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

& sra_id_part);

m_Seq_ids.front();

m_Seq_ids.front();

m_Seq_id_Handle;

m_RefMapByName;

m_RefMapBySeq_id;

OpenRefTable(

);

OpenAlnTable(

is_secondary);

OpenSeqTable(

);

OpenAlnTable(is_secondary);

x_MakeRefSeq_ids(SRefInfo&

,

& csra_path,

& csra_path,

& sra_id_part,

& dir_path,

& csra_file);

CCSraDb_Impl::TRefInfoList::const_iterator iter)

!m_Db || m_Iter == m_Db->GetRefInfoList().end();

*(void)

{

!*

? 0:

;

m_Iter->m_SeqId;

m_Iter->GetMainSeq_id();

m_Iter->GetMainSeq_id_Handle();

m_Iter->m_Seq_ids;

IsCircular(

)

;

GetAlignCountAtPos(

pos, TAlignType

= fAnyAlign)

;

GetRefBioseq(ELoadData load = eLoadData)

;

GetRefLiterals(

& literals,

vector<TSeqPos>& GetAlnOverStarts(

)

;

GetEstimatedNumberOfAlignments(

)

;

m_Db.GetNCObject();

CCSraDb_Impl::TRefInfoList::const_iterator

;

& ref_id,

ESearchMode search_mode = eSearchByOverlap,

TAlignType align_type = fAnyAlign);

ESearchMode search_mode,

TAlignType align_type = fAnyAlign);

TAlignType align_type = fAnyAlign);

ESearchMode search_mode = eSearchByOverlap,

TAlignType align_type = fAnyAlign);

*(void)

{

m_Error? 0:

;

m_AlnRowIsSecondary;

GetRefMinusStrand(

)

;

GetMapQuality(

)

;

GetShortPos(

)

;

GetShortLen(

)

;

IsSetName(

)

;

MakeFullMismatch(

&

,

m_RefIter->GetMainSeq_id();

m_RefIter.GetDb();

max_value_length,

max_cache_size)

;

EClipType clip_type = eDefaultClip);

EClipType clip_type = eDefaultClip);

EClipType clip_type = eDefaultClip);

*(void)

{

m_Error? 0:

;

GetReadId()-1;

GetMaxReadId();

GetMateCount(

)

;

IsSetName(

)

;

HasClippingInfo(

)

;

m_ClipByQuality && HasClippingInfo();

!m_ClipByQuality && HasClippingInfo();

GetReadData(EClipType clip_type = eDefaultClip)

;

IsTechnicalRead(

)

;

GetReadRange().GetLength();

GetClipQualityLeft(

)

;

GetClipQualityLength(

)

;

GetClipQualityLeft() + GetClipQualityLength() - 1;

fQualityGraph = 1<<0,

fDefaultBioseqFlags = 0

m_Db.GetNCObject();

x_Init(

& csra_db, EClipType clip_type);

x_ValidRead(

)

;

x_Settle(

single_spot =

);

x_GetMaxReadId(

);

x_GetReadData(TOpenRange range)

;

* annot_name)

;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Extensions to std::atomic<>

bool operator!(void) const

CRef< CSeq_annot > x_GetMatchAnnot(const string *annot_name) const

CRef< CSeq_annot > GetEmptyMatchAnnot(void) const

CCSraRefSeqIterator m_RefIter

CRef< CObject_id > TObjectIdCache

CRef< CSeq_entry > GetMatchEntry(void) const

static CRef< CSeq_annot > MakeSeq_annot(const string &annot_name)

CCSraDb_Impl & GetDb(void) const

CRef< CSeq_id > GetRefSeq_id(void) const

CRef< CSeq_annot > GetQualityGraphAnnot(void) const

TSeqPos GetRefSeqLen(void) const

map< CTempString, CRef< CUser_field > > TUserFieldCache

const TVDBRowId * m_AlnRowCur

CRef< CSeq_annot > x_GetSeq_annot(const string *annot_name) const

CRef< CSeq_annot > GetSeq_annot(void) const

TSeqPos GetRefSeqPos(void) const

CRef< CSeq_entry > x_GetMatchEntry(const string *annot_name) const

CRef< CCSraDb_Impl::SRefTableCursor > m_Ref

CCSraAlignIterator & operator++(void)

