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NCBI C++ ToolKit: include/sra/readers/sra/wgsread.hpp Source File

*m_MainObject;

m_IdPrefixWithVersion;

NormalizePathOrAccession(

path_or_acc,

eRowType_scaffold =

,

eRowType_protein =

fAllowRowType_contig = 1<<0,

fAllowRowType_scaffold = 1<<1,

fAllowRowType_protein = 1<<2

pair<TVDBRowId, ERowType> ParseRowType(

acc,

TAllowRowType allow);

ParseRowType(acc, fAllowRowType_contig).first;

ParseRowType(acc, fAllowRowType_scaffold).first;

ParseRowType(acc, fAllowRowType_protein).first;

m_IdRowDigits;

IsTSA(

)

;

fGnlId_NoWGSVersion = 1<<0,

fGnlId_NoWGSId = 1<<1,

TGnlIdFlags gnl_id_flags = fGnlId_Default)

;

TGnlIdFlags gnl_id_flags = fGnlId_Default)

;

GetMasterGi(

)

;

m_IsSetMasterDescr;

m_MasterDescr;

ResetMasterDescr(

);

SetMasterDescr(

& descr,

filter);

LoadMasterDescr(

filter);

pair<TGi, TGi> GetNucGiRange(

);

pair<TGi, TGi> GetProtGiRange(

);

pair<TVDBRowId, bool> GetGiRowId(

gi);

GetContigNameRowId(

& name);

GetScaffoldNameRowId(

& name);

GetProteinNameRowId(

& name);

GetProductNameRowId(

& name);

GetAcc(

)

;

( m_IdLength !=

.m_IdLength ) {

m_IdLength <

.m_IdLength;

m_AccPrefix <

.m_AccPrefix;

m_IdLength ==

.m_IdLength &&

m_AccPrefix ==

.m_AccPrefix;

!(*

==

);

HasStandardFeatLocIdType();

m_ProjectGBState;

!m_ReplacedBy.empty();

m_HasCommonTaxId;

m_CommonTaxId;

SAmbiguityInfo;

( !m_ScfTableIsOpened.load(memory_order_acquire) ) {

( !m_ProtTableIsOpened.load(memory_order_acquire) ) {

( !m_FeatTableIsOpened.load(memory_order_acquire) ) {

( !m_GiIdxTableIsOpened.load(memory_order_acquire) ) {

( !m_ProtIdxTableIsOpened.load(memory_order_acquire) ) {

m_ProtIdxTable;

( !m_ProtAccIndexIsOpened.load(memory_order_acquire) ) {

m_ProtAccIndex;

( !m_ContigNameIndexIsOpened.load(memory_order_acquire) ) {

OpenContigNameIndex();

m_ContigNameIndex;

( !m_ScaffoldNameIndexIsOpened.load(memory_order_acquire) ) {

OpenScaffoldNameIndex();

m_ScaffoldNameIndex;

( !m_ProteinNameIndexIsOpened.load(memory_order_acquire) ) {

OpenProteinNameIndex();

m_ProteinNameIndex;

( !m_ProductNameIndexIsOpened.load(memory_order_acquire) ) {

OpenProductNameIndex();

m_ProductNameIndex;

SSeq0TableCursor& cur,

SScfTableCursor& cur,

SProt0TableCursor& cur,

atomic<bool>& table_is_opened,

atomic<Int1>& index_is_opened,

* index_name,

* backup_index_name = 0);

OpenScfTable(

);

OpenProtTable(

);

OpenFeatTable(

);

OpenGiIdxTable(

);

OpenProtIdxTable(

);

OpenProtAccIndex(

);

OpenContigNameIndex(

);

OpenScaffoldNameIndex(

);

OpenProteinNameIndex(

);

OpenProductNameIndex(

);

x_InitIdParams(

);

x_LoadMasterDescr(

filter);

x_SortGiRanges(TGiRanges& ranges);

fExcludeProjectGBState = 1 << 8,

fIncludeDefault = fIncludeLive | fIncludeUnverified

TIncludeFlags

,

TIncludeFlags

,

TIncludeFlags

,

TIncludeFlags

,

m_FirstGoodId;

GetFirstBadRowId() - 1;

GetFirstBadRowId() - GetCurrentRowId();

