CCSRADataLoader::SLoaderParams Struct Reference

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#include <sra/data_loaders/csra/csraloader.hpp>

Collaboration diagram for CCSRADataLoader::SLoaderParams:

Public Types
enum	{   kMinMapQuality_config = -1 , kPileupGraphs_config = -1 , kQualityGraphs_config = -1 , kSpotGroups_config = -1 ,   kSpotReadAlign_config = -1 , kPathInId_config = -1 }

Public Member Functions
	SLoaderParams (void)
string	GetLoaderName (void) const
int	GetEffectiveMinMapQuality (void) const
bool	GetEffectivePileupGraphs (void) const
bool	GetEffectiveQualityGraphs (void) const
int	GetEffectiveSpotGroups (void) const
bool	GetEffectiveSpotReadAlign (void) const

Public Attributes
string	m_DirPath
vector< string >	m_CSRAFiles
AutoPtr< IIdMapper >	m_IdMapper
string	m_AnnotName
int	m_MinMapQuality
int	m_PileupGraphs
int	m_QualityGraphs
int	m_SpotGroups
int	m_SpotReadAlign
int	m_PathInId

Detailed Description

Definition at line 54 of file csraloader.hpp.

Member Enumeration Documentation

anonymous enum

anonymous enum

Enumerator
kMinMapQuality_config
kPileupGraphs_config
kQualityGraphs_config
kSpotGroups_config
kSpotReadAlign_config
kPathInId_config

Definition at line 56 of file csraloader.hpp.

Constructor & Destructor Documentation

SLoaderParams()

CCSRADataLoader::SLoaderParams::SLoaderParams ( void  )

inline

Definition at line 66 of file csraloader.hpp.

Member Function Documentation

GetEffectiveMinMapQuality()

int CCSRADataLoader::SLoaderParams::GetEffectiveMinMapQuality

(

void

)

const

Definition at line 180 of file csraloader.cpp.

References CCSRADataLoader::GetMinMapQualityParamDefault(), kMinMapQuality_config, and m_MinMapQuality.

Referenced by CCSRADataLoader_Impl::CCSRADataLoader_Impl().

GetEffectivePileupGraphs()

bool CCSRADataLoader::SLoaderParams::GetEffectivePileupGraphs

(

void

)

const

Definition at line 187 of file csraloader.cpp.

References CCSRADataLoader::GetPileupGraphsParamDefault().

Referenced by CCSRADataLoader_Impl::CCSRADataLoader_Impl().

GetEffectiveQualityGraphs()

bool CCSRADataLoader::SLoaderParams::GetEffectiveQualityGraphs

(

void

)

const

Definition at line 194 of file csraloader.cpp.

References CCSRADataLoader::GetQualityGraphsParamDefault().

Referenced by CCSRADataLoader_Impl::CCSRADataLoader_Impl().

GetEffectiveSpotGroups()

int CCSRADataLoader::SLoaderParams::GetEffectiveSpotGroups

(

void

)

const

Definition at line 208 of file csraloader.cpp.

References CCSRADataLoader::GetSpotGroupsParamDefault().

Referenced by CCSRADataLoader_Impl::CCSRADataLoader_Impl().

GetEffectiveSpotReadAlign()

bool CCSRADataLoader::SLoaderParams::GetEffectiveSpotReadAlign

(

void

)

const

Definition at line 201 of file csraloader.cpp.

References CCSRADataLoader::GetSpotReadAlignParamDefault().

Referenced by CCSRADataLoader_Impl::CCSRADataLoader_Impl().

GetLoaderName()

string CCSRADataLoader::SLoaderParams::GetLoaderName

(

void

)

const

Definition at line 215 of file csraloader.cpp.

References ITERATE, and str().

Referenced by CCSRADataLoader::GetLoaderNameFromArgs().

Member Data Documentation

m_AnnotName

string CCSRADataLoader::SLoaderParams::m_AnnotName

Definition at line 79 of file csraloader.hpp.

Referenced by CCSRADataLoader_Impl::CCSRADataLoader_Impl().

m_CSRAFiles

vector<string> CCSRADataLoader::SLoaderParams::m_CSRAFiles

Definition at line 77 of file csraloader.hpp.

Referenced by CCSRADataLoader_Impl::CCSRADataLoader_Impl(), CCSRADataLoader::GetLoaderNameFromArgs(), and CCSRADataLoader::RegisterInObjectManager().

m_DirPath

string CCSRADataLoader::SLoaderParams::m_DirPath

Definition at line 76 of file csraloader.hpp.

Referenced by CCSRADataLoader::CCSRADataLoader(), CCSRADataLoader_Impl::CCSRADataLoader_Impl(), CCSRADataLoader::GetLoaderNameFromArgs(), and CCSRADataLoader::RegisterInObjectManager().

m_IdMapper

AutoPtr<IIdMapper> CCSRADataLoader::SLoaderParams::m_IdMapper

Definition at line 78 of file csraloader.hpp.

m_MinMapQuality

int CCSRADataLoader::SLoaderParams::m_MinMapQuality

Definition at line 80 of file csraloader.hpp.

Referenced by GetEffectiveMinMapQuality().

m_PathInId

int CCSRADataLoader::SLoaderParams::m_PathInId

Definition at line 85 of file csraloader.hpp.

Referenced by CCSRADataLoader_Impl::CCSRADataLoader_Impl().

m_PileupGraphs

int CCSRADataLoader::SLoaderParams::m_PileupGraphs

Definition at line 81 of file csraloader.hpp.

m_QualityGraphs

int CCSRADataLoader::SLoaderParams::m_QualityGraphs

Definition at line 82 of file csraloader.hpp.

m_SpotGroups

int CCSRADataLoader::SLoaderParams::m_SpotGroups

Definition at line 83 of file csraloader.hpp.

m_SpotReadAlign

int CCSRADataLoader::SLoaderParams::m_SpotReadAlign

Definition at line 84 of file csraloader.hpp.

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

• include/sra/data_loaders/csra/csraloader.hpp
• src/sra/data_loaders/csra/csraloader.cpp