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

: m_BlobType(blob_type),

m_RefIdType(ref.

->m_File->GetRefIdType()),

m_File(ref.

->m_File->GetCSRAName()),

m_SeqId(ref.

->GetRefSeqId()),

m_FileLock(ref.second)

: m_BlobType(eBlobType_reads),

m_RefIdType(

.

->GetRefIdType()),

m_FirstSpotId(first_spot_id),

m_FileLock(

.second)

* begin =

.data();

* ptr = begin+

.size();

* end = ptr;

number_digit = 1;

parsing_read_id =

;

( ; ptr != begin; ) {

( parsing_read_id ) {

+= (c-

)*number_digit;

( c ==

) {

( ptr[1] ==

) {

( parsing_read_id ) {

parsing_read_id =

;

( ptr == begin ) {

& dbtag =

->GetGeneral();

( srr_len !=

) {

( srr_len ==

) {

( srr->size() != srr_len ) {

* srr_acc_ptr,

&

=

->GetGeneral().GetTag().GetStr();

( srr_end ==

) {

*srr_acc_ptr =

.substr(0, srr_end);

*label_ptr =

.substr(srr_end+1);

* srr_acc_ptr,

( srr_end ==

) {

*srr_acc_ptr =

.substr(0, srr_end);

<<str0);

<<str0);

<<str0);

m_IdMapper(params.m_IdMapper)

<

Call>

retry_count)

( retry_count == 0 ) {

(

= 1;

< retry_count; ++

) {

(

<<

<<name<<

<<

<<

<<exc);

( exception& exc ) {

(

<<

<<name<<

<<

<<

<<exc.

());

(

<<

<<name<<

<<

<<

);

(

<<

<<wait_sec<<

);

( !

.first ) {

(

.first->GetRefSeqInfo(idh), std::move(

.second));

(1,

<<idh<<

<<ret.first->m_File->GetCSRAName()<<

<<

->m_File->GetCSRAName());

( it->second->m_CSRADb->GetSraIdPart() == acc ) {

(2,

<<idh<<

<<it->second->GetCSRAName()<<

<<ret.first->GetCSRAName());

ret.first = it->second;

( !ret.first->IsValidReadId(spot_id, read_id, ref_ptr, ref_pos_ptr) ) {

*spot_id_ptr = spot_id;

*read_id_ptr = read_id;

data_source, cref(blob_id)),

data_source, cref(idh), choice),

need_seq =

, need_align =

, need_graph =

, need_orphan =

;

need_seq = need_align = need_graph =

;

need_align = need_graph =

;

( need_align || need_graph ) {

( need_seq || need_graph || (need_align && !ref_info) ) {

( need_align && !ref_info ) {

( need_align && ref_info ) {

( chunk_id >= 0 ) {

file_info.first->GetRefSeqInfo(blob_id)->LoadAnnotBlob(load_lock);

file_info.first->GetRefSeqInfo(blob_id)->LoadRefSeqBlob(load_lock);

file_info.first->LoadReadsBlob(blob_id, load_lock);

cref(blob_id), ref(chunk_info)),

file_info.first->GetRefSeqInfo(blob_id)->LoadAnnotChunk(chunk_info);

file_info.first->GetRefSeqInfo(blob_id)->LoadRefSeqChunk(chunk_info);

it->second->GetPossibleAnnotNames(

);

.first->GetRefSeqIterator();

cref(idh), ref(ids)),

( (*it)->GetTextseq_Id() ) {

( (*it)->IsGi() ) {

ret.

= (*it)->GetGi();

);

iter.GetSeqLength();

iter.GetShortLen();

);

& csra,

refseq_label = seq_id.

();

& csra,

(

.GetPathInId() ) {

.m_DirPath, csra),

.m_IdMapper.get(),

<<csra<<

<<

->GetSraIdPart());

max_separate_spot_groups =

.GetSpotGroups();

( max_separate_spot_groups > 1 ) {

( !name.empty() ) {

( align_annot_name.empty() ) {

<<refseq_label<<

<<refseq_id);

( ref_pos_ptr ) {

( ref_ptr || ref_pos_ptr ) {

<<blob_id.

