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:

Go to the source code of this file.

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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

(

2

)

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

Definition at line 99 of file csraread.cpp.

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

Referenced by CCSraAlignIterator::GetMatchAlign().

s_GetClipByQuality()

static bool s_GetClipByQuality ( void  )

static

Definition at line 113 of file csraread.cpp.

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

Referenced by CCSraShortReadIterator::x_Init().

s_GetExplicitMateInfoParam()

static bool s_GetExplicitMateInfoParam ( void  )

static

Definition at line 92 of file csraread.cpp.

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

Referenced by CCSraAlignIterator::GetMatchAlign(), and CCSraAlignIterator::x_GetEmptyMatchAnnot().

s_GetIncludeTechnicalReads()

static bool s_GetIncludeTechnicalReads ( void  )

static

Definition at line 106 of file csraread.cpp.

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

Referenced by CCSraShortReadIterator::x_Init().

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

Definition at line 127 of file csraread.cpp.

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

Referenced by CCSraAlignIterator::GetMatchAlign().

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.