NCBI C++ ToolKit
Classes | Macros | Enumerations | Functions | Variables
csraloader_impl.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objects/general/general__.hpp>
#include <objects/seqloc/seqloc__.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/impl/tse_split_info.hpp>
#include <objmgr/data_loader_factory.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <serial/objistr.hpp>
#include <serial/serial.hpp>
#include <sra/error_codes.hpp>
#include <sra/readers/ncbi_traces_path.hpp>
#include <sra/data_loaders/csra/csraloader.hpp>
#include <sra/data_loaders/csra/impl/csraloader_impl.hpp>
#include <util/sequtil/sequtil_manip.hpp>
#include <algorithm>
#include <cmath>
+ Include dependency graph for csraloader_impl.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes

struct  SBaseStat
 
struct  SBaseStats
 
struct  SChunkAnnots
 

Macros

#define NCBI_USE_ERRCODE_X   cSRALoader
 
#define SPOT_GROUP_SEPARATOR   ": "
 
#define PILEUP_NAME_SUFFIX   "pileup graphs"
 

Enumerations

enum  EBaseStat {
  kStat_A = 0 , kStat_C = 1 , kStat_G = 2 , kStat_T = 3 ,
  kStat_Insert = 4 , kStat_Match = 5 , kNumStat = 6
}
 

Functions

 NCBI_DEFINE_ERR_SUBCODE_X (16)
 
 NCBI_PARAM_DECL (int, CSRA_LOADER, DEBUG)
 
 NCBI_PARAM_DEF_EX (int, CSRA_LOADER, DEBUG, 0, eParam_NoThread, CSRA_LOADER_DEBUG)
 
static int GetDebugLevel (void)
 
 NCBI_PARAM_DECL (size_t, CSRA_LOADER, GC_SIZE)
 
 NCBI_PARAM_DEF_EX (size_t, CSRA_LOADER, GC_SIZE, 100, eParam_NoThread, CSRA_LOADER_GC_SIZE)
 
static size_t GetGCSize (void)
 
 NCBI_PARAM_DECL (unsigned, CSRA_LOADER, RETRY_COUNT)
 
 NCBI_PARAM_DEF (unsigned, CSRA_LOADER, RETRY_COUNT, 3)
 
static unsigned GetRetryCountParam (void)
 

Variables

static const int kTSEId = 1
 
static const int kMainChunkId = CTSE_Chunk_Info::kDelayedMain_ChunkId
 
static const bool kUseFullAlignCounts = true
 
static const bool kEstimateAlignCounts = true
 
static const bool kOmitEmptyPileup = true
 
static const unsigned kAlignChunkSize = 1000
 
static const unsigned kGraphChunkSize = 10000
 
static const unsigned kAlignEmptyPages = 16
 
static const unsigned kGraphEmptyPages = 4
 
static const unsigned kChunkGraphMul = 8
 
static const unsigned kChunkSeqDataMul = 8
 
static const unsigned kReadsPerBlob = 1
 
static const unsigned kMaxReadId = 999
 
static const Uint8 kMaxSpotId = NCBI_CONST_UINT8(999999999999999999)
 
static const char kBlobPrefixAnnot [] = "annot|"
 
static const char kBlobPrefixRefSeq [] = "refseq|"
 
static const char kBlobPrefixReads [] = "reads|"
 
static const char kBlobPrefixReadsAlign [] = "align|"
 
static const char kRefIdPrefixGeneral [] = "gnl|"
 
static const char kRefIdPrefixId [] = "id|"
 
static const char kFileEnd [] = "|||"
 
static const Uint4 k_align_bytes = 300
 
static const double k_read_byte_seconds = 7.5e-9
 
static const double k_make_graph_seconds = 20e-9
 
static const double k_make_align_seconds = 80e-9
 
 BEGIN_LOCAL_NAMESPACE
 
 END_LOCAL_NAMESPACE
 

Macro Definition Documentation

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   cSRALoader

Definition at line 63 of file csraloader_impl.cpp.

◆ PILEUP_NAME_SUFFIX

#define PILEUP_NAME_SUFFIX   "pileup graphs"

Definition at line 95 of file csraloader_impl.cpp.

◆ SPOT_GROUP_SEPARATOR

#define SPOT_GROUP_SEPARATOR   ": "

Definition at line 94 of file csraloader_impl.cpp.

Enumeration Type Documentation

◆ EBaseStat

enum EBaseStat
Enumerator
kStat_A 
kStat_C 
kStat_G 
kStat_T 
kStat_Insert 
kStat_Match 
kNumStat 

Definition at line 1984 of file csraloader_impl.cpp.

Function Documentation

◆ GetDebugLevel()

static int GetDebugLevel ( void  )
static

◆ GetGCSize()

static size_t GetGCSize ( void  )
static

◆ GetRetryCountParam()

static unsigned GetRetryCountParam ( void  )
static

Definition at line 123 of file csraloader_impl.cpp.

References NCBI_PARAM_TYPE, and rapidjson::value.

