BamTools 2.5.2
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BamTools::SamReadGroup Struct Reference

Represents a SAM read group entry. More...

#include <SamReadGroup.h>

Public Member Functions

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

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
iddesired 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

std::string BamTools::SamReadGroup::Description

corresponds to @RG DS:<Description>

◆ FlowOrder

std::string BamTools::SamReadGroup::FlowOrder

corresponds to @RG FO:<FlowOrder>

◆ ID

std::string BamTools::SamReadGroup::ID

corresponds to @RG ID:<ID>

Required for valid SAM header.

◆ KeySequence

std::string BamTools::SamReadGroup::KeySequence

corresponds to @RG KS:<KeySequence>

◆ Library

std::string BamTools::SamReadGroup::Library

corresponds to @RG LB:<Library>

◆ PlatformUnit

std::string BamTools::SamReadGroup::PlatformUnit

corresponds to @RG PU:<PlatformUnit>

◆ PredictedInsertSize

std::string BamTools::SamReadGroup::PredictedInsertSize

corresponds to @RG PI:<PredictedInsertSize>

◆ ProductionDate

std::string BamTools::SamReadGroup::ProductionDate

corresponds to @RG DT:<ProductionDate>

◆ Program

std::string BamTools::SamReadGroup::Program

corresponds to @RG PG:<Program>

◆ Sample

std::string BamTools::SamReadGroup::Sample

corresponds to @RG SM:<Sample>

◆ SequencingCenter

std::string BamTools::SamReadGroup::SequencingCenter

corresponds to @RG CN:<SequencingCenter>

◆ SequencingTechnology

std::string BamTools::SamReadGroup::SequencingTechnology

corresponds to @RG PL:<SequencingTechnology>


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