NCBI C++ ToolKit
Classes | Macros | Functions | Variables
csraread.cpp File Reference
#include <ncbi_pch.hpp>
#include <sra/readers/sra/csraread.hpp>
#include <corelib/ncbistr.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/ncbi_param.hpp>
#include <objects/general/general__.hpp>
#include <objects/seq/seq__.hpp>
#include <objects/seqset/seqset__.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <objects/seqalign/seqalign__.hpp>
#include <objects/seqres/seqres__.hpp>
#include <objtools/readers/iidmapper.hpp>
#include <sra/error_codes.hpp>
#include <sra/readers/sra/kdbread.hpp>
#include <klib/rc.h>
#include <insdc/sra.h>
#include <vdb/vdb-priv.h>
#include <sstream>
#include <algorithm>
+ Include dependency graph for csraread.cpp:

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Classes

struct  CCSraDb_Impl::SRefTableCursor
 
struct  CCSraDb_Impl::SAlnTableCursor
 
struct  CCSraDb_Impl::SSeqTableCursor
 

Macros

#define NCBI_USE_ERRCODE_X   cSRAReader
 
#define RC_NO_MORE_ALIGNMENTS   RC(rcApp, rcQuery, rcSearching, rcRow, rcNotFound)
 

Functions

 NCBI_DEFINE_ERR_SUBCODE_X (2)
 
 BEGIN_NAMESPACE (objects)
 
 NCBI_PARAM_DECL (bool, CSRA, EXPLICIT_MATE_INFO)
 
 NCBI_PARAM_DEF_EX (bool, CSRA, EXPLICIT_MATE_INFO, false, eParam_NoThread, CSRA_EXPLICIT_MATE_INFO)
 
 NCBI_PARAM_DECL (bool, CSRA, CIGAR_IN_ALIGN_EXT)
 
 NCBI_PARAM_DEF_EX (bool, CSRA, CIGAR_IN_ALIGN_EXT, true, eParam_NoThread, CSRA_CIGAR_IN_ALIGN_EXT)
 
 NCBI_PARAM_DECL (bool, CSRA, INCLUDE_TECHNICAL_READS)
 
 NCBI_PARAM_DEF_EX (bool, CSRA, INCLUDE_TECHNICAL_READS, false, eParam_NoThread, CSRA_INCLUDE_TECHNICAL_READS)
 
 NCBI_PARAM_DECL (bool, CSRA, CLIP_BY_QUALITY)
 
 NCBI_PARAM_DEF_EX (bool, CSRA, CLIP_BY_QUALITY, true, eParam_NoThread, CSRA_CLIP_BY_QUALITY)
 
 NCBI_PARAM_DECL (bool, CSRA, PATH_IN_ID)
 
 NCBI_PARAM_DEF_EX (bool, CSRA, PATH_IN_ID, true, eParam_NoThread, CSRA_PATH_IN_ID)
 
 NCBI_PARAM_DECL (bool, CSRA, READ_FILTER_IN_ALIGN_EXT)
 
 NCBI_PARAM_DEF (bool, CSRA, READ_FILTER_IN_ALIGN_EXT, true)
 
static bool s_GetExplicitMateInfoParam (void)
 
static bool s_GetCigarInAlignExt (void)
 
static bool s_GetIncludeTechnicalReads (void)
 
static bool s_GetClipByQuality (void)
 
static bool s_GetPathInId (void)
 
static bool s_GetReadFilterInAlignExt (void)
 
 END_NAMESPACE (objects)
 

Variables

 BEGIN_NCBI_NAMESPACE
 
 END_NCBI_NAMESPACE
 

Macro Definition Documentation

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   cSRAReader

Definition at line 57 of file csraread.cpp.

◆ RC_NO_MORE_ALIGNMENTS

#define RC_NO_MORE_ALIGNMENTS   RC(rcApp, rcQuery, rcSearching, rcRow, rcNotFound)

Definition at line 134 of file csraread.cpp.

