BamTools  2.4.0
Public Member Functions | Public Attributes | List of all members
BamTools::SamReadGroup Struct Reference

Represents a SAM read group entry. More...

#include <SamReadGroup.h>

Public Member Functions

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

default constructor

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

constructs read group with id

Parameters
iddesired 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

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