CRef< CSeq_annot > GetMatchAnnot(void) const

bool IsSecondary(void) const

CRef< CSeq_annot > x_GetQualityGraphAnnot(const string *annot_name) const

CRef< CSeq_annot > x_GetEmptyMatchAnnot(const string *annot_name) const

AutoPtr< SCreateCache > m_CreateCache

CRef< CCSraDb_Impl::SAlnTableCursor > m_Aln

const TVDBRowId * m_AlnRowEnd

CFastMutex m_OverlapMutex

const CVDBTable & SeqTable(void)

void GetSpotGroups(TSpotGroups &spot_groups)

list< SRefInfo > TRefInfoList

CVDBObjectCache< SSeqTableCursor > m_Seq

const CVDBTable & RefTable(void)

vector< string > TSpotGroups

void SetSraIdPart(const string &s)

const TRefInfoMapBySeq_id & GetRefInfoMapBySeq_id(void) const

TRefInfoMapByName m_RefMapByName

CVDBObjectCache< SRefTableCursor > m_Ref

const string & GetCSraPath(void) const

TRefInfoMapBySeq_id m_RefMapBySeq_id

TSeqPos GetRowSize(void) const

const CVDBTable & AlnTable(bool is_secondary)

const string & GetSraIdPart(void) const

map< string, TRefInfoList::iterator, PNocase > TRefInfoMapByName

const TRefInfoList & GetRefInfoList(void) const

map< CSeq_id_Handle, TRefInfoList::iterator > TRefInfoMapBySeq_id

const TRefInfoMapByName & GetRefInfoMapByName(void) const

CCSraDb_Impl::TSpotGroups TSpotGroups

void GetSpotGroups(TSpotGroups &spot_groups)

TSeqPos GetRowSize(void) const

static string MakeSraIdPart(EPathInIdType path_in_id_type, const string &dir_path, const string &csra_file)

const CCSraDb_Impl::SRefInfo & operator*(void) const

static CRef< CSeq_annot > MakeSeq_annot(const string &annot_name)

CRef< CSeq_annot > GetSeq_annot(void) const

CCSraDb_Impl::TRefInfoList::const_iterator m_Iter

CCSraRefSeqIterator(const CCSraDb &csra_db, CCSraDb_Impl::TRefInfoList::const_iterator iter)

const CBioseq::TId & GetRefSeq_ids(void) const

bool operator!(void) const

CCSraRefSeqIterator & operator++(void)

const string & GetRefSeqId(void) const

CRef< CSeq_annot > x_GetSeq_annot(const string *annot_name) const

list< CRef< CSeq_literal > > TLiterals

const CCSraDb_Impl::SRefInfo * operator->(void) const

CCSraRefSeqIterator(void)

const CSeq_id_Handle & GetRefSeq_id_Handle(void) const

CRef< CSeq_id > GetRefSeq_id(void) const

CCSraDb_Impl & GetDb(void) const

uint32_t GetReadId(void) const

COpenRange< TSeqPos > TOpenRange

TSeqPos GetClipQualityRight(void) const

bool x_Settle(bool single_spot=false)

bool m_IncludeTechnicalReads

CCSraShortReadIterator & operator++(void)

TVDBRowId GetShortId1(void) const

bool IsClippedByQuality(void) const

CRef< CSeq_annot > GetQualityGraphAnnot(void) const

CRef< CSeq_annot > x_GetQualityGraphAnnot(const string *annot_name) const

TVDBRowId GetSpotId(void) const

CCSraDb_Impl & GetDb(void) const

uint32_t GetMaxReadId(void) const

TVDBRowId GetMaxSpotId(void) const

uint32_t GetMateIndex(void) const

CRef< CCSraDb_Impl::SSeqTableCursor > m_Seq

uint32_t GetReadCount(void) const

TSeqPos GetShortLen(void) const

uint32_t GetShortId2(void) const

bool ShouldBeClippedByQuality(void) const

bool operator!(void) const

CRef< CSeq_annot > x_GetSeq_annot(const string *annot_name) const

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

General IdMapper interface.

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

uint8_t INSDC_read_filter

int GetSeqLength(const CBioseq &bioseq)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

TObjectType & GetObject(void)

Get object.

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define NCBI_SRAREAD_EXPORT

list< CRef< CSeq_id > > TId

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

const GenericPointer< typename T::ValueType > T2 value

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

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

static CObject_id & x_GetObject_id(CRef< CObject_id > &cache, const char *name)

#define row(bind, expected)

TObjectIdCache m_ObjectIdMISMATCH

TObjectIdCache m_ObjectIdRefPos

CRef< CUser_object > m_SecondaryIndicator

TObjectIdCache m_ObjectIdTracebacks

TUserFieldCache m_UserFieldCacheCigar

TObjectIdCache m_ObjectIdCIGAR

TObjectIdCache m_ObjectIdLcl

TObjectIdCache m_ObjectIdRefId

TUserFieldCache m_UserFieldCacheMismatch

TObjectIdCache m_ObjectIdMateRead

CRef< CAnnotdesc > m_MatchAnnotIndicator

const CSeq_id_Handle & GetMainSeq_id_Handle(void) const

CSeq_id_Handle m_Seq_id_Handle

CRef< CSeq_id > & GetMainSeq_id(void)

copyable_relaxed_atomic< TSeqPos > m_SeqLength

const CRef< CSeq_id > & GetMainSeq_id(void) const

vector< TSeqPos > m_AlnOverStarts

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