GetFirstBadRowId() - GetFirstGoodRowId();

HasGi(

)

;

GetLatestAccVersion(

)

;

GetAccVersionCount(

)

;

HasAccVersion(

)

;

GetLatestAccVersion() + m_AccVersion.m_Offset;

SelectAccVersion(

);

HasTitle(

)

;

GetClipQualityLeft(

)

;

GetClipQualityLength(

)

;

GetClipQualityLeft() + GetClipQualityLength() - 1;

HasClippingInfo(

)

;

m_ClipByQuality && HasClippingInfo();

!m_ClipByQuality && HasClippingInfo();

(clip_type == eDefaultClip?

clip_type == eClipByQuality);

GetRawSeqLength(

)

;

GetSeqOffset(EClipType clip_type = eDefaultClip)

;

HasTaxId(

)

;

HasSeqHash(

)

;

GetSeqHash(

)

;

( gaps_linkage ) {

(

, GetToOpen()-pos);

!*

?

:

(

, GetFrom()-pos);

} TWGSContigGapInfo;

HasGapInfo(

)

;

GetGapInfo(TWGSContigGapInfo& gap_info)

;

vector<Uint1> GetAmbiguityBytes()

;

HasSeqDescrBytes(

)

;

HasNucProtDescrBytes(

)

;

HasSeq_descr(TFlags

= fDefaultFlags)

;

HasAnnotSet(

)

;

GetAnnotSet(

& annot_set, TFlags

= fDefaultFlags)

;

CanHaveQualityGraph(

)

;

HasQualityGraph(

)

;

GetQualityVec(vector<INSDC_quality_phred>& quality_vec)

;

GetQualityAnnot(

& annot_set,

TFlags

= fDefaultFlags)

;

GetQualityAnnotName(

)

;

HasPublicComment(

)

;

IsCircular(

)

;

GetSplitInfoAndVersion(TFlags

= fDefaultFlags)

;

GetSplitInfoDataAndVersion(TFlags

= fDefaultFlags)

;

TFlags

= fDefaultFlags)

;

TFlags

= fDefaultFlags)

;

fInst_MakeData = 1<<0,

fInst_MakeGaps = 1<<1,

fInst_Minimal = 1<<3

x_Select(

& wgs_db,

TIncludeFlags include_flags,

x_Select(

& wgs_db,

TIncludeFlags include_flags,

x_Select(

& wgs_db,

TIncludeFlags include_flags,

x_Select(

& wgs_db,

TIncludeFlags include_flags,

x_Init(

& wgs_db,

TIncludeFlags include_flags,

m_Db.GetNCObject();

x_Settle(

);

x_Excluded(

)

;

x_ReportInvalid(

* method)

;

x_ReportInvalid(method);

SVersionSelector x_GetAccVersionSelector(

)

;

index)

;

index)

;

index)

;

index)

;

x_GetQualityArraySize(

)

;

x_GetQualityAnnot(TAnnotSet& annot_set,

TInstSegmentFlags

)

;

x_GetSegmentsWithRecoveredGaps(

& segments,

m_FirstGoodId;

m_FirstBadId;

GetFirstBadRowId() - GetCurrentRowId();

GetFirstBadRowId() - GetFirstGoodRowId();

GetAccVersion(

)

;

HasSeq_descr(TFlags

= fDefaultFlags)

;

IsCircular(

)

;

x_Init(

& wgs_db);

m_Db.GetNCObject();

x_ReportInvalid(

* method)

;

x_ReportInvalid(method);

m_CurrSeqType;

x_Init(

& wgs_db, ESeqType seq_type);

m_Db.GetNCObject();

x_Settle(

);

x_Excluded(

);

m_FirstGoodId;

m_FirstBadId;

GetFirstBadRowId() - GetCurrentRowId();

GetFirstBadRowId() - GetFirstGoodRowId();

HasGi(

)

;

GetAccVersion(

)

;

HasTaxId(

)

;

HasSeqHash(

)

;

GetSeqHash(

)

;

GetProductFeatCount(

)

;

GetProductFeatRowId(

index)

;

GetBestProductFeatRowId(

)

;

GetProductFeatRowId(

)

;

GetReplacedByRowId(

)

;

GetReplacesRowId(

)

;

