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NCBI C++ ToolKit: src/sra/data_loaders/bam/bamloader_impl.cpp File Reference

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  NCBI_DEFINE_ERR_SUBCODE_X (30)     NCBI_PARAM_DECL (int, BAM_LOADER, DEBUG)     NCBI_PARAM_DEF_EX (int, BAM_LOADER, DEBUG, 0, eParam_NoThread, BAM_LOADER_DEBUG)   static int  GetDebugLevel (void)     NCBI_PARAM_DECL (string, BAM_LOADER, MAPPER_FILE)     NCBI_PARAM_DEF_EX (string, BAM_LOADER, MAPPER_FILE, "", eParam_NoThread, BAM_LOADER_MAPPER_FILE)   static string  GetMapperFileName (void)     NCBI_PARAM_DECL (string, BAM_LOADER, MAPPER_CONTEXT)     NCBI_PARAM_DEF_EX (string, BAM_LOADER, MAPPER_CONTEXT, "", eParam_NoThread, BAM_LOADER_MAPPER_CONTEXT)   static string  GetMapperContext (void)     NCBI_PARAM_DECL (bool, BAM_LOADER, PILEUP_GRAPHS)     NCBI_PARAM_DEF (bool, BAM_LOADER, PILEUP_GRAPHS, true)   static bool  GetPileupGraphsParam (void)     NCBI_PARAM_DECL (bool, BAM_LOADER, SKIP_EMPTY_PILEUP_GRAPHS)     NCBI_PARAM_DEF (bool, BAM_LOADER, SKIP_EMPTY_PILEUP_GRAPHS, true)   static bool  GetSkipEmptyPileupGraphsParam (void)     NCBI_PARAM_DECL (int, BAM_LOADER, GAP_TO_INTRON_THRESHOLD)     NCBI_PARAM_DEF (int, BAM_LOADER, GAP_TO_INTRON_THRESHOLD, -1)   static TSeqPos  s_GetGapToIntronThreshold (void)     NCBI_PARAM_DECL (bool, BAM_LOADER, INTRON_GRAPH)     NCBI_PARAM_DEF (bool, BAM_LOADER, INTRON_GRAPH, false)   static bool  s_GetMakeIntronGraph (void)     NCBI_PARAM_DECL (bool, BAM_LOADER, ESTIMATED_COVERAGE_GRAPH)     NCBI_PARAM_DEF (bool, BAM_LOADER, ESTIMATED_COVERAGE_GRAPH, true)   static bool  GetEstimatedCoverageGraphParam (void)     NCBI_PARAM_DECL (bool, BAM_LOADER, PREFER_RAW_INDEX_OVER_COVERAGE_GRAPH)     NCBI_PARAM_DEF_EX (bool, BAM_LOADER, PREFER_RAW_INDEX_OVER_COVERAGE_GRAPH, false, eParam_NoThread, BAM_LOADER_PREFER_RAW_INDEX_OVER_COVERAGE_GRAPH)   static bool  GetPreferRawIndexOverCoverageGraphParam (void)     NCBI_PARAM_DECL (bool, BAM_LOADER, PREOPEN)     NCBI_PARAM_DEF (bool, BAM_LOADER, PREOPEN, false)     NCBI_PARAM_DECL (string, BAM_LOADER, INCLUDE_ALIGN_TAGS)     NCBI_PARAM_DEF_EX (string, BAM_LOADER, INCLUDE_ALIGN_TAGS, "", eParam_NoThread, "")   static string  GetIncludeAlignTagsParam (void)     NCBI_PARAM_DECL (int, BAM_LOADER, MIN_MAP_QUALITY)     NCBI_PARAM_DEF (int, BAM_LOADER, MIN_MAP_QUALITY, 1)   static bool  GetMinMapQualityParam (void)     NCBI_PARAM_DECL (Uint8, BAM_LOADER, SPLIT_BIN_DATA_SIZE)     NCBI_PARAM_DEF_EX (Uint8, BAM_LOADER, SPLIT_BIN_DATA_SIZE, kDefaultSplitBinDataSize, eParam_NoThread, BAM_LOADER_SPLIT_BIN_DATA_SIZE)   static Uint8  GetSplitBinDataSize (void)     NCBI_PARAM_DECL (TSeqPos, BAM_LOADER, SPLIT_BIN_MIN_LENGTH)     NCBI_PARAM_DEF_EX (TSeqPos, BAM_LOADER, SPLIT_BIN_MIN_LENGTH, kDefaultSplitBinMinLength, eParam_NoThread, BAM_LOADER_SPLIT_BIN_MIN_LENGTH)   static TSeqPos  GetSplitBinMinLength (void)   template<class Call > std::invoke_result< Call >::type  CallWithRetry (Call &&call, const char *name, int retry_count=0)   static const CUser_field &  GetIdField (const CUser_field &field, int id)   static TSeqPos  s_GetEnd (const vector< TSeqPos > &over_ends, TSeqPos i, TSeqPos bin_size)   static Uint1  sx_GetBaseRaw (CTempString read_raw, TSeqPos pos)   ◆ NCBI_USE_ERRCODE_X ◆ PILEUP_NAME_SUFFIX ◆ RETRY ◆ SEPARATE_PILEUP_READS ◆ USE_NEW_PILEUP_COLLECTOR ◆ EChunkIdType Enumerator eChunk_pileup_graph  eChunk_align  eChunk_align1  eChunk_align2  eChunk_short_seq_pileup  eChunk_short_seq  eChunk_short_seq1  eChunk_short_seq2  kChunkIdMul 

