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NCBI C++ ToolKit: src/sra/readers/sra/csraread.cpp Source File

m_IsSecondary(is_secondary),

& sra_id_part)

(2,

<<

<<csra_path<<

);

(2,

<<

<<csra_path);

name_row_range = ref->m_NAME.GetRowIdRange(ref->m_Cursor);

end_row = name_row_range.first + name_row_range.second;

ref->m_Cursor.SetParam(

, name);

.m_SeqId = *ref->SEQ_ID(

);

CBioseq::TId::iterator best_id =

.m_Seq_ids.begin();

(

.GetMainSeq_id(), *best_id);

.m_Seq_id_Handle =

.m_RowFirst = range.first;

.m_RowLast = range.second;

.m_Circular = *ref->CIRCULAR(

);

& dir_path,

& csra_file)

& csra_path,

& csra_path,

& sra_id_part,

* name =

[

];

spot_groups.push_back(name);

.m_Seq_ids.clear();

( ref_id_mapper ) {

.m_Seq_ids.push_back(ret);

( !ret->

(*old) ) {

.m_Seq_ids.push_back(ret);

(

.m_SeqId.find(

) !=

) {

.m_Seq_ids.clear();

(

.m_Seq_ids.empty() ) {

.m_Seq_ids.push_back(ret);

( ref_id_mapper ) {

:

));

[curs->m_IsSecondary].Put(curs);

last_len = *ref->SEQ_LEN(

.m_RowLast);

m_Iter(csra_db->GetRefInfoList().begin())

& seq_id)

( iter != csra_db->m_RefMapBySeq_id.end() ) {

(1,

<<seq_id<<

);

csra_db->m_RefMapByName.find(name);

( iter != csra_db->m_RefMapByName.end() ) {

csra_db->m_RefMapBySeq_id.find(seq_id);

( iter != csra_db->m_RefMapBySeq_id.end() ) {

);

.m_SeqLength;

);

ret += ref->PRIMARY_ALIGNMENT_IDS(

).size();

ret += ref->SECONDARY_ALIGNMENT_IDS(

).size();

loc_int.

(

.GetMainSeq_id().GetNCObject());

values.resize(

);

(

= 0;

<

; ++

) {

(

==

.m_RowLast ) {

annot->

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

annot->

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

& csra_path =

->GetCSraPath();

+

seq->

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

seq->SetLiteral(**it);

inst.

().SetDelta().Set().push_back(seq);

(

==

.m_RowLast ) {

segment_len = *ref->SEQ_LEN(

);

->SetLength(segment_len);

->SetSeq_data().SetIupacna().Set() = *ref->READ(

);

(

.m_AlnOverStarts.empty() ) {

( ref->m_OVERLAP_REF_POS ) {

(

.m_AlnOverStarts.empty() ) {

(

= 0;

< 2 &&

< vv.

(); ++

) {

( p && p < pos ) {

max_aln_end = 1;

(

secondary = 0; secondary < 2; ++secondary ) {

( !ref->m_SECONDARY_ALIGNMENT_IDS ) {

aln_ids = ref->SECONDARY_ALIGNMENT_IDS(

.m_RowFirst);

aln_ids = ref->PRIMARY_ALIGNMENT_IDS(

.m_RowFirst);

( aln_ids.

() ) {

(

aln_id : aln_ids ) {

end = pos + *aln->REF_LEN(aln_id);

max_aln_end =

(max_aln_end, end);

pp[

(pp.size()-1, (max_aln_end-1)/segment_len)] = 0;

(

= pp.size();

-- > 1; ) {

pp[

-1] =

(pp[

-1], pp[

]);

(

vector<TSeqPos>&

(

.m_AlnOverStarts), pp);

.m_AlnOverStarts;

( seg+1 < pp.size() && pp[seg+1] < range.

() ) {

first_align_id = 0, last_align_id = 0;

first_align_id = *min_element(ids.

(), ids.

()+

);

( first_align_id ) {

( !first_align_id ) {

last_align_id = *max_element(ids.

(), ids.

()+

);

( last_align_id ) {

last_align_id-first_align_id+1;

(

!= &iter ) {

& ref_id,

m_Ref(m_RefIter.GetDb().

