSize
	corresponds to @RG PI:<PredictedInsertSize> More...

std::string	ProductionDate
	corresponds to @RG DT:<ProductionDate> More...

std::string	Program
	corresponds to @RG PG:<Program> More...

std::string	Sample
	corresponds to @RG SM:<Sample> More...

std::string	SequencingCenter
	corresponds to @RG CN:<SequencingCenter> More...

std::string	SequencingTechnology
	corresponds to @RG PL:<SequencingTechnology> More...

std::vector< CustomHeaderTag >	CustomTags

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() [1/2]

SamReadGroup::SamReadGroup ( )

default constructor

◆ SamReadGroup() [2/2]

SamReadGroup::SamReadGroup ( const std::string & id )

constructs read group with id

Parameters

id	desired read group ID

Member Function Documentation

◆ Clear()

void SamReadGroup::Clear ( )

Clears all data fields.

◆ HasDescription()

bool SamReadGroup::HasDescription ( ) const

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

◆ HasFlowOrder()

bool SamReadGroup::HasFlowOrder ( ) const

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

◆ HasID()

bool SamReadGroup::HasID ( ) const

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

◆ HasKeySequence()

bool SamReadGroup::HasKeySequence ( ) const

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

◆ HasLibrary()

bool SamReadGroup::HasLibrary ( ) const

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

◆ HasPlatformUnit()

bool SamReadGroup::HasPlatformUnit ( ) const

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

◆ HasPredictedInsertSize()

bool SamReadGroup::HasPredictedInsertSize ( ) const

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

◆ HasProductionDate()

bool SamReadGroup::HasProductionDate ( ) const

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

◆ HasProgram()

bool SamReadGroup::HasProgram ( ) const

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

◆ HasSample()

bool SamReadGroup::HasSample ( ) const

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

◆ HasSequencingCenter()

bool SamReadGroup::HasSequencingCenter ( ) const

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

◆ HasSequencingTechnology()

bool SamReadGroup::HasSequencingTechnology ( ) const

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

Member Data Documentation

◆ CustomTags

std::vector<CustomHeaderTag> BamTools::SamReadGroup::CustomTags

◆ Description

SamReadGroup::Description

corresponds to @RG DS:<Description>

◆ FlowOrder

SamReadGroup::FlowOrder

corresponds to @RG FO:<FlowOrder>

◆ ID

SamReadGroup::ID

corresponds to @RG ID:<ID>

Required for valid SAM header.

◆ KeySequence

SamReadGroup::KeySequence

corresponds to @RG KS:<KeySequence>

◆ Library

SamReadGroup::Library

corresponds to @RG LB:<Library>

◆ PlatformUnit

SamReadGroup::PlatformUnit

corresponds to @RG PU:<PlatformUnit>

◆ PredictedInsertSize

SamReadGroup::PredictedInsertSize

corresponds to @RG PI:<PredictedInsertSize>

◆ ProductionDate

SamReadGroup::ProductionDate

corresponds to @RG DT:<ProductionDate>

◆ Program

SamReadGroup::Program

corresponds to @RG PG:<Program>

◆ Sample

SamReadGroup::Sample

corresponds to @RG SM:<Sample>

◆ SequencingCenter

SamReadGroup::SequencingCenter

corresponds to @RG CN:<SequencingCenter>

◆ SequencingTechnology

SamReadGroup::SequencingTechnology

corresponds to @RG PL:<SequencingTechnology>

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

Public Member Functions

Public Attributes