()<<

<<

first_spot_id<<

<<last_spot_id);

( ; it; ++it ) {

( ; it; ++it ) {

annot->

().SetAlign().push_back(ait.GetMatchAlign());

: m_File(csra_file),

m_MinMapQuality(csra_file->GetMinMapQuality())

GetStatCount(

)

{

GetStatLen(

)

{

m_RefPosLast - m_RefPosFirst + .5;

( ; ait; ++ait ) {

( min_quality > 0 && ait.GetMapQuality() < min_quality ) {

pos = ait.GetRefSeqPos();

( pos < m_RefPosFirst ) {

m_RefPosFirst = pos;

( pos > m_RefPosLast ) {

( ++m_Count ==

) {

<<ref_pos<<

<<m_Count<<

<<

m_RefPosFirst<<

<<m_RefPosLast<<

<<skipped);

<<k<<

<<range<<

<<k<<

<<range<<

a_empty = 0, g_empty = 0;

(

p = 0; p < ref_length; p += segment_len ) {

end =

(ref_length, p + segment_len);

( (p >

.start_pos &&

.align_count+c >= 2*kAlignLimitCount) ||

(p >=

.start_pos+kAlignEmptyLength && c && !

.align_count) ) {

.align_count += c;

(

.align_count && end >= a_empty+kAlignEmptyLength ) {

.start_pos = a_empty;

(

.align_count >= kAlignLimitCount ) {

( (p >

.start_pos &&

.align_count+c >= 2*kGraphLimitCount) ||

(p >=

.start_pos+kGraphEmptyLength && c && !

.align_count) ) {

.align_count += c;

(

.align_count && end >= g_empty+kGraphEmptyLength ) {

.start_pos = g_empty;

(

.align_count >= kGraphLimitCount ||

(p + segment_len -

.start_pos) >= kGraphLimitLength) ) {

(

.align_count ) {

(

.start_pos < ref_length);

.start_pos = ref_length;

(

.start_pos <= ref_length);

(

.align_count ) {

(

.start_pos < ref_length);

.start_pos = ref_length;

(

.start_pos <= ref_length);

align_chunks = 0;

( it->align_count ) {

graph_chunks = 0;

( it->align_count ) {

<<total<<

<<align_chunks<<

<<graph_chunks<<

chunk_len =

(chunk_len, segment_len);

(

pos = 0; pos < ref_length; pos += chunk_len ) {

<<est_count<<

<<pp.size());

pp.push_back(ref_length);

kStatCount = 1000;

ref_begin = 0, ref_end = ref_length;

stat_len = 0, stat_cnt = 0;

scan_first = 1;

( stat[0].m_Count != kStatCount ) {

( stat[0].m_Count > 0 ) {

ref_begin = stat[0].m_RefPosFirst;

stat_len = stat[0].GetStatLen();

stat_cnt = stat[0].GetStatCount();

(

k = scan_first; k <

; ++k ) {

( k && ref_pos < stat[k-1].m_RefPosLast ) {

ref_pos = stat[k-1].m_RefPosLast;

(

<<k<<

<<ref_pos);

stat_len += stat[k].GetStatLen();

stat_cnt += stat[k].GetStatCount();

density = stat_cnt / stat_len;

exp_count = (ref_end-ref_begin)*density;

chunks =

(chunks,

(sqrt(exp_count)+1));

<<ref_begin<<

<<ref_end-1<<

<<exp_count<<

<<chunks);

pp.resize(chunks+1);

(

k = 1; k < chunks; ++k ) {

(

(ref_end-ref_begin)*k/chunks);

pp[chunks] = ref_end;

( vector<TSeqPos>, it, pp ) {

TChunks::const_iterator it =

align_name, pileup_name;

( !separate_spot_groups ) {

( separate_spot_groups ) {

<<

( !separate_spot_groups ) {

vector<CRef<CSeq_annot>> new_annots;

vector<CRef<CTSE_Chunk_Info>> new_chunks;

( separate_spot_groups ) {

annot->

().Set().push_back(desc);

new_annots.push_back(annot);

(

k = 0; k+1 < chunks.size(); ++k ) {

( !chunks[k].align_count ) {

range.

(chunks[k].start_pos);

range.

(chunks[k+1].start_pos);

( separate_spot_groups ) {

new_chunks.push_back(chunk);

(

k = 0; k+1 < chunks.size(); ++k ) {

range.

(chunks[k].start_pos);

range.

(chunks[k+1].start_pos);

( separate_spot_groups ) {

new_chunks.push_back(chunk);

(

& annot : new_annots ) {

(

& chunk : new_chunks ) {

vector<CTSE_Chunk_Info::TLocation> loc_set(1);

range.

(range_id*chunk_data_size);

<<

list< CRef<CSeq_literal> >

;

[pos].cnts[stat];

[pos].cnts[stat] += 1;

( pos <

() ) {

: stat =

;

;

: stat =

;

;

: stat =

;

;

: stat =

;

;

pair<unsigned, unsigned> c_min_max;

( !

.empty() && !

(stat) ) {

c_min_max.first = c_min_max.second =

(stat, 0);

c =

(stat,

);

c_min_max.first =

(c_min_max.first, c);

c_min_max.second =

(c_min_max.second, c);

vv.reserve(

());

vv.reserve(

());

(

& name);

m_SeparateSpotGroups(!m_File->GetSeparateSpotGroups().

()),

m_LastAnnot(m_Annots.end())

(spot_group_name);

<<

skipped = 0,

= 0;

( ; ait; ++ait ){

( min_quality > 0 && ait.

() < min_quality ) {

chunk_info.

(place, *it->second.first);

pos<<

<<(end-1)<<

<<

<<

<<skipped);

<<

= 0, skipped = 0;

( ; ait; ++ait ) {

( min_quality > 0 && ait.

() < min_quality ) {

* ptr = cigar.

();

* end = cigar.

();

( ptr != end ) {

( ; ptr != end; ) {

( c >=

&& c <=

) {

seglen = seglen*10+(c-

);

( seglen == 0 ) {

<<

<<

(

==

) {

(

==

||

==

) {

(

= 0;

< seglen; ++

) {

( ref_pos <

) {

ss.

(read[read_pos], ref_pos);

(

==

||

==

) {

(

==

) {

(

==

) {

(

==

) {

(

!=

) {

<<

<<

<<cigar);

pos<<

<<(end-1)<<

<<

<<

<<skipped);

total_bytes = 0;

(

k = 0; k <

; ++k ) {

*

titles[6] = {

,

,

,

,

,

( c_min_max.second == 0 ) {

.SetValues().resize(

);

total_bytes +=

.SetValues().size();

( c_min_max.second < 256 ) {

.SetMin(c_min_max.first);

.SetMax(c_min_max.second);

total_bytes += vv.size();

.SetMin(c_min_max.first);

.SetMax(c_min_max.second);

total_bytes += vv.size()*

(vv[0]);

it->second.first->SetData().SetGraph().push_back(graph);

pos<<

<<(end-1)<<

<<

chunk_info.

(place, *it->second.first);

pos<<

<<(end-1)<<

<<total_bytes<<

);

Blob state exceptions, used by GenBank loader.

CCSraDb::ERefIdType m_RefIdType

pair< CRef< CCSRARefSeqInfo >, TSRRFiles::CLock > TRefLock

string ToString(void) const

Get string representation of blob id.

static bool GetGeneralSRAAccLabel(const CSeq_id_Handle &idh, string *srr_acc_ptr=0, string *label_ptr=0)

pair< CRef< CCSRAFileInfo >, TSRRFiles::CLock > TFileLock

bool operator==(const CBlobId &id) const

static EGeneralIdType GetGeneralIdType(const CSeq_id_Handle &idh, EGeneralIdType allow_type, const string *srr=0)

static bool GetGeneralSRAAccReadId(const CSeq_id_Handle &idh, string *srr_acc_ptr=0, TVDBRowId *spot_id_ptr=0, Uint4 *read_id_ptr=0)

bool operator<(const CBlobId &id) const

void FromString(CTempString str)

TSRRFiles::CLock m_FileLock

CCSRABlobId(const CTempString &str)

static SIZE_TYPE ParseReadId(CTempString str, TVDBRowId *spot_id_ptr=0, Uint4 *read_id_ptr=0)

TFileLock GetReadsFileInfo(const CSeq_id_Handle &idh, TVDBRowId *spot_id_ptr=0, Uint4 *read_id_ptr=0, CRef< CCSRARefSeqInfo > *ref_ptr=0, TSeqPos *ref_pos_ptr=0)

CTSE_LoadLock GetBlobById(CDataSource *data_source, const CCSRABlobId &blob_id)

CRef< TSRRFiles > m_SRRFiles

CRef< CCSRABlobId > GetReadsBlobId(const TFileLock &lock, TVDBRowId spot_id)

CCSRADataLoader_Impl(const CCSRADataLoader::SLoaderParams &params)

TRefLock GetRefSeqInfo(const CSeq_id_Handle &idh)

CDataSource::STypeFound GetSequenceTypeOnce(const CSeq_id_Handle &idh)

CDataSource::SGiFound GetGi(const CSeq_id_Handle &idh)

void SetSpotReadAlign(bool value)

void GetChunkOnce(const CCSRABlobId &blob_id, CTSE_Chunk_Info &chunk)

CRef< CCSRABlobId > GetBlobId(const CSeq_id_Handle &idh)

vector< CSeq_id_Handle > TIds

CDataLoader::TTSE_LockSet GetRecords(CDataSource *data_source, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

void GetIds(const CSeq_id_Handle &idh, TIds &ids)

string GetLabel(const CSeq_id_Handle &idh)

CDataSource::STypeFound GetSequenceType(const CSeq_id_Handle &idh)

void AddCSRAFileOnce(const string &csra)

CCSRADataLoader::TAnnotNames TAnnotNames

CRef< CCSRABlobId > GetBlobIdOnce(const CSeq_id_Handle &idh)

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

void GetIdsOnce(const CSeq_id_Handle &idh, TIds &ids)

CTSE_LoadLock GetBlobByIdOnce(CDataSource *data_source, const CCSRABlobId &blob_id)

CDataSource::SGiFound GetGiOnce(const CSeq_id_Handle &idh)

~CCSRADataLoader_Impl(void)

CDataSource::SAccVerFound GetAccVerOnce(const CSeq_id_Handle &idh)

void AddCSRAFile(const string &csra)

pair< CRef< CCSRARefSeqInfo >, TSRRFiles::CLock > TRefLock

friend class CCSRAFileInfo

TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

string GetLabelOnce(const CSeq_id_Handle &idh)

TFileLock GetSRRFile(const string &acc)

CCSraRefSeqIterator GetRefSeqIterator(const CSeq_id_Handle &idh)

CDataSource::SAccVerFound GetAccVer(const CSeq_id_Handle &idh)

TFileLock GetFileInfo(const CCSRABlobId &blob_id)

bool GetSpotReadAlign(void) const

CCSraShortReadIterator GetShortReadIterator(const CSeq_id_Handle &idh)

void LoadBlob(const CCSRABlobId &blob_id, CTSE_LoadLock &load_lock)

TTaxId GetTaxIdOnce(const CSeq_id_Handle &idh)

TSeqPos GetSequenceLengthOnce(const CSeq_id_Handle &idh)

TAnnotNames GetPossibleAnnotNames(void) const

TTaxId GetTaxId(const CSeq_id_Handle &idh)

CDataLoader::TTSE_LockSet GetRecordsOnce(CDataSource *data_source, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

pair< CRef< CCSRAFileInfo >, TSRRFiles::CLock > TFileLock

void GetChunk(const CCSRABlobId &blob_id, CTSE_Chunk_Info &chunk)

vector< CAnnotName > TAnnotNames

void x_Initialize(CCSRADataLoader_Impl &impl, const string &csra, CCSraDb::ERefIdType ref_id_type)

void GetPossibleAnnotNames(TAnnotNames &names) const

void LoadReadsBlob(const CCSRABlobId &blob_id, CTSE_LoadLock &load_lock)

CCSRADataLoader::TAnnotNames TAnnotNames

string GetPileupAnnotName(void) const

CCSraDb::ERefIdType m_RefIdType

void AddRefSeq(const string &refseq_label, const CSeq_id_Handle &refseq_id)

bool GetPileupGraphs(void) const

const vector< string > & GetSeparateSpotGroups(void) const

CRef< CCSRARefSeqInfo > GetRefSeqInfo(const CSeq_id_Handle &seq_id)

CCSRAFileInfo(CCSRADataLoader_Impl &impl, const string &csra, CCSraDb::ERefIdType ref_id_type)

const string & GetCSRAName(void) const

const string & GetBaseAnnotName(void) const

bool IsValidReadId(TVDBRowId spot_id, Uint4 read_id, CRef< CCSRARefSeqInfo > *ref_ptr=0, TSeqPos *ref_pos_ptr=0)

string GetAnnotName(const string &spot_group, ECSRAAnnotChunkIdType type) const

string GetAlignAnnotName(void) const

vector< string > m_SeparateSpotGroups

CRef< CSeq_annot > m_CovAnnot

void LoadAnnotMainChunk(CTSE_Chunk_Info &chunk_info)

const CSeq_id_Handle & GetRefSeqId(void) const

void LoadRefSeqBlob(CTSE_LoadLock &load_lock)

CCSraRefSeqIterator GetRefSeqIterator(void) const

void LoadAnnotPileupChunk(CTSE_Chunk_Info &chunk_info)

int GetAnnotChunkId(TSeqPos ref_pos) const

vector< SChunkInfo > TChunks

CCSRARefSeqInfo(CCSRAFileInfo *csra_file, const CSeq_id_Handle &seq_id)

void LoadAnnotAlignChunk(CTSE_Chunk_Info &chunk_info)

void LoadAnnotChunk(CTSE_Chunk_Info &chunk_info)

void LoadAnnotBlob(CTSE_LoadLock &load_lock)

void LoadRefSeqChunk(CTSE_Chunk_Info &chunk_info)

void LoadAnnotMainSplit(CTSE_LoadLock &load_lock)

void LoadRefSeqMainEntry(CTSE_LoadLock &load_lock)

void x_LoadRangesStat(void)

CTempString GetSpotGroup(void) const

TSeqPos GetShortPos(void) const

CTempString GetMismatchRead(void) const

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

CRef< CSeq_id > GetRefSeq_id(void) const

int GetMapQuality(void) const

TSeqPos GetRefSeqPos(void) const

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

CRef< CSeq_align > GetMatchAlign(void) const

CTempString GetCIGARLong(void) const

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)

Uint8 GetEstimatedNumberOfAlignments(void) const

size_t GetAlignCountAtPos(TSeqPos pos, TAlignType type=fAnyAlign) const

void GetRefLiterals(TLiterals &literals, TRange range, ELoadData load=eLoadData) const

TSeqPos GetAlnOverToOpen(TRange range) const

CRef< CBioseq > GetRefBioseq(ELoadData load=eLoadData) const

TSeqPos GetSeqLength(void) const

const CSeq_id_Handle & GetRefSeq_id_Handle(void) const

CRef< CSeq_annot > GetCoverageAnnot(void) const

CRef< CBioseq > GetShortBioseq(TBioseqFlags flags=fDefaultBioseqFlags) const

void SetLastSpotId(TVDBRowId spot_id)

CCSraAlignIterator GetAlignIter() const

CCSraRefSeqIterator GetRefSeqIter(TSeqPos *ref_pos_ptr=NULL) const

CFastMutex & GetValueMutex()

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

void SetNameDesc(const string &name)

@ eProtectedDb

DB is protected.

@ eNotFoundDb

DB main file not found.

virtual TErrCode GetErrCode(void) const

pair< TBioseqId, TBioseq_setId > TPlace

void x_AddAnnotPlace(const TBioseqId &id)

TBlobId GetBlobId(void) const

void x_LoadAnnot(const TPlace &place, const CSeq_annot &annot)

void x_SetLoadSeconds(double seconds)

void x_AddUsedMemory(size_t size)

void x_LoadSequence(const TPlace &place, TSeqPos pos, const TSequence &seq)

void SetLoaded(CObject *obj=0)

TChunkId GetChunkId(void) const

void x_AddAnnotType(const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id)

void x_SetLoadBytes(Uint4 bytes)

void x_AddSeq_data(const TLocationSet &location)

const CTSE_Split_Info & GetSplitInfo(void) const

void x_LoadChunk(TChunkId chunk_id) const

CTSE_Split_Info & GetSplitInfo(void)

void SetSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

bool IsLoaded(void) const

void AddChunk(CTSE_Chunk_Info &chunk_info)

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

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static const int chunk_size

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

static const char kFileEnd[]

static const char kRefIdPrefixGeneral[]

static const unsigned kMaxReadId

static unsigned GetRetryCountParam(void)

static const unsigned kGraphEmptyPages

#define SPOT_GROUP_SEPARATOR

NCBI_PARAM_DEF(unsigned, CSRA_LOADER, RETRY_COUNT, 3)

static const double k_make_align_seconds

static const unsigned kGraphChunkSize

static const unsigned kAlignEmptyPages

static const double k_read_byte_seconds

static const char kBlobPrefixReads[]

static const char kBlobPrefixAnnot[]

static size_t GetGCSize(void)

NCBI_PARAM_DECL(int, CSRA_LOADER, DEBUG)

static const unsigned kAlignChunkSize

static const unsigned kReadsPerBlob

static int GetDebugLevel(void)

static const unsigned kChunkSeqDataMul

static const double k_make_graph_seconds

static const char kRefIdPrefixId[]

static const Uint4 k_align_bytes

static const bool kOmitEmptyPileup

static const unsigned kChunkGraphMul

NCBI_PARAM_DEF_EX(int, CSRA_LOADER, DEBUG, 0, eParam_NoThread, CSRA_LOADER_DEBUG)

static const bool kUseFullAlignCounts

NCBI_DEFINE_ERR_SUBCODE_X(16)

static const char kBlobPrefixReadsAlign[]

static const int kMainChunkId

static const char kBlobPrefixRefSeq[]

#define PILEUP_NAME_SUFFIX

static const bool kEstimateAlignCounts

static const Uint8 kMaxSpotId

@ eCSRAAnnotChunk_pileup_graph

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

main entry point for tests

static const struct name_t names[]

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define LOG_POST_X(err_subcode, message)

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Warning(CExceptionArgs_Base &args)

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

static string MakePath(const string &dir=kEmptyStr, const string &base=kEmptyStr, const string &ext=kEmptyStr)

Assemble a path from basic components.

#define MSerial_AsnText

I/O stream manipulators –.

CConstRef< CSeq_id > GetSeqId(void) const

void Reset(void)

Reset the handle (remove seq-id reference)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

string AsString(void) const

CSeq_id::E_Choice Which(void) const

string GetLabel(const CSeq_id &id)

string ToString(void) const

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

@ eExtFeatures

external features

@ eExtAnnot

all external annotations

@ eExtAlign

external aligns

@ eAll

all blobs (main and external)

@ eOrphanAnnot

all external annotations if no Bioseq exists

@ eGraph

graph annotations from main blob

@ eAnnot

all annotations from main blob

@ eBioseq

main blob with complete bioseq

@ eAlign

aligns from main blob

@ eBioseqCore

main blob with bioseq core (no seqdata and annots)

@ eExtGraph

external graph annotations

@ eFeatures

features from main blob

CRef< C > Ref(C *object)

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

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

@ eParam_NoThread

Do not use per-thread values.

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

TThisType & SetToOpen(position_type toOpen)

TThisType & SetLength(position_type length)

static TThisType GetWhole(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

NCBI_NS_STD::string::size_type SIZE_TYPE

const_iterator end() const

Return an iterator to the string's ending position (one past the end of the represented sequence)

const char * data(void) const

Return a pointer to the array represented.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

static const char label[]

void SetFrom(TFrom value)

Assign a value to From data member.

TFrom GetFrom(void) const

Get the From member data.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

void SetTo(TTo value)

Assign a value to To data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

@ e_General

for other databases

void SetTitle(const TTitle &value)

Assign a value to Title data member.

void SetNumval(TNumval value)

Assign a value to Numval data member.

void SetGraph(TGraph &value)

Assign a value to Graph data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

TSet & SetSet(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

void SetId(TId &value)

Assign a value to Id data member.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

void SetData(TData &value)

Assign a value to Data data member.

const TGraph & GetGraph(void) const

Get the variant data.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

TName & SetName(void)

Select the variant.

list< CRef< CSeq_id > > TId

const TData & GetData(void) const

Get the Data member data.

@ eMol_na

just a nucleic acid

unsigned int

A callback function used to compare two keys in a database.

Definition of all error codes used in SRA C++ support libraries.

constexpr auto sort(_Init &&init)

constexpr bool empty(list< Ts... >) noexcept

double value_type

The numeric datatype used by the parser.

string s_Value(TValue value)

const GenericPointer< typename T::ValueType > T2 value

#define NCBI_CONST_UINT8(v)

void SleepMilliSec(unsigned long ml_sec, EInterruptOnSignal onsignal=eRestartOnSignal)

Helper classes and templates to implement plugins.

bool GetEffectiveQualityGraphs(void) const

int GetEffectiveMinMapQuality(void) const

int GetEffectiveSpotGroups(void) const

bool GetEffectiveSpotReadAlign(void) const

bool GetEffectivePileupGraphs(void) const

vector< string > m_CSRAFiles

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

Better replacement of GetSequenceType(), this method should be defined in data loaders,...

void add_stat(EBaseStat stat, TSeqPos pos)

void get_bytes(EBaseStat stat, CByte_graph::TValues &vv)

void add_match(TSeqPos pos)

pair< unsigned, unsigned > get_min_max(EBaseStat stat) const

void add_insert(TSeqPos pos, TSeqPos count)

void x_add(EBaseStat stat, TSeqPos pos)

bool x_empty(EBaseStat stat) const

void add_base(TSeqPos pos, char b)

void add_base(char b, TSeqPos pos)

void get_ints(EBaseStat stat, CInt_graph::TValues &vv)

void add_match(TSeqPos pos, TSeqPos count)

unsigned x_get(EBaseStat stat, TSeqPos pos) const

void add_stat(EBaseStat stat, TSeqPos pos, TSeqPos count)

TAnnots::iterator m_LastAnnot

ECSRAAnnotChunkIdType m_Type

SChunkAnnots(CCSRAFileInfo *file_info, ECSRAAnnotChunkIdType type)

TSlot & Select(const CCSraAlignIterator &ait)

pair< CRef< CSeq_annot >, SBaseStats > TSlot

void Create(const string &name)

bool m_SeparateSpotGroups

map< string, TSlot > TAnnots

CRef< CCSRAFileInfo > m_File

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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