()),

(ref_pos, window, search_mode, align_type);

: m_RefIter(csra_db, ref_id),

m_Ref(m_RefIter.GetDb().

()),

(ref_pos, window, search_mode, align_type);

: m_RefIter(csra_db, ref_id),

m_Ref(m_RefIter.GetDb().

()),

( align_type ) {

);

start_pos =

(ref_pos, row_size)-row_size;

start_pos = pp[ref_pos/row_size];

start_pos = ref_pos;

(

->m_SECONDARY_ALIGNMENT_IDS ) {

( !

->m_READ_FILTER ) {

SRA_READ_FILTER_PASS;

dbtag.

(

);

(

.empty() ) {

->SEQ_READ_ID(mate_id));

(

->m_REF_OFFSET_TYPE &&

ret.reserve(mismatch.

()+2);

* cptr = cigar.

();

* cend = cigar.

();

* mptr = mismatch.

();

* mend = mismatch.

();

( cptr != cend ) {

( cptr != cend ) {

( c >=

&& c <=

) {

seglen = seglen*10+(c-

);

<< cigar);

( seglen == 0 ) {

<<

<<

(

==

) {

(

==

) {

( mptr + seglen > mend ) {

<<cigar<<

<<mismatch);

ret.append(mptr, seglen);

(

==

||

==

) {

( seqpos + seglen > has_mismatch.

() ) {

<<cigar<<

<<mismatch);

(

= 0;

< seglen; ++

, ++seqpos ) {

( has_mismatch[seqpos] ==

) {

( mptr == mend ) {

<<cigar<<

<<mismatch);

(

==

||

==

||

==

) {

<<

<<

<<cigar);

( mptr != mend ) {

<<cigar<<

<<mismatch);

* ptr = cigar.

();

* end = cigar.

();

(

* p = ptr; p != end; ++p ) {

( c < '0' || c >

) {

( c ==

|| c ==

) {

starts.reserve(2*segcount);

lens.reserve(segcount);

refstart = 0, seqstart = 0;

( ptr != end ) {

( ptr != end ) {

( c >=

&& c <=

) {

seglen = seglen*10+(c-

);

<< cigar);

( seglen == 0 ) {

<<

<<

(

==

||

==

) {

insert_size += seglen;

(

==

) {

(

==

||

==

) {

(

==

) {

(

!=

) {

<<

<<

<<cigar);

starts.push_back(refstart);

starts.push_back(seqstart);

lens.push_back(seglen);

strands.reserve(2*segcount);

(

= 0;

< segcount; ++

) {

starts[

*2+1] = end - (pos +

);

( !mate_id_v.

() ) {

, mate_ref_id,

, *

->REF_POS(mate_id),

->SEQ_SPOT_ID(mate_id),

->SEQ_READ_ID(mate_id));

obj->

().push_back(field);

align->

().push_back(obj);

( insert_size == 0 ) {

align->

().push_back(obj);

( filter > SRA_READ_FILTER_PASS &&

filter <= SRA_READ_FILTER_REDACTED ) {

*

[4] = {

,

graph->

(

);

values.resize(

);

(

= 0;

<

; ++

) {

TValue q = qual[

];

seq->

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

& iupac = inst.

().SetIupacna().Set();

iupac.assign(

.data(), length);

obj.

().SetStr(

);

obj.

(

,

);

obj.

().push_back(field);

max_value_length,

max_cache_size)

(

.size() > max_value_length || cache.

() > max_cache_size ) {

( iter == cache.

() || iter->first !=

) {

obj.

().push_back(iter->second);

(

!= &iter ) {

m_IncludeTechnicalReads(

),

m_ClipByQuality(

),

(csra_db, clip_type);

(csra_db, clip_type);

(csra_db, clip_type);

(spot_id, read_id);

( clip_type ) {

( single_spot ) {

(

= 0;

< read_types.

(); ++

) {

INSDC_read_type

= read_types[

];

( (

& (SRA_READ_TYPE_TECHNICAL | SRA_READ_TYPE_BIOLOGICAL)) ==

SRA_READ_TYPE_TECHNICAL ) {

(

& (SRA_READ_TYPE_TECHNICAL | SRA_READ_TYPE_BIOLOGICAL)) ==

SRA_READ_TYPE_TECHNICAL;

( !

->m_READ_FILTER ) {

SRA_READ_FILTER_PASS;

(

->IsCSRA() ) {

( trim_pos > pos ) {

trim_end = trim_pos + trim_len;

( trim_end < end ) {

clip_by_quality = !

->IsCSRA() &&

( clip_by_quality ) {

pos =

(pos, trim_pos);

trim_end = trim_pos + trim_len;

end =

(end, trim_end);

seq->

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

& iupac = inst.

().SetIupacna().Set();

iupac.assign(

.data(),

.size());

graph->

(

);

values.resize(

);

(

= 0;

<

; ++

) {

TValue q = qual[start+

];

annot->

().SetAlign();

annot->

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

* annot_name)

(

->m_PRIMARY_ALIGNMENT_ID ) {

( ref_pos_ptr ) {

*ref_pos_ptr = *aln->REF_POS(row_id);

(

->m_PRIMARY_ALIGNMENT_ID ) {

#define NCBI_THROW3(exc_cls, err_code, msg, extra1, extra2)

#define READ(buf, off, bytes, endian)

void Select(TSeqPos ref_pos, TSeqPos window=0, ESearchMode search_mode=eSearchByOverlap, TAlignType align_type=fAnyAlign)

CRef< CSeq_id > GetShortSeq_id(void) const

TVDBRowId GetAlignmentId(void) const

CTempString GetSpotGroup(void) const

CUser_field & x_AddField(CUser_object &obj, const char *name, TObjectIdCache &cache) const

SCreateCache & x_GetCreateCache(void) const

static CRef< CAnnotdesc > MakeMatchAnnotIndicator(void)

bool IsSetName(void) const

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

CCSraRefSeqIterator m_RefIter

TSeqPos GetShortPos(void) const

bool GetRefMinusStrand(void) const

CRef< CSeq_id > GetMateShortSeq_id(void) const

CTempString GetMismatchRead(void) const

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

CCSraDb_Impl & GetDb(void) const

CRef< CSeq_id > GetRefSeq_id(void) const

CCSraAlignIterator & operator=(const CCSraAlignIterator &iter)

CTempString GetCIGAR(void) const

CRef< CBioseq > GetShortBioseq(void) const

~CCSraAlignIterator(void)

INSDC_read_filter GetReadFilter(void) const

CRef< CSeq_graph > GetQualityGraph(void) const

CTempString GetMismatchRaw(void) const

int GetMapQuality(void) const

const TVDBRowId * m_AlnRowCur

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

TSeqPos GetRefSeqPos(void) const

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

CRef< CCSraDb_Impl::SRefTableCursor > m_Ref

CTempString GetName(void) const

CTempString GetRefSeqId(void) const

bool IsSecondary(void) const

CRef< CUser_object > x_GetSecondaryIndicator(void) const

TVDBRowId GetShortId1(void) const

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

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

void MakeFullMismatch(string &str, CTempString cigar, CTempString mismatch) const

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

AutoPtr< SCreateCache > m_CreateCache

TSeqPos GetShortLen(void) const

CObject_id & x_GetObject_id(const char *name, TObjectIdCache &cache) const

CRef< CCSraDb_Impl::SAlnTableCursor > m_Aln

CRef< CSeq_align > GetMatchAlign(void) const

CTempString GetCIGARLong(void) const

INSDC_coord_one GetShortId2(void) const

const TVDBRowId * m_AlnRowEnd

CVDBObjectCache< SAlnTableCursor > m_Aln[2]

const CVDBTable & SeqTable(void)

void GetSpotGroups(TSpotGroups &spot_groups)

list< SRefInfo > TRefInfoList

CRef< SRefTableCursor > Ref(void)

virtual ~CCSraDb_Impl(void)

void x_MakeRefSeq_ids(SRefInfo &info, IIdMapper *ref_id_mapper, int ref_id_type)

CVDBObjectCache< SSeqTableCursor > m_Seq

CRef< SSeqTableCursor > Seq(void)

const CVDBTable & RefTable(void)

vector< string > TSpotGroups

TRefInfoMapByName m_RefMapByName

CVDBObjectCache< SRefTableCursor > m_Ref

void Put(CRef< SRefTableCursor > &curs)

void x_CalcSeqLength(const SRefInfo &info)

const string & GetCSraPath(void) