#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objects/general/general__.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seq/seq__.hpp>
#include <objects/seqres/seqres__.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objmgr/impl/tse_loadlock.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/data_loader_factory.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <sra/data_loaders/csra/csraloader.hpp>
#include <sra/data_loaders/csra/impl/csraloader_impl.hpp>

Include dependency graph for csraloader.cpp:

Go to the SVN repository for this file.

Classes
class	CLoaderFilter

class	CRevoker

class	CCSRA_DataLoaderCF

Functions
	NCBI_PARAM_DECL (string, CSRA, ACCESSIONS)

	NCBI_PARAM_DEF (string, CSRA, ACCESSIONS, "")

	NCBI_PARAM_DECL (bool, CSRA_LOADER, PILEUP_GRAPHS)

	NCBI_PARAM_DEF_EX (bool, CSRA_LOADER, PILEUP_GRAPHS, true, eParam_NoThread, CSRA_LOADER_PILEUP_GRAPHS)

	NCBI_PARAM_DECL (bool, CSRA_LOADER, QUALITY_GRAPHS)

	NCBI_PARAM_DEF_EX (bool, CSRA_LOADER, QUALITY_GRAPHS, false, eParam_NoThread, CSRA_LOADER_QUALITY_GRAPHS)

	NCBI_PARAM_DECL (int, CSRA_LOADER, MIN_MAP_QUALITY)

	NCBI_PARAM_DEF_EX (int, CSRA_LOADER, MIN_MAP_QUALITY, 0, eParam_NoThread, CSRA_LOADER_MIN_MAP_QUALITY)

	NCBI_PARAM_DECL (int, CSRA_LOADER, MAX_SEPARATE_SPOT_GROUPS)

	NCBI_PARAM_DEF_EX (int, CSRA_LOADER, MAX_SEPARATE_SPOT_GROUPS, 0, eParam_NoThread, CSRA_LOADER_MAX_SEPARATE_SPOT_GROUPS)

	NCBI_PARAM_DECL (bool, CSRA_LOADER, SPOT_READ_ALIGN)

	NCBI_PARAM_DEF (bool, CSRA_LOADER, SPOT_READ_ALIGN, false)

	USING_SCOPE (objects)

void	DataLoaders_Register_CSRA (void)

void	NCBI_EntryPoint_DataLoader_CSRA (CPluginManager< CDataLoader >::TDriverInfoList &info_list, CPluginManager< CDataLoader >::EEntryPointRequest method)

void	NCBI_EntryPoint_xloader_csra (CPluginManager< objects::CDataLoader >::TDriverInfoList &info_list, CPluginManager< objects::CDataLoader >::EEntryPointRequest method)

Variables
	BEGIN_LOCAL_NAMESPACE

static CSafeStatic< CRevoker >	s_Revoker (CSafeStaticLifeSpan(CSafeStaticLifeSpan::eLifeLevel_AppMain, CSafeStaticLifeSpan::eLifeSpan_Long))

	END_LOCAL_NAMESPACE

const char	kDataLoader_CSRA_DriverName [] = "csra"

Function Documentation

◆ DataLoaders_Register_CSRA()

void DataLoaders_Register_CSRA ( void )

Definition at line 507 of file csraloader.cpp.

References NCBI_EntryPoint_DataLoader_CSRA().

◆ NCBI_EntryPoint_DataLoader_CSRA()

void NCBI_EntryPoint_DataLoader_CSRA	(	CPluginManager< CDataLoader >::TDriverInfoList &	info_list,
		CPluginManager< CDataLoader >::EEntryPointRequest	method
	)

Definition at line 545 of file csraloader.cpp.

References CHostEntryPointImpl< TClassFactory >::NCBI_EntryPointImpl().

Referenced by DataLoaders_Register_CSRA(), and NCBI_EntryPoint_xloader_csra().

◆ NCBI_EntryPoint_xloader_csra()

void NCBI_EntryPoint_xloader_csra	(	CPluginManager< objects::CDataLoader >::TDriverInfoList &	info_list,
		CPluginManager< objects::CDataLoader >::EEntryPointRequest	method
	)

Definition at line 553 of file csraloader.cpp.

References NCBI_EntryPoint_DataLoader_CSRA().

◆ NCBI_PARAM_DECL() [1/6]

NCBI_PARAM_DECL	(	bool	,
		CSRA_LOADER	,
		PILEUP_GRAPHS
	)

◆ NCBI_PARAM_DECL() [2/6]

NCBI_PARAM_DECL	(	bool	,
		CSRA_LOADER	,
		QUALITY_GRAPHS
	)

◆ NCBI_PARAM_DECL() [3/6]

NCBI_PARAM_DECL	(	bool	,
		CSRA_LOADER	,
		SPOT_READ_ALIGN
	)

◆ NCBI_PARAM_DECL() [4/6]

NCBI_PARAM_DECL	(	int	,
		CSRA_LOADER	,
		MAX_SEPARATE_SPOT_GROUPS
	)

◆ NCBI_PARAM_DECL() [5/6]

NCBI_PARAM_DECL	(	int	,
		CSRA_LOADER	,
		MIN_MAP_QUALITY
	)

◆ NCBI_PARAM_DECL() [6/6]

NCBI_PARAM_DECL	(	string	,
		CSRA	,
		ACCESSIONS
	)

◆ NCBI_PARAM_DEF() [1/2]

NCBI_PARAM_DEF	(	bool	,
		CSRA_LOADER	,
		SPOT_READ_ALIGN	,
		false
	)

◆ NCBI_PARAM_DEF() [2/2]

NCBI_PARAM_DEF	(	string	,
		CSRA	,
		ACCESSIONS	,
		""
	)

◆ NCBI_PARAM_DEF_EX() [1/4]

NCBI_PARAM_DEF_EX	(	bool	,
		CSRA_LOADER	,
		PILEUP_GRAPHS	,
		true	,
		eParam_NoThread	,
		CSRA_LOADER_PILEUP_GRAPHS
	)

◆ NCBI_PARAM_DEF_EX() [2/4]

NCBI_PARAM_DEF_EX	(	bool	,
		CSRA_LOADER	,
		QUALITY_GRAPHS	,
		false	,
		eParam_NoThread	,
		CSRA_LOADER_QUALITY_GRAPHS
	)

◆ NCBI_PARAM_DEF_EX() [3/4]

NCBI_PARAM_DEF_EX	(	int	,
		CSRA_LOADER	,
		MAX_SEPARATE_SPOT_GROUPS	,
		0	,
		eParam_NoThread	,
		CSRA_LOADER_MAX_SEPARATE_SPOT_GROUPS
	)

◆ NCBI_PARAM_DEF_EX() [4/4]

NCBI_PARAM_DEF_EX	(	int	,
		CSRA_LOADER	,
		MIN_MAP_QUALITY	,
		0	,
		eParam_NoThread	,
		CSRA_LOADER_MIN_MAP_QUALITY
	)

◆ USING_SCOPE()

USING_SCOPE ( objects )

Variable Documentation

◆ BEGIN_LOCAL_NAMESPACE

BEGIN_LOCAL_NAMESPACE

Definition at line 56 of file csraloader.cpp.

◆ END_LOCAL_NAMESPACE

END_LOCAL_NAMESPACE

Definition at line 77 of file csraloader.cpp.

◆ kDataLoader_CSRA_DriverName

const char kDataLoader_CSRA_DriverName[] = "csra"

Definition at line 513 of file csraloader.cpp.

◆ s_Revoker

CSafeStatic<CRevoker> s_Revoker(CSafeStaticLifeSpan( CSafeStaticLifeSpan::eLifeLevel_AppMain, CSafeStaticLifeSpan::eLifeSpan_Long)) ( CSafeStaticLifeSpan( CSafeStaticLifeSpan::eLifeLevel_AppMain, CSafeStaticLifeSpan::eLifeSpan_Long) )

static

Classes

Functions

Variables