#include <ncbi_pch.hpp>
#include <sra/data_loaders/snp/impl/id2snp_impl.hpp>
#include <objects/id2/id2processor_interface.hpp>
#include <sra/data_loaders/snp/id2snp_params.h>
#include <sra/readers/sra/snpread.hpp>
#include <sra/error_codes.hpp>
#include <corelib/reader_writer.hpp>
#include <corelib/rwstream.hpp>
#include <util/compress/zlib.hpp>
#include <serial/objostrasnb.hpp>
#include <serial/serial.hpp>
#include <objects/id2/id2__.hpp>
#include <objects/seqsplit/seqsplit__.hpp>
#include <objects/general/general__.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <objects/seqres/seqres__.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqsplit/ID2S_Split_Info.hpp>
#include <objects/seqsplit/ID2S_Chunk.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/annot_selector.hpp>

Include dependency graph for id2snp_impl.cpp:

Go to the SVN repository for this file.

Classes
class	COSSWriter

Macros
#define	NCBI_USE_ERRCODE_X ID2SNPProcessor

#define	TRACE_PROCESSING

#define	DEFAULT_VDB_CACHE_SIZE 10

#define	DEFAULT_INDEX_UPDATE_TIME 600

#define	DEFAULT_COMPRESS_DATA CID2SNPContext::eCompressData_some

#define	START_TRACE() do { if(s_DebugLevel()>0)sw.Restart(); } while(0)

#define	TRACE_X(t, l, m)

Enumerations
enum	EResolveMaster { eResolveMaster_never , eResolveMaster_without_gi , eResolveMaster_always , eResolveMaster_never , eResolveMaster_without_gi , eResolveMaster_always }

enum	EDebugLevel { eTraceError = 1 , eTraceOpen = 2 , eTraceConn = 4 , eTraceASN = 5 , eTraceASNData = 8 , eDebug_none = 0 , eDebug_error = 1 , eDebug_open = 2 , eDebug_request = 5 , eDebug_replies = 6 , eDebug_resolve = 7 , eDebug_data = 8 , eDebug_all = 9 }

Functions
	NCBI_DEFINE_ERR_SUBCODE_X (24)

	BEGIN_NAMESPACE (objects)

	NCBI_PARAM_DECL (bool, ID2SNP, ENABLE)

	NCBI_PARAM_DEF_EX (bool, ID2SNP, ENABLE, true, eParam_NoThread, ID2SNP_ENABLE)

	NCBI_PARAM_DECL (int, ID2SNP, DEBUG)

	NCBI_PARAM_DEF_EX (int, ID2SNP, DEBUG, eDebug_error, eParam_NoThread, ID2SNP_DEBUG)

	NCBI_PARAM_DECL (bool, ID2SNP, FILTER_ALL)

	NCBI_PARAM_DEF_EX (bool, ID2SNP, FILTER_ALL, true, eParam_NoThread, ID2SNP_FILTER_ALL)

static bool	s_Enabled (void)

static int	s_DebugLevel (void)

static bool	s_DebugEnabled (EDebugLevel level)

static bool	s_FilterAll (void)

template<class Cont >
Cont::value_type::TObjectType &	sx_AddNew (Cont &cont)

void	sx_SetZoomLevel (CSeq_annot &annot, int zoom_level)

bool	IsValidNAIndex (size_t na_index)

bool	IsValidNAVersion (size_t na_version)

bool	IsValidSeqIndex (size_t seq_index)

bool	IsValidFilterIndex (size_t filter_index)

string	GetNAAccession (const SSNPDbTrackInfo &track)

string	FormatTrack (const SSNPDbTrackInfo &track)

SSNPDbTrackInfo	ParseTrack (CTempString acc_filter)

CNcbiOstream &	operator<< (CNcbiOstream &out, const CID2SNPProcessor_Impl::SSNPEntryInfo &seq)

size_t	sx_GetSize (const CID2_Reply_Data &data)

template<class Values >
bool	sx_HasNonZero (const Values &values, TSeqPos index, TSeqPos count)

template<class TValues >
void	sx_AddBits2 (vector< char > &bits, TSeqPos bit_values, TSeqPos pos_index, const TValues &values)

static void	sx_AddBits (vector< char > &bits, TSeqPos kChunkSize, const CSeq_graph &graph)

	END_NAMESPACE (objects)

Variables
	BEGIN_NCBI_NAMESPACE

static const EResolveMaster	kResolveMaster = eResolveMaster_never

const int	kSNPSatBase = 2000

const int	kNAIndexDigits = 9

const int	kNAIndexMin = 1

const int	kNAIndexMax = 999999999

const int	kNAVersionDigitsMin = 1

const int	kNAVersionDigitsMax = 2

const int	kNALengthMin = 2 + kNAIndexDigits + 1 + kNAVersionDigitsMin

const int	kNALengthMax = 2 + kNAIndexDigits + 1 + kNAVersionDigitsMax

const int	kNAVersionMin = 1

const int	kNAVersionMax = 99

const int	kSeqIndexCount = 1000000

const int	kFilterIndexCount = 2000

const int	kFilterIndexMaxLength = 4

static const int	kTSEId = 1

static const int	kChunkIdFeat = 0

static const int	kChunkIdGraph = 1

static const int	kChunkIdMul = 2

static const TSeqPos	kFeatChunkSize = 1000000

static const TSeqPos	kGraphChunkSize = 10000000

	BEGIN_LOCAL_NAMESPACE

static CStopWatch	sw

	END_LOCAL_NAMESPACE

	END_NCBI_NAMESPACE

Macro Definition Documentation

◆ DEFAULT_COMPRESS_DATA

#define DEFAULT_COMPRESS_DATA CID2SNPContext::eCompressData_some

Definition at line 79 of file id2snp_impl.cpp.

◆ DEFAULT_INDEX_UPDATE_TIME

#define DEFAULT_INDEX_UPDATE_TIME 600

Definition at line 78 of file id2snp_impl.cpp.

◆ DEFAULT_VDB_CACHE_SIZE

#define DEFAULT_VDB_CACHE_SIZE 10

Definition at line 77 of file id2snp_impl.cpp.

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X ID2SNPProcessor

Definition at line 61 of file id2snp_impl.cpp.

◆ START_TRACE

#define START_TRACE ( ) do { if(s_DebugLevel()>0)sw.Restart(); } while(0)

Definition at line 279 of file id2snp_impl.cpp.

◆ TRACE_PROCESSING

#define TRACE_PROCESSING

Definition at line 67 of file id2snp_impl.cpp.

◆ TRACE_X

#define TRACE_X	(	t,
		l,
		m
	)

Value:

    do {                                                                \
        if ( s_DebugEnabled(l) ) {                                      \
            LOG_POST_X(t, Info<<sw.Elapsed()<<": ID2SNP: "<<m);         \
        }                                                               \
    } while(0)

Definition at line 286 of file id2snp_impl.cpp.

Enumeration Type Documentation

◆ EDebugLevel

enum EDebugLevel

Enumerator
eTraceError
eTraceOpen
eTraceConn
eTraceASN
eTraceASNData
eDebug_none
eDebug_error
eDebug_open
eDebug_request
eDebug_replies
eDebug_resolve
eDebug_data
eDebug_all