Definition at line 121 of file bamloader_impl.cpp.

◆ CallWithRetry()

template<class Call >

std::invoke_result<Call>::type CallWithRetry ( Call &&  call, const char *  name, int  retry_count = 0  )

Definition at line 343 of file bamloader_impl.cpp.

References kDefaultRetryCount, LOG_POST, SleepMilliSec(), t, Warning(), and CException::what().

Referenced by CWGSDataLoader_Impl::GetAccVer(), CWGSDataLoader_Impl::GetBlobById(), CWGSDataLoader_Impl::GetBlobId(), CWGSDataLoader_Impl::GetChunk(), CWGSDataLoader_Impl::GetGi(), CWGSDataLoader_Impl::GetIds(), CWGSDataLoader_Impl::GetRecords(), CWGSDataLoader_Impl::GetSequenceHash(), CWGSDataLoader_Impl::GetSequenceLength(), CWGSDataLoader_Impl::GetSequenceType(), and CWGSDataLoader_Impl::GetTaxId().

◆ GetDebugLevel()

Definition at line 139 of file bamloader_impl.cpp.

References DEBUG, NCBI_PARAM_TYPE, and rapidjson::value.

Referenced by CBamFileInfo::AddRefSeq(), CBamFileInfo::CBamFileInfo(), CBamRefSeqInfo::CreateChunks(), CBamRefSeqInfo::LoadAlignChunk(), CBamRefSeqInfo::LoadMainSplit(), CBamRefSeqInfo::LoadPileupChunk(), CBamRefSeqInfo::LoadSeqChunk(), CBamRefSeqInfo::x_AddSeqChunk(), CBamRefSeqInfo::x_LoadRangesCov(), CBamRefSeqInfo::x_LoadRangesEstimated(), CBamRefSeqInfo::x_LoadRangesScan(), CBamRefSeqInfo::x_LoadRangesStat(), and CBAMDataLoader_Impl::~CBAMDataLoader_Impl().