◆ NCBI_DEFINE_ERR_SUBCODE_X()

NCBI_DEFINE_ERR_SUBCODE_X ( 16  )

◆ NCBI_PARAM_DECL() [1/3]

NCBI_PARAM_DECL ( int  ,
CSRA_LOADER  ,
DEBUG   
)

◆ NCBI_PARAM_DECL() [2/3]

NCBI_PARAM_DECL ( size_t  ,
CSRA_LOADER  ,
GC_SIZE   
)

◆ NCBI_PARAM_DECL() [3/3]

NCBI_PARAM_DECL ( unsigned  ,
CSRA_LOADER  ,
RETRY_COUNT   
)

◆ NCBI_PARAM_DEF()

NCBI_PARAM_DEF ( unsigned  ,
CSRA_LOADER  ,
RETRY_COUNT  ,
 
)

◆ NCBI_PARAM_DEF_EX() [1/2]

NCBI_PARAM_DEF_EX ( int  ,
CSRA_LOADER  ,
DEBUG  ,
,
eParam_NoThread  ,
CSRA_LOADER_DEBUG   
)

◆ NCBI_PARAM_DEF_EX() [2/2]

NCBI_PARAM_DEF_EX ( size_t  ,
CSRA_LOADER  ,
GC_SIZE  ,
100  ,
eParam_NoThread  ,
CSRA_LOADER_GC_SIZE   
)

Variable Documentation

◆ BEGIN_LOCAL_NAMESPACE

BEGIN_LOCAL_NAMESPACE

Definition at line 1982 of file csraloader_impl.cpp.

◆ END_LOCAL_NAMESPACE

END_LOCAL_NAMESPACE

Definition at line 2190 of file csraloader_impl.cpp.

◆ k_align_bytes

const Uint4 k_align_bytes = 300
static

Definition at line 1763 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::LoadAnnotMainChunk().

◆ k_make_align_seconds

const double k_make_align_seconds = 80e-9
static

Definition at line 1766 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::LoadAnnotMainChunk().

◆ k_make_graph_seconds

const double k_make_graph_seconds = 20e-9
static

Definition at line 1765 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::LoadAnnotMainChunk().

◆ k_read_byte_seconds

const double k_read_byte_seconds = 7.5e-9
static

Definition at line 1764 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::LoadAnnotMainChunk().

◆ kAlignChunkSize

const unsigned kAlignChunkSize = 1000
static

Definition at line 80 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::x_LoadRangesStat().

◆ kAlignEmptyPages

const unsigned kAlignEmptyPages = 16
static

Definition at line 82 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::x_LoadRangesStat().

◆ kBlobPrefixAnnot

const char kBlobPrefixAnnot[] = "annot|"
static

Definition at line 337 of file csraloader_impl.cpp.

Referenced by CCSRABlobId::FromString(), and CCSRABlobId::ToString().

◆ kBlobPrefixReads

const char kBlobPrefixReads[] = "reads|"
static

Definition at line 339 of file csraloader_impl.cpp.

Referenced by CCSRABlobId::FromString(), and CCSRABlobId::ToString().

◆ kBlobPrefixReadsAlign

const char kBlobPrefixReadsAlign[] = "align|"
static

Definition at line 340 of file csraloader_impl.cpp.

Referenced by CCSRABlobId::FromString(), and CCSRABlobId::ToString().

◆ kBlobPrefixRefSeq

const char kBlobPrefixRefSeq[] = "refseq|"
static

Definition at line 338 of file csraloader_impl.cpp.

Referenced by CCSRABlobId::FromString(), and CCSRABlobId::ToString().

◆ kChunkGraphMul

const unsigned kChunkGraphMul = 8
static

Definition at line 84 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::x_LoadRangesStat().

◆ kChunkSeqDataMul

const unsigned kChunkSeqDataMul = 8
static

◆ kEstimateAlignCounts

const bool kEstimateAlignCounts = true
static

Definition at line 76 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::x_LoadRangesStat().

◆ kFileEnd

const char kFileEnd[] = "|||"
static

Definition at line 343 of file csraloader_impl.cpp.

Referenced by CCSRABlobId::FromString(), and CCSRABlobId::ToString().

◆ kGraphChunkSize

const unsigned kGraphChunkSize = 10000
static

◆ kGraphEmptyPages

const unsigned kGraphEmptyPages = 4
static

Definition at line 83 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::x_LoadRangesStat().

◆ kMainChunkId

◆ kMaxReadId

const unsigned kMaxReadId = 999
static

Definition at line 91 of file csraloader_impl.cpp.

Referenced by CCSRABlobId::ParseReadId().

◆ kMaxSpotId

const Uint8 kMaxSpotId = NCBI_CONST_UINT8(999999999999999999)
static

Definition at line 92 of file csraloader_impl.cpp.

Referenced by CCSRABlobId::ParseReadId().

◆ kOmitEmptyPileup

const bool kOmitEmptyPileup = true
static

Definition at line 77 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::LoadAnnotPileupChunk().

◆ kReadsPerBlob

const unsigned kReadsPerBlob = 1
static

◆ kRefIdPrefixGeneral

const char kRefIdPrefixGeneral[] = "gnl|"
static

Definition at line 341 of file csraloader_impl.cpp.

Referenced by CCSRABlobId::FromString(), and CCSRABlobId::ToString().

◆ kRefIdPrefixId

const char kRefIdPrefixId[] = "id|"
static

Definition at line 342 of file csraloader_impl.cpp.

Referenced by CCSRABlobId::FromString(), and CCSRABlobId::ToString().

◆ kTSEId

const int kTSEId = 1
static

◆ kUseFullAlignCounts

const bool kUseFullAlignCounts = true
static

Definition at line 75 of file csraloader_impl.cpp.

Referenced by CCSRARefSeqInfo::x_LoadRangesStat().

Modified on Sun Apr 21 03:43:47 2024 by modify_doxy.py rev. 669887