Function Documentation

◆ BEGIN_NAMESPACE()

BEGIN_NAMESPACE ( objects  )

◆ END_NAMESPACE()

END_NAMESPACE ( objects  )

◆ NCBI_DEFINE_ERR_SUBCODE_X()

NCBI_DEFINE_ERR_SUBCODE_X ( )

◆ NCBI_PARAM_DECL() [1/6]

NCBI_PARAM_DECL ( bool  ,
CSRA  ,
CIGAR_IN_ALIGN_EXT   
)

◆ NCBI_PARAM_DECL() [2/6]

NCBI_PARAM_DECL ( bool  ,
CSRA  ,
CLIP_BY_QUALITY   
)

◆ NCBI_PARAM_DECL() [3/6]

NCBI_PARAM_DECL ( bool  ,
CSRA  ,
EXPLICIT_MATE_INFO   
)

◆ NCBI_PARAM_DECL() [4/6]

NCBI_PARAM_DECL ( bool  ,
CSRA  ,
INCLUDE_TECHNICAL_READS   
)

◆ NCBI_PARAM_DECL() [5/6]

NCBI_PARAM_DECL ( bool  ,
CSRA  ,
PATH_IN_ID   
)

◆ NCBI_PARAM_DECL() [6/6]

NCBI_PARAM_DECL ( bool  ,
CSRA  ,
READ_FILTER_IN_ALIGN_EXT   
)

◆ NCBI_PARAM_DEF()

NCBI_PARAM_DEF ( bool  ,
CSRA  ,
READ_FILTER_IN_ALIGN_EXT  ,
true   
)

◆ NCBI_PARAM_DEF_EX() [1/5]

NCBI_PARAM_DEF_EX ( bool  ,
CSRA  ,
CIGAR_IN_ALIGN_EXT  ,
true  ,
eParam_NoThread  ,
CSRA_CIGAR_IN_ALIGN_EXT   
)

◆ NCBI_PARAM_DEF_EX() [2/5]

NCBI_PARAM_DEF_EX ( bool  ,
CSRA  ,
CLIP_BY_QUALITY  ,
true  ,
eParam_NoThread  ,
CSRA_CLIP_BY_QUALITY   
)

◆ NCBI_PARAM_DEF_EX() [3/5]

NCBI_PARAM_DEF_EX ( bool  ,
CSRA  ,
EXPLICIT_MATE_INFO  ,
false  ,
eParam_NoThread  ,
CSRA_EXPLICIT_MATE_INFO   
)

◆ NCBI_PARAM_DEF_EX() [4/5]

NCBI_PARAM_DEF_EX ( bool  ,
CSRA  ,
INCLUDE_TECHNICAL_READS  ,
false  ,
eParam_NoThread  ,
CSRA_INCLUDE_TECHNICAL_READS   
)

◆ NCBI_PARAM_DEF_EX() [5/5]

NCBI_PARAM_DEF_EX ( bool  ,
CSRA  ,
PATH_IN_ID  ,
true  ,
eParam_NoThread  ,
CSRA_PATH_IN_ID   
)

◆ s_GetCigarInAlignExt()

static bool s_GetCigarInAlignExt ( void  )
static

◆ s_GetClipByQuality()

static bool s_GetClipByQuality ( void  )
static

◆ s_GetExplicitMateInfoParam()

static bool s_GetExplicitMateInfoParam ( void  )
static

◆ s_GetIncludeTechnicalReads()

static bool s_GetIncludeTechnicalReads ( void  )
static

◆ s_GetPathInId()

static bool s_GetPathInId ( void  )
static

Definition at line 120 of file csraread.cpp.

References NCBI_PARAM_TYPE, and ncbi::grid::netcache::search::s_Value().

Referenced by CCSraDb::MakeSraIdPart().

◆ s_GetReadFilterInAlignExt()

static bool s_GetReadFilterInAlignExt ( void  )
static

Variable Documentation

◆ BEGIN_NCBI_NAMESPACE

BEGIN_NCBI_NAMESPACE

Definition at line 55 of file csraread.cpp.

◆ END_NCBI_NAMESPACE

END_NCBI_NAMESPACE

Definition at line 2373 of file csraread.cpp.

Modified on Mon Feb 26 04:00:58 2024 by modify_doxy.py rev. 669887