NCBI C++ ToolKit
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#include <ncbi_pch.hpp>
#include <sra/readers/sra/wgsread.hpp>
#include <sra/readers/ncbi_traces_path.hpp>
#include <corelib/ncbistr.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/ncbi_param.hpp>
#include <util/line_reader.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 <objects/seqfeat/seqfeat__.hpp>
#include <objects/seqsplit/seqsplit__.hpp>
#include <serial/objistrasnb.hpp>
#include <serial/objostrasnb.hpp>
#include <serial/serial.hpp>
#include <serial/pack_string.hpp>
#include <serial/objhook.hpp>
#include <serial/objectio.hpp>
#include <sra/error_codes.hpp>
#include <sra/readers/sra/kdbread.hpp>
#include <ncbi/ncbi.h>
#include <insdc/insdc.h>
#include <sra/readers/sra/impl/wgs-contig.h>
#include <vdb/vdb-priv.h>
#include <numeric>
Go to the source code of this file.
Go to the SVN repository for this file.
Classes | |
class | CWGSAsnBinData |
struct | CWGSAsnBinData::SFtableInfo |
class | CFtableWriteHook |
class | CDescrWriteHook |
struct | CWGSDb_Impl::SSeq0TableCursor |
struct | CWGSDb_Impl::SSeqTableCursor |
struct | CWGSDb_Impl::SSeq4naTableCursor |
struct | CWGSDb_Impl::SScfTableCursor |
struct | CWGSDb_Impl::SProt0TableCursor |
struct | CWGSDb_Impl::SProtTableCursor |
struct | CWGSDb_Impl::SFeatTableCursor |
struct | CWGSDb_Impl::SGiIdxTableCursor |
struct | CWGSDb_Impl::SProtIdxTableCursor |
struct | CWGSDb_Impl::SAmbiguityInfo |
struct | CWGSDb_Impl::SAmbiguityInfo::S4naBlock |
struct | CWGSDb_Impl::SAmbiguityInfo::S4naReader |
class | SStaticGlobalAmbiguityCacheCallbacks |
struct | SWGSCreateInfo |
struct | CWGSSeqIterator::SAmbiguityAccess |
struct | SWGSFeatChunkInfo |
struct | SWGSFeatChunkInfo::SFeatureSet |
Macros | |
#define | USE_GLOBAL_AMBIGUITY_CACHE |
#define | DEFAULT_AMBIGUITY_CACHE_SIZE "128MB" |
#define | NCBI_USE_ERRCODE_X WGSReader |
#define | PROFILE(var) |
Typedefs | |
typedef limited_resource_map< pair< string, TVDBRowId >, CRef< CWGSDb_Impl::SAmbiguityInfo >, size_t > | TGlobalAmbiguityCache |
Enumerations | |
enum | EChunkType { eChunk_prod , eChunk_data , eChunk_feat , eChunk_qual , kChunkIdStep = 4 } |
enum | EFromFlags { eFromFlags } |
enum | EFromSplitVersion { eFromSplitVersion } |
enum | EDeltaType { eDelta_all , eDelta_split } |
#define DEFAULT_AMBIGUITY_CACHE_SIZE "128MB" |
Definition at line 70 of file wgsread.cpp.
#define NCBI_USE_ERRCODE_X WGSReader |
Definition at line 77 of file wgsread.cpp.
#define PROFILE | ( | var | ) |
Definition at line 306 of file wgsread.cpp.
#define USE_GLOBAL_AMBIGUITY_CACHE |
Definition at line 67 of file wgsread.cpp.
typedef limited_resource_map<pair<string, TVDBRowId>, CRef<CWGSDb_Impl::SAmbiguityInfo>, size_t> TGlobalAmbiguityCache |
Definition at line 2202 of file wgsread.cpp.
enum EChunkType |
Enumerator | |
---|---|
eChunk_prod | |
eChunk_data | |
eChunk_feat | |
eChunk_qual | |
kChunkIdStep |
Definition at line 190 of file wgsread.cpp.
enum EDeltaType |
Enumerator | |
---|---|
eDelta_all | |
eDelta_split |
Definition at line 5110 of file wgsread.cpp.
enum EFromFlags |
Enumerator | |
---|---|
eFromFlags |
Definition at line 3797 of file wgsread.cpp.
enum EFromSplitVersion |
Enumerator | |
---|---|
eFromSplitVersion |
Definition at line 3800 of file wgsread.cpp.
