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NCBI C++ ToolKit: src/sra/data_loaders/csra/csraloader_impl.cpp File Reference

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) ◆ NCBI_USE_ERRCODE_X ◆ PILEUP_NAME_SUFFIX ◆ SPOT_GROUP_SEPARATOR ◆ EBaseStat Enumerator kStat_A kStat_C kStat_G kStat_T kStat_Insert kStat_Match kNumStat

Definition at line 1984 of file csraloader_impl.cpp.

◆ GetDebugLevel()

Definition at line 101 of file csraloader_impl.cpp.

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

Referenced by CCSRAFileInfo::AddRefSeq(), CCSRARefSeqInfo::LoadAnnotAlignChunk(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CCSRARefSeqInfo::LoadRanges(), CCSRAFileInfo::LoadReadsBlob(), CCSRARefSeqInfo::LoadRefSeqChunk(), CCSRAFileInfo::x_Initialize(), and CCSRARefSeqInfo::x_LoadRangesStat().

◆ GetGCSize() static size_t GetGCSize ( void ) static ◆ GetRetryCountParam() static unsigned GetRetryCountParam ( void ) static ◆ 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 , 3 ) ◆ NCBI_PARAM_DEF_EX() [1/2] ◆ NCBI_PARAM_DEF_EX() [2/2] NCBI_PARAM_DEF_EX ( size_t , CSRA_LOADER , GC_SIZE , 100 , eParam_NoThread , CSRA_LOADER_GC_SIZE ) ◆ BEGIN_LOCAL_NAMESPACE ◆ END_LOCAL_NAMESPACE ◆ k_align_bytes ◆ k_make_align_seconds const double k_make_align_seconds = 80e-9 static ◆ k_make_graph_seconds const double k_make_graph_seconds = 20e-9 static ◆ k_read_byte_seconds const double k_read_byte_seconds = 7.5e-9 static ◆ kAlignChunkSize const unsigned kAlignChunkSize = 1000 static ◆ kAlignEmptyPages const unsigned kAlignEmptyPages = 16 static ◆ kBlobPrefixAnnot const char kBlobPrefixAnnot[] = "annot|" static ◆ kBlobPrefixReads const char kBlobPrefixReads[] = "reads|" static ◆ kBlobPrefixReadsAlign const char kBlobPrefixReadsAlign[] = "align|" static ◆ kBlobPrefixRefSeq const char kBlobPrefixRefSeq[] = "refseq|" static ◆ kChunkGraphMul const unsigned kChunkGraphMul = 8 static ◆ kChunkSeqDataMul const unsigned kChunkSeqDataMul = 8 static ◆ kEstimateAlignCounts ◆ kFileEnd const char kFileEnd[] = "|||" static ◆ kGraphChunkSize const unsigned kGraphChunkSize = 10000 static ◆ kGraphEmptyPages const unsigned kGraphEmptyPages = 4 static ◆ kMainChunkId ◆ kMaxReadId const unsigned kMaxReadId = 999 static ◆ kMaxSpotId ◆ kOmitEmptyPileup ◆ kReadsPerBlob const unsigned kReadsPerBlob = 1 static ◆ kRefIdPrefixGeneral const char kRefIdPrefixGeneral[] = "gnl|" static ◆ kRefIdPrefixId const char kRefIdPrefixId[] = "id|" static ◆ kTSEId ◆ kUseFullAlignCounts

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