HasRefAcc(

)

;

HasPublicComment(

)

;

HasSeq_descr(TFlags

= fDefaultFlags)

;

HasTitle(

)

;

HasAnnotSet(

)

;

GetAnnotSet(

& annot_set, TFlags

= fDefaultFlags)

;

x_Init(

& wgs_db);

x_Cur()

;

m_Db.GetNCObject();

x_ReportInvalid(

* method)

;

x_ReportInvalid(method);

m_FirstGoodId;

m_FirstBadId;

GetFirstBadRowId() - GetCurrentRowId();

GetFirstBadRowId() - GetFirstGoodRowId();

GetProductRowId(

)

;

GetLocStart(

)

;

GetLocLength(

)

;

m_Db.GetNCObject();

x_Init(

& wgs_db);

x_ReportInvalid(

* method)

;

x_ReportInvalid(method);

CRef< CSerialObject > m_MainObject

const CSerialObject & GetMainObject(void) const

CObjectOStreamAsnBinary –.

@Seq_descr.hpp User-defined methods of the data storage class.

namespace ncbi::objects::

Base class for all serializable objects.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

CVDBTableIndex m_ProteinNameIndex

DECLARE_SAFE_FLAGS_TYPE(EGnlIdFlags, TGnlIdFlags)

const string & GetIdPrefixWithVersion(void) const

CVDBObjectCache< SProtIdxTableCursor > m_ProtIdx

map< SProtAccInfo, TIdRange > TProtAccRanges

CVDBObjectCache< SProt0TableCursor > m_Prot0

atomic< bool > m_GiIdxTableIsOpened

NCBI_gb_state m_ProjectGBState

const CVDBTableIndex & ContigNameIndex(void)

const CVDBTableIndex & ProductNameIndex(void)

pair< TGi, TGi > GetNucGiRange(void)

bool LoadMasterDescr(int filter)

const CVDBTable & GiIdxTable(void)

COpenRange< TIntId > TGiRange

static TVDBRowId ParseContigRow(CTempString acc)

DECLARE_SAFE_FLAGS_TYPE(EAllowRowType, TAllowRowType)

atomic< bool > m_FeatTableIsOpened

CVDBTableIndex m_ScaffoldNameIndex

atomic< bool > m_ScfTableIsOpened

string m_IdPrefixDbWithVersion

bool HasCommonTaxId(void) const

const string & GetReplacedBy() const

TAmbiguityCache m_AmbiguityCache

TVDBRowId GetNucGiRowId(TGi gi)

const CVDBTableIndex & ScaffoldNameIndex(void)

void SetMasterDescr(const TMasterDescr &descr, int filter)

TTaxId GetCommonTaxId(void) const

pair< TVDBRowId, bool > GetGiRowId(TGi gi)

const CVDBTable & ScfTable(void)

const CRef< CSeq_id > & GetPatentId(void) const

CVDBTableIndex m_ProtAccIndex

TMasterDescr m_MasterDescr

CRef< CSeq_entry > m_MasterEntry

TVDBRowId GetScaffoldNameRowId(const string &name)

TVDBRowId GetContigNameRowId(const string &name)

Uint4 GetIdRowDigits(void) const

CVDBObjectCache< SSeqTableCursor > m_Seq

COpenRange< Uint4 > TIdRange

atomic< Int1 > m_ScaffoldNameIndexIsOpened

atomic< bool > m_ProtIdxTableIsOpened

NCBI_gb_state GetProjectGBState() const

TVDBRowId GetProductNameRowId(const string &name)

TVDBRowId GetProtAccRowId(const string &acc, int version=-1)

CVDBObjectCache< SProtTableCursor > m_Prot

TVDBRowId GetProteinNameRowId(const string &name)

atomic< Int1 > m_ProductNameIndexIsOpened

vector< TGiRange > TGiRanges

list< CRef< CSeqdesc > > TMasterDescr

CSimpleBufferT< char > TMasterDescrBytes

TProtAccRanges GetProtAccRanges(void)

CFastMutex m_AmbiguityCacheMutex

const CVDBTableIndex & ProteinNameIndex(void)

TGiRanges GetProtGiRanges(void)