BEGIN_NAMESPACE | ( | objects | ) |
DEFINE_STATIC_FAST_MUTEX | ( | s_GlobalAmbiguityCacheMutex | ) |
END_NAMESPACE | ( | objects | ) |
NCBI_DEFINE_ERR_SUBCODE_X | ( | 19 | ) |
NCBI_PARAM_DECL | ( | bool | , |
WGS | , | ||
CLIP_BY_QUALITY | |||
) |
NCBI_PARAM_DECL | ( | bool | , |
WGS | , | ||
MASTER_DESCR | |||
) |
NCBI_PARAM_DECL | ( | bool | , |
WGS | , | ||
USE_AMBIGUITY_4NA | |||
) |
NCBI_PARAM_DECL | ( | bool | , |
WGS | , | ||
USE_AMBIGUITY_MASK | |||
) |
NCBI_PARAM_DECL | ( | bool | , |
WGS | , | ||
USE_FULL_4NA_BLOCKS | |||
) |
NCBI_PARAM_DECL | ( | bool | , |
WGS | , | ||
USE_GAP_INFO | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
AMBIGUITY_CACHE | |||
) |
NCBI_PARAM_DEF_EX | ( | bool | , |
WGS | , | ||
CLIP_BY_QUALITY | , | ||
true | , | ||
eParam_NoThread | , | ||
CSRA_CLIP_BY_QUALITY | |||
) |
NCBI_PARAM_DEF_EX | ( | bool | , |
WGS | , | ||
USE_AMBIGUITY_4NA | , | ||
true | , | ||
eParam_NoThread | , | ||
WGS_USE_AMBIGUITY_4NA | |||
) |
NCBI_PARAM_DEF_EX | ( | bool | , |
WGS | , | ||
USE_AMBIGUITY_MASK | , | ||
true | , | ||
eParam_NoThread | , | ||
WGS_USE_AMBIGUITY_MASK | |||
) |
NCBI_PARAM_DEF_EX | ( | bool | , |
WGS | , | ||
USE_FULL_4NA_BLOCKS | , | ||
false | , | ||
eParam_NoThread | , | ||
WGS_USE_FULL_4NA_BLOCKS | |||
) |
NCBI_PARAM_DEF_EX | ( | bool | , |
WGS | , | ||
USE_GAP_INFO | , | ||
true | , | ||
eParam_NoThread | , | ||
WGS_USE_GAP_INFO | |||
) |
NCBI_PARAM_DEF_EX | ( | int | , |
WGS | , | ||
DEBUG | , | ||
0 | , | ||
eParam_NoThread | , | ||
WGS_DEBUG | |||
) |
NCBI_PARAM_DEF_EX | ( | string | , |
WGS | , | ||
AMBIGUITY_CACHE | , | ||
"128MB" | , | ||
eParam_NoThread | , | ||
WGS_AMBIGUITY_CACHE | |||
) |
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Definition at line 5636 of file wgsread.cpp.
References GI_CONST, GI_TO, CID2S_Gi_Range_Base::SetCount(), CID2S_Gi_Range_Base::SetStart(), CID2S_Seq_loc_Base::SetWhole_gi(), and CID2S_Seq_loc_Base::SetWhole_gi_range().
Referenced by SWGSFeatChunkInfo::CreateChunkInfo().
Definition at line 3182 of file wgsread.cpp.
References set< Key, Compare >::insert(), and s_GetUserObjectType().
Referenced by CWGSDb_Impl::AddMasterDescr().
Definition at line 1460 of file wgsread.cpp.
References s_ConvertBits_2na_to_4na_1st(), and s_ConvertBits_2na_to_4na_2nd().
Referenced by CWGSDb_Impl::SAmbiguityInfo::Get4na(), and s_Convert_2na_to_4na().
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Definition at line 1488 of file wgsread.cpp.
References s_Convert_2na_to_4na().
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inlinestatic |
Definition at line 1428 of file wgsread.cpp.
References table.
Referenced by s_ConvertBits_2na_to_4na_1st(), and s_ConvertBits_2na_to_4na_2nd().
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inlinestatic |
Definition at line 1443 of file wgsread.cpp.
References s_ConvertBits_2na_to_4na().
Referenced by s_Convert_2na_to_4na().
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inlinestatic |
Definition at line 1452 of file wgsread.cpp.
References s_ConvertBits_2na_to_4na().
Referenced by s_Convert_2na_to_4na().
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Definition at line 1545 of file wgsread.cpp.
Referenced by s_SetAmbiguitiesBlocks().
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Definition at line 163 of file wgsread.cpp.
References NCBI_PARAM_TYPE, and NStr::StringToUInt8_DataSize().
Referenced by SStaticGlobalAmbiguityCacheCallbacks::Create().
Definition at line 103 of file wgsread.cpp.
References NCBI_PARAM_TYPE, and ncbi::grid::netcache::search::s_Value().
Referenced by CWGSSeqIterator::x_Init().
Definition at line 87 of file wgsread.cpp.
References DEBUG, NCBI_PARAM_TYPE, and rapidjson::value.
Referenced by CWGSDb_Impl::SAmbiguityInfo::SAmbiguityInfo(), CWGSDb_Impl::SAmbiguityInfo::x_Calculate4na(), CWGSDb_Impl::SAmbiguityInfo::x_CalculateAmbiguityMask(), and CWGSDb_Impl::SAmbiguityInfo::~SAmbiguityInfo().
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inlinestatic |
Definition at line 4712 of file wgsread.cpp.
References arr, max(), min(), ncbi::grid::netcache::search::fields::size, and v2.
Referenced by CWGSSeqIterator::x_GetQualityAnnot().
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Definition at line 4393 of file wgsread.cpp.
References TAX_ID_FROM, rapidjson::value, and ZERO_TAX_ID.
Referenced by CWGSSeqIterator::GetTaxId(), and CWGSProteinIterator::GetTaxId().
Definition at line 3158 of file wgsread.cpp.
References data, CUser_object_Base::GetData(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), NStr::IntToString(), CObject_id_Base::IsStr(), CSeqdesc_Base::IsUser(), ITERATE, and string.
Referenced by CWGSDb_Impl::AddMasterDescr(), and s_AddUserObjectType().
Definition at line 1604 of file wgsread.cpp.
Referenced by CWGSDb_Impl::SAmbiguityInfo::x_AddAmbiguousBlock().
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inlinestatic |
Definition at line 1503 of file wgsread.cpp.
References offset.
Referenced by s_SetAmbiguitiesPos().
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inlinestatic |
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Definition at line 1641 of file wgsread.cpp.
References blocks, kAmbiguityBlockSize, len, min(), and s_Copy_4na().
Referenced by CWGSDb_Impl::SAmbiguityInfo::Get4na().
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Definition at line 1626 of file wgsread.cpp.
References len, and s_Set_4na().
Referenced by CWGSDb_Impl::SAmbiguityInfo::Get4na().
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Definition at line 1670 of file wgsread.cpp.
References _ASSERT, CWGSSeqIterator::SWGSContigGapInfo::GetDataLength(), CWGSSeqIterator::SWGSContigGapInfo::GetFrom(), CWGSSeqIterator::SWGSContigGapInfo::GetGapLength(), CWGSSeqIterator::SWGSContigGapInfo::IsInGap(), len, s_Set_4na_gap(), and CWGSSeqIterator::SWGSContigGapInfo::SetPos().
Referenced by CWGSDb_Impl::SAmbiguityInfo::Get4na().
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inlinestatic |
Definition at line 4059 of file wgsread.cpp.
References CWGSSeqIterator::eIncludeWithdrawn, CWGSSeqIterator::fIncludeDefault, and CWGSSeqIterator::fIncludeWithdrawn.
Referenced by CWGSSeqIterator::CWGSSeqIterator().
Definition at line 3299 of file wgsread.cpp.
References GI_FROM, and NCBI_THROW_FMT.
Referenced by CWGSSeqIterator::GetGi(), CWGSProteinIterator::GetGi(), CWGSDb_Impl::GetNucGiRange(), CWGSDb_Impl::GetNucGiRanges(), and CWGSDb_Impl::GetProtGiRange().
Definition at line 139 of file wgsread.cpp.
References NCBI_PARAM_TYPE.
Referenced by CWGSDb_Impl::SSeqTableCursor::SSeqTableCursor().
Definition at line 115 of file wgsread.cpp.
References NCBI_PARAM_TYPE.
Referenced by CWGSDb_Impl::SSeqTableCursor::SSeqTableCursor().
Definition at line 151 of file wgsread.cpp.
References NCBI_PARAM_TYPE.
Referenced by CWGSDb_Impl::SAmbiguityInfo::x_Calculate4na(), and CWGSDb_Impl::SAmbiguityInfo::x_CalculateAmbiguityMask().
Definition at line 127 of file wgsread.cpp.
References NCBI_PARAM_TYPE.
Referenced by CWGSDb_Impl::SSeqTableCursor::SSeqTableCursor().
void sx_AddAnnotBytes | ( | CBioseq::TAnnot & | annot_set, |
CTempString | bytes | ||
) |
Definition at line 2698 of file wgsread.cpp.
References CTempString::data(), CTempString::empty(), in(), and CTempString::size().
Referenced by CWGSSeqIterator::GetAnnotSet(), and CWGSProteinIterator::GetAnnotSet().
void sx_AddDescrBytes | ( | CSeq_descr & | descr, |
CTempString | bytes | ||
) |
Definition at line 2673 of file wgsread.cpp.
References CTempString::data(), CTempString::empty(), in(), kSeq_descrFirstByte, CSeq_descr_Base::Set(), CTempString::size(), and tmp.
Referenced by CWGSSeqIterator::GetSeq_descr(), CWGSProteinIterator::GetSeq_descr(), SWGSCreateInfo::x_AddDescr(), and CWGSSeqIterator::x_CreateEntry().
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Definition at line 4978 of file wgsread.cpp.
References CSeq_gap_Base::SetLinkage_evidence().
Referenced by sx_MakeGapLiteral().
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Definition at line 6032 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_CreateEntry(), and CWGSScaffoldIterator::x_CreateEntry().
void sx_AddSplitId | ( | CID2S_Bioseq_Ids::Tdata & | split_ids, |
CSeq_id & | id | ||
) |
Definition at line 2733 of file wgsread.cpp.
References sx_SetSplitId().
Referenced by sx_AddSplitIds().
void sx_AddSplitIds | ( | CID2S_Bioseq_Ids::Tdata & | split_ids, |
const CBioseq::TId & | ids | ||
) |
Definition at line 2741 of file wgsread.cpp.
References ITERATE, and sx_AddSplitId().
Referenced by SWGSCreateInfo::x_CreateProtSet().
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Definition at line 1168 of file wgsread.cpp.
References CVDBValueFor< V >::begin(), and CVDBValue::size().
Referenced by CWGSDb_Impl::SAmbiguityInfo::SAmbiguityInfo().
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inlinestatic |
Definition at line 1378 of file wgsread.cpp.
References i, offset, sx_Get_4na(), and sx_Is2na().
Referenced by CWGSDb_Impl::SAmbiguityInfo::Get2naLengthExact().
Definition at line 1354 of file wgsread.cpp.
References sx_Is2na().
Referenced by sx_HasAmbiguity().
Definition at line 1366 of file wgsread.cpp.
Referenced by CWGSDb_Impl::SAmbiguityInfo::GetBaseType(), and sx_Find_4na_Ambiguity().
int sx_GetStringId | ( | CTempString | str | ) |
Definition at line 2619 of file wgsread.cpp.
References str(), and sx_StringToNonNegativeInt().
Referenced by CWGSDb_Impl::GetGeneralOrPatentSeq_id(), CWGSScaffoldIterator::GetGeneralOrPatentSeq_id(), and sx_SetTag().
Definition at line 1391 of file wgsread.cpp.
References sx_FindAmbiguity().
Referenced by sx_HasAmbiguity(), and CWGSDb_Impl::SAmbiguityInfo::x_AddAmbiguousBlock().
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Definition at line 5914 of file wgsread.cpp.
References count, and compile_time_bits::range().
Referenced by CWGSSeqIterator::x_InitSplit().
Definition at line 1346 of file wgsread.cpp.
References b.
Referenced by CWGSDb_Impl::SAmbiguityInfo::GetBaseType(), sx_Find_4na_Ambiguity(), sx_FindAmbiguity(), and CWGSDb_Impl::SAmbiguityInfo::x_AddAmbiguities().
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Definition at line 4987 of file wgsread.cpp.
References _ASSERT, CInt_fuzz_Base::eLim_unk, CSeq_gap_Base::eLinkage_linked, CSeq_gap_Base::eType_centromere, CSeq_gap_Base::eType_contig, CSeq_gap_Base::eType_heterochromatin, CLinkage_evidence_Base::eType_paired_ends, CSeq_gap_Base::eType_repeat, CSeq_gap_Base::eType_scaffold, CSeq_gap_Base::eType_short_arm, CSeq_gap_Base::eType_telomere, CSeq_gap_Base::eType_unknown, len, literal(), NCBI_WGS_gap_centromere, NCBI_WGS_gap_contig, NCBI_WGS_gap_heterochromatin, NCBI_WGS_gap_known, NCBI_WGS_gap_linkage_evidence_paired_ends, NCBI_WGS_gap_linkage_linked, NCBI_WGS_gap_repeat, NCBI_WGS_gap_scaffold, NCBI_WGS_gap_short_arm, NCBI_WGS_gap_telomere, NCBI_WGS_gap_unknown, NCBI_WGS_gap_unknown_type, CSeq_gap_Base::SetLinkage(), CSeq_gap_Base::SetType(), sx_AddEvidence(), and type.
Referenced by CWGSScaffoldIterator::GetSeq_inst(), and CWGSSeqIterator::x_AddGap().
int sx_NewStringToNonNegativeInt | ( | CTempString | str | ) |
Definition at line 2568 of file wgsread.cpp.
References i, len, CNcbiError::SetErrno(), and str().
Referenced by sx_StringToNonNegativeInt().
bool sx_SetAccession | ( | CSeq_id & | id, |
CTempString | accession | ||
) |
Definition at line 2549 of file wgsread.cpp.
Referenced by CWGSDb_Impl::GetAccSeq_id().
void sx_SetSplitId | ( | CID2S_Bioseq_Ids::C_E & | split_id, |
CSeq_id & | id | ||
) |
Definition at line 2711 of file wgsread.cpp.
References CID2S_Bioseq_Ids_Base::C_E::SetGi(), and CID2S_Bioseq_Ids_Base::C_E::SetSeq_id().
Referenced by SWGSFeatChunkInfo::SWGSFeatChunkInfo(), sx_AddSplitId(), CWGSSeqIterator::x_AddQualityChunkInfo(), CWGSSeqIterator::x_CreateDataChunk(), and CWGSSeqIterator::x_CreateQualityChunk().
void sx_SetSplitId | ( | CID2S_Chunk_Data::TId & | split_id, |
CSeq_id & | id | ||
) |
Definition at line 2722 of file wgsread.cpp.
References CID2S_Chunk_Data_Base::C_Id::SetGi(), and CID2S_Chunk_Data_Base::C_Id::SetSeq_id().
void sx_SetSplitInterval | ( | CID2S_Seq_loc & | split_loc, |
CSeq_id & | id, | ||
TSeqPos | pos, | ||
TSeqPos | end | ||
) |
Definition at line 2750 of file wgsread.cpp.
References CID2S_Gi_Interval_Base::SetGi(), CID2S_Seq_loc_Base::SetGi_interval(), CID2S_Gi_Interval_Base::SetLength(), CID2S_Seq_id_Interval_Base::SetLength(), CID2S_Seq_id_Interval_Base::SetSeq_id(), CID2S_Seq_loc_Base::SetSeq_id_interval(), CID2S_Gi_Interval_Base::SetStart(), and CID2S_Seq_id_Interval_Base::SetStart().
Referenced by CWGSSeqIterator::x_AddQualityChunkInfo(), and CWGSSeqIterator::x_GetSeq_inst().
void sx_SetTag | ( | CDbtag & | tag, |
CTempString | str | ||
) |
Definition at line 2660 of file wgsread.cpp.
References CObject_id_Base::SetId(), CObject_id_Base::SetStr(), str(), sx_GetStringId(), and tag.
Referenced by CWGSDb_Impl::GetGeneralSeq_id().
Definition at line 2539 of file wgsread.cpp.
References dtl::version.
Referenced by CWGSDb_Impl::GetAccSeq_id(), and CWGSDb_Impl::GetMasterSeq_id().
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Definition at line 2563 of file wgsread.cpp.
References str(), and sx_NewStringToNonNegativeInt().
Referenced by sx_GetStringId().
BEGIN_LOCAL_NAMESPACE |
Definition at line 2537 of file wgsread.cpp.
BEGIN_NCBI_NAMESPACE |
Definition at line 75 of file wgsread.cpp.
END_LOCAL_NAMESPACE |
Definition at line 2768 of file wgsread.cpp.
END_NCBI_NAMESPACE |
Definition at line 7928 of file wgsread.cpp.
Definition at line 179 of file wgsread.cpp.
Referenced by CWGSDb_Impl::SAmbiguityInfo::Advance(), CWGSDb_Impl::SAmbiguityInfo::Get2naLengthBlock(), CWGSDb_Impl::SAmbiguityInfo::Get2naLengthExact(), CWGSDb_Impl::SAmbiguityInfo::Get4naLengthBlock(), CWGSDb_Impl::SAmbiguityInfo::Get4naReader(), s_SetAmbiguitiesBlocks(), CWGSDb_Impl::SAmbiguityInfo::x_Calculate4na(), CWGSDb_Impl::SAmbiguityInfo::x_CalculateAmbiguityMask(), and CWGSDb_Impl::SAmbiguityInfo::x_IsValid().
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Definition at line 188 of file wgsread.cpp.
Referenced by SWGSCreateInfo::x_SetFlags(), and SWGSCreateInfo::x_SetSplitVersion().
Definition at line 5101 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), and CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps().
Definition at line 5100 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), and CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps().
Definition at line 203 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_CreateDataChunk(), CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), and CWGSSeqIterator::x_GetSeq_inst().
Definition at line 183 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_InitSplit().
Definition at line 185 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_InitSplit().
Definition at line 184 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_InitSplit().
Definition at line 182 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_InitSplit().
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Definition at line 201 of file wgsread.cpp.
Referenced by SWGSCreateInfo::x_AddFeaturesSplit(), and CWGSSeqIterator::x_CreateFeaturesChunk().
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Definition at line 189 of file wgsread.cpp.
Referenced by SWGSFeatChunkInfo::CreateChunkInfo(), SWGSCreateInfo::x_AddProducts(), CWGSSeqIterator::x_CreateFeaturesChunk(), SWGSCreateInfo::x_CreateProtSet(), and SWGSCreateInfo::x_GetProtSet().
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Definition at line 5097 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), and CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps().
Definition at line 204 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_InitSplit().
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Definition at line 200 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_InitSplit().
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Definition at line 199 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_CreateProductsChunk(), SWGSCreateInfo::x_CreateProtSet(), and CWGSSeqIterator::x_InitSplit().
Definition at line 202 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_AddQualityChunkInfo(), and CWGSSeqIterator::x_CreateQualityChunk().
Definition at line 1335 of file wgsread.cpp.
Referenced by CWGSDb_Impl::SAmbiguityInfo::Get4naLengthExact(), and CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps().
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Definition at line 178 of file wgsread.cpp.
Referenced by CWGSAsnBinData::AddDescr(), sx_AddDescrBytes(), and CDescrWriteHook::WriteClassMember().
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Definition at line 5105 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), and CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps().
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Definition at line 5104 of file wgsread.cpp.
Referenced by CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), and CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps().
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Definition at line 2208 of file wgsread.cpp.
Referenced by CWGSDb_Impl::GetAmbiguityInfo(), and CWGSDb_Impl::PutAmbiguityInfo().