◆ GetEstimatedCoverageGraphParam() static bool GetEstimatedCoverageGraphParam ( void  ) inlinestatic ◆ GetIdField() ◆ GetIncludeAlignTagsParam() ◆ GetMapperContext() ◆ GetMapperFileName() ◆ GetMinMapQualityParam() ◆ GetPileupGraphsParam() ◆ GetPreferRawIndexOverCoverageGraphParam() static bool GetPreferRawIndexOverCoverageGraphParam ( void  ) static ◆ GetSkipEmptyPileupGraphsParam() static bool GetSkipEmptyPileupGraphsParam ( void  ) inlinestatic ◆ GetSplitBinDataSize() ◆ GetSplitBinMinLength() ◆ NCBI_DEFINE_ERR_SUBCODE_X() NCBI_DEFINE_ERR_SUBCODE_X ( 30  ) ◆ NCBI_PARAM_DECL() [1/14] NCBI_PARAM_DECL ( bool  , BAM_LOADER  , ESTIMATED_COVERAGE_GRAPH    ) ◆ NCBI_PARAM_DECL() [2/14] NCBI_PARAM_DECL ( bool  , BAM_LOADER  , INTRON_GRAPH    ) ◆ NCBI_PARAM_DECL() [3/14] NCBI_PARAM_DECL ( bool  , BAM_LOADER  , PILEUP_GRAPHS    ) ◆ NCBI_PARAM_DECL() [4/14] NCBI_PARAM_DECL ( bool  , BAM_LOADER  , PREFER_RAW_INDEX_OVER_COVERAGE_GRAPH    ) ◆ NCBI_PARAM_DECL() [5/14] NCBI_PARAM_DECL ( bool  , BAM_LOADER  , PREOPEN    ) ◆ NCBI_PARAM_DECL() [6/14] NCBI_PARAM_DECL ( bool  , BAM_LOADER  , SKIP_EMPTY_PILEUP_GRAPHS    ) ◆ NCBI_PARAM_DECL() [7/14] NCBI_PARAM_DECL ( int  , BAM_LOADER  , DEBUG    ) ◆ NCBI_PARAM_DECL() [8/14] NCBI_PARAM_DECL ( int  , BAM_LOADER  , GAP_TO_INTRON_THRESHOLD    ) ◆ NCBI_PARAM_DECL() [9/14] NCBI_PARAM_DECL ( int  , BAM_LOADER  , MIN_MAP_QUALITY    ) ◆ NCBI_PARAM_DECL() [10/14] NCBI_PARAM_DECL ( string  , BAM_LOADER  , INCLUDE_ALIGN_TAGS    ) ◆ NCBI_PARAM_DECL() [11/14] NCBI_PARAM_DECL ( string  , BAM_LOADER  , MAPPER_CONTEXT    ) ◆ NCBI_PARAM_DECL() [12/14] NCBI_PARAM_DECL ( string  , BAM_LOADER  , MAPPER_FILE    ) ◆ NCBI_PARAM_DECL() [13/14] NCBI_PARAM_DECL ( TSeqPos  , BAM_LOADER  , SPLIT_BIN_MIN_LENGTH    ) ◆ NCBI_PARAM_DECL() [14/14] NCBI_PARAM_DECL ( Uint8  , BAM_LOADER  , SPLIT_BIN_DATA_SIZE    ) ◆ NCBI_PARAM_DEF() [1/7] NCBI_PARAM_DEF ( bool  , BAM_LOADER  , ESTIMATED_COVERAGE_GRAPH  , true    ) ◆ NCBI_PARAM_DEF() [2/7] NCBI_PARAM_DEF ( bool  , BAM_LOADER  , INTRON_GRAPH  , false    ) ◆ NCBI_PARAM_DEF() [3/7] NCBI_PARAM_DEF ( bool  , BAM_LOADER  , PILEUP_GRAPHS  , true    ) ◆ NCBI_PARAM_DEF() [4/7] NCBI_PARAM_DEF ( bool  , BAM_LOADER  , PREOPEN  , false    ) ◆ NCBI_PARAM_DEF() [5/7] NCBI_PARAM_DEF ( bool  , BAM_LOADER  , SKIP_EMPTY_PILEUP_GRAPHS  , true    ) ◆ NCBI_PARAM_DEF() [6/7] NCBI_PARAM_DEF ( int  , BAM_LOADER  , GAP_TO_INTRON_THRESHOLD  , -  1  ) ◆ NCBI_PARAM_DEF() [7/7] NCBI_PARAM_DEF ( int  , BAM_LOADER  , MIN_MAP_QUALITY  , 1    ) ◆ NCBI_PARAM_DEF_EX() [1/7] NCBI_PARAM_DEF_EX ( bool  , BAM_LOADER  , PREFER_RAW_INDEX_OVER_COVERAGE_GRAPH  , false  , eParam_NoThread  , BAM_LOADER_PREFER_RAW_INDEX_OVER_COVERAGE_GRAPH    ) ◆ NCBI_PARAM_DEF_EX() [2/7] ◆ NCBI_PARAM_DEF_EX() [3/7] ◆ NCBI_PARAM_DEF_EX() [4/7] NCBI_PARAM_DEF_EX ( string  , BAM_LOADER  , MAPPER_CONTEXT  , ""  , eParam_NoThread  , BAM_LOADER_MAPPER_CONTEXT    ) ◆ NCBI_PARAM_DEF_EX() [5/7] ◆ NCBI_PARAM_DEF_EX() [6/7] ◆ NCBI_PARAM_DEF_EX() [7/7] ◆ s_GetEnd() ◆ s_GetGapToIntronThreshold() ◆ s_GetMakeIntronGraph() ◆ sx_GetBaseRaw() ◆ BEGIN_LOCAL_NAMESPACE ◆ END_LOCAL_NAMESPACE ◆ k_make_align_seconds const double k_make_align_seconds = 250e-9 static ◆ k_make_graph_seconds const double k_make_graph_seconds = 7.5e-9 static ◆ k_make_read_seconds const double k_make_read_seconds = 80e-9 static ◆ kChunkDataSize const size_t kChunkDataSize = 250000 static ◆ kChunkSize ◆ kDefaultSplitBinDataSize ◆ kDefaultSplitBinMinLength ◆ kMainChunkId ◆ kSingleAlignBytes ◆ kSplitLevelsChunkDataSize ◆ kTSEId ◆ s_AttachTime ◆ s_CreateTime

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