TVDBRowId ParseRow(CTempString acc, bool *is_scaffold) const

TGiRanges GetNucGiRanges(void)

limited_resource_map< TVDBRowId, CRef< SAmbiguityInfo >, size_t > TAmbiguityCache

CVDBObjectCache< SScfTableCursor > m_Scf

static TVDBRowId ParseScaffoldRow(CTempString acc)

bool IsSetMasterDescr(void) const

CVDBTableIndex m_ContigNameIndex

CVDBObjectCache< SSeq0TableCursor > m_Seq0

CRef< CSeq_id > m_PatentId

atomic< bool > m_ProtTableIsOpened

const CVDBTable & FeatTable(void)

const CVDBTableIndex & ProtAccIndex(void)

const CVDBTable & SeqTable(void)

pair< TGi, TGi > GetProtGiRange(void)

CSeq_inst::TMol m_ContigMolType

string m_IdPrefixWithVersion

atomic< Int1 > m_ProtAccIndexIsOpened

CSeq_id::E_Choice m_SeqIdType

const TMasterDescr & GetMasterDescr(void) const

atomic< EFeatLocIdType > m_FeatLocIdType

CVDBTableIndex m_ProductNameIndex

static TVDBRowId ParseProteinRow(CTempString acc)

CVDBObjectCache< SFeatTableCursor > m_Feat

const CVDBTable & ProtIdxTable(void)

const CVDBTable & ProtTable(void)

CVDBObjectCache< SGiIdxTableCursor > m_GiIdx

const string & GetIdPrefix(void) const

atomic< Int1 > m_ProteinNameIndexIsOpened

TVDBRowId GetProtGiRowId(TGi gi)

const string & GetWGSPath(void) const

atomic< Int1 > m_ContigNameIndexIsOpened

CWGSDb(CVDBMgr &mgr, CTempString path_or_acc, CTempString vol_path=CTempString())

TGiRanges GetProtGiRanges(void)

pair< TVDBRowId, bool > GetGiRowId(TGi gi) const

TVDBRowId GetProductNameRowId(const string &name) const

CWGSDb(CWGSDb_Impl *impl)

TGiRanges GetNucGiRanges(void) const

CWGSDb_Impl::SProtAccInfo SProtAccInfo

TProtAccRanges GetProtAccRanges(void)

static TVDBRowId ParseProteinRow(CTempString acc)

const string & GetWGSPath(void) const

static TVDBRowId ParseScaffoldRow(CTempString acc)

TVDBRowId GetContigNameRowId(const string &name) const

TVDBRowId GetNucGiRowId(TGi gi) const

void SetMasterDescr(const TMasterDescr &descr, EDescrFilter filter=eDescrDefaultFilter) const

CWGSDb_Impl::TIdRange TIdRange

pair< TGi, TGi > GetProtGiRange(void) const

pair< TGi, TGi > GetNucGiRange(void) const

CWGSDb_Impl::TGiRange TGiRange

CWGSDb_Impl::TProtAccRanges TProtAccRanges

TVDBRowId GetProteinNameRowId(const string &name) const

TVDBRowId GetProtAccRowId(const string &acc, int version=-1) const

list< CRef< CSeqdesc > > TMasterDescr

TVDBRowId ParseRow(CTempString acc, bool *is_scaffold=NULL) const

TVDBRowId GetProtGiRowId(TGi gi) const

bool LoadMasterDescr(EDescrFilter filter=eDescrDefaultFilter) const

static EDescrType GetMasterDescrType(const CSeqdesc &desc)

CWGSDb_Impl::TGiRanges TGiRanges

static TVDBRowId ParseContigRow(CTempString acc)

TVDBRowId GetScaffoldNameRowId(const string &name) const

CWGSDb_Impl & GetDb(void) const

TVDBRowCount GetSize(void) const

CWGSFeatureIterator & operator++(void)

TVDBRowId GetFirstBadRowId(void) const

DECLARE_OPERATOR_BOOL(m_CurrId< m_FirstBadId)

TVDBRowCount GetRemainingCount(void) const

TVDBRowId GetFirstGoodRowId(void) const

TVDBRowId GetCurrentRowId(void) const

CRef< CWGSDb_Impl::SFeatTableCursor > m_Cur

void x_CheckValid(const char *method) const

CWGSGiIterator & operator++(void)

ESeqType GetSeqType(void) const

TVDBRowId GetRowId(void) const

CRef< CWGSDb_Impl::SGiIdxTableCursor > m_Cur

CWGSDb_Impl & GetDb(void) const

DECLARE_OPERATOR_BOOL(m_CurrGi< m_FirstBadGi)

TVDBRowId GetFirstBadRowId(void) const

CBioseq::TAnnot TAnnotSet

TVDBRowId GetCurrentRowId(void) const

TVDBRowId GetFirstGoodRowId(void) const

DECLARE_OPERATOR_BOOL(m_CurrId< m_FirstBadId)

CWGSDb_Impl & GetDb(void) const

TVDBRowCount GetRemainingCount(void) const

void x_CheckValid(const char *method) const

CRef< CWGSDb_Impl::SProtTableCursor > m_Cur

TVDBRowCount GetSize(void) const

CWGSProteinIterator & operator++(void)

CRef< CWGSDb_Impl::SProt0TableCursor > m_Cur0

TVDBRowCount GetSize(void) const

TVDBRowId GetFirstBadRowId(void) const

TVDBRowCount GetRemainingCount(void) const

TVDBRowId GetFirstGoodRowId(void) const

CRef< CWGSDb_Impl::SScfTableCursor > m_Cur

void x_CheckValid(const char *method) const

CWGSDb_Impl & GetDb(void) const

CWGSScaffoldIterator & operator++(void)

TVDBRowId GetCurrentRowId(void) const

DECLARE_OPERATOR_BOOL(m_CurrId< m_FirstBadId)

TVDBRowId GetRemainingCount(void) const

TIncludeFlags m_IncludeFlags

TSeqPos x_Get4naLength(TSeqPos pos, TSeqPos len, SAmbiguityAccess &ambiguity) const

TSeqPos x_Get2naLength(TSeqPos pos, TSeqPos len, SAmbiguityAccess &ambiguity) const

DECLARE_SAFE_FLAGS_TYPE(EIncludeFlags, TIncludeFlags)

TSeqPos x_Get4naLengthExact(TSeqPos pos, TSeqPos len, TSeqPos stop_2na_len, TSeqPos stop_gap_len, SAmbiguityAccess &ambiguity) const

bool x_AmbiguousBlock(TSeqPos block_index, SAmbiguityAccess &ambiguity) const

CWGSDb_Impl::SAmbiguityInfo SAmbiguityInfo

TVDBRowId GetCurrentRowId(void) const

CRef< CWGSDb_Impl::SSeq0TableCursor > m_Cur0

bool IsClippedByQuality(void) const

int GetAccVersion(void) const

CRef< CDelta_ext > GetDelta(TSeqPos pos, TSeqPos len) const

TSeqPos x_GetGapLengthExact(TSeqPos pos, TSeqPos len, SAmbiguityAccess &ambiguity) const

CRef< CSeq_data > Get4na(TSeqPos pos, TSeqPos len, SAmbiguityAccess &ambiguity) const

TVDBRowId GetFirstBadRowId(void) const

CWGSDb_Impl::SSeq4naTableCursor SSeq4naTableCursor

CBioseq::TAnnot TAnnotSet

CRef< CWGSDb_Impl::SAmbiguityInfo > m_AmbiguityInfo

SVersionSelector m_AccVersion

CRef< CWGSDb_Impl::SSeqTableCursor > m_Cur

TVDBRowId GetSize(void) const

DECLARE_SAFE_FLAGS_TYPE(EInstSegmentFlags, TInstSegmentFlags)

TSeqPos x_Get2naLengthExact(TSeqPos pos, TSeqPos len, SAmbiguityAccess &ambiguity) const

CRef< CSeq_data > Get2na(TSeqPos pos, TSeqPos len, SAmbiguityAccess &ambiguity) const

vector< SSegment > TSegments

DECLARE_OPERATOR_BOOL(m_CurrId< m_FirstBadId)

bool ShouldBeClippedByQuality(void) const

TVDBRowId GetLastRowId(void) const

const Uint1 * x_GetUnpacked4na(TSeqPos pos, TSeqPos len, SAmbiguityAccess &ambiguity) const

bool GetClipByQualityFlag(EClipType clip_type=eDefaultClip) const

void x_CheckValid(const char *method) const

CRef< CDelta_ext > GetDelta(TSeqPos pos, TSeqPos len, TWGSContigGapInfo gap_info, vector< COpenRange< TSeqPos > > *split=0) const

CWGSDb_Impl & GetDb(void) const

TVDBRowId GetFirstGoodRowId(void) const

TSeqPos GetClipQualityRight(void) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

int GetSeqLength(const CBioseq &bioseq)

std::ofstream out("events_result.xml")

main entry point for tests

static const char table_name[]

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

string GetProteinName(const CBioseq_Handle &seq)

Return protein name from corresponding Prot-ref feature.

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

CObject & operator=(const CObject &src) THROWS_NONE

Assignment operator.

TObjectType & GetObject(void)

Get object.

TObjectType & GetNCObject(void) const

Get object.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int8_t Int1

1-byte (8-bit) signed integer

#define NCBI_SRAREAD_EXPORT

E_Choice

Choice variants.

list< CRef< CSeq_id > > TId

EMol

molecule class in living organism

list< CRef< CSeq_annot > > TAnnot

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

Generic map with additional resource limited by some value.

CSeq_entry_Info & GetSeq_entry(CTSE_Info &tse, const CBioObjectId &id)

CBioseq_Info & GetBioseq(CTSE_Info &tse, const CBioObjectId &id)

static string GetProductName(const CProt_ref &prot)

const string version

version string

Multi-threading – mutexes; rw-locks; semaphore.

void split(std::vector< std::string > *strVec, const std::string &str_, const std::string &split_)

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

#define row(bind, expected)

bool operator<(const SProtAccInfo &b) const

bool operator==(const SProtAccInfo &b) const

bool operator!=(const SProtAccInfo &b) const

DECLARE_OPERATOR_BOOL(m_IdLength !=0)

CRef< CSeq_literal > literal

COpenRange< TSeqPos > range

SVersionSelector(ELatest)

const INSDC_coord_len * gaps_len

bool IsInGap(TSeqPos pos) const

TSeqPos GetGapLength(TSeqPos pos, TSeqPos len) const

TSeqPos GetLength(void) const

TSeqPos GetToOpen(void) const

DECLARE_OPERATOR_BOOL(gaps_count > 0)

const NCBI_WGS_component_props * gaps_props

TSeqPos GetFrom(void) const

TSeqPos GetTo(void) const

const INSDC_coord_zero * gaps_start

TSeqPos GetDataLength(TSeqPos pos, TSeqPos len) const

const NCBI_WGS_gap_linkage * gaps_linkage

DECLARE_SAFE_FLAGS_TYPE(EFlags, TFlags)

@ eFeatLocIdUninitialized

static const TSplitVersion kDefaultSplitVersion

pair< TVDBRowId, TVDBRowCount > TVDBRowIdRange

void Serialize(CNcbiOstream &, const CRawScoreVector< Key, Score > &)

Generics These throw an exception; we must implement serialization for each type.

int32_t NCBI_WGS_gap_linkage

int16_t NCBI_WGS_component_props

void AddMasterDescr(CBioseq_Info &seq, const CSeq_descr &src, EDescrType type)

int32_t NCBI_WGS_gap_linkage

@ NCBI_gb_state_eWGSGenBankUnverified

@ NCBI_gb_state_eWGSGenBankReplaced

@ NCBI_gb_state_eWGSGenBankSuppressed

@ NCBI_gb_state_eWGSGenBankMissing

@ NCBI_gb_state_eWGSGenBankMigrated

@ NCBI_gb_state_eWGSGenBankLive

@ NCBI_gb_state_eWGSGenBankWithdrawn

DECLARE_SAFE_FLAGS(SWGSDb_Defs::EFlags)

@ NCBI_WGS_seqtype_scaffold

@ NCBI_WGS_seqtype_protein

@ NCBI_WGS_seqtype_contig

@ NCBI_WGS_loc_strand_both

@ NCBI_WGS_loc_strand_minus

@ NCBI_WGS_loc_strand_plus

@ NCBI_WGS_loc_strand_unknown

uint8_t INSDC_quality_phred

int16_t NCBI_WGS_component_props

uint8_t NCBI_WGS_loc_strand

uint8_t NCBI_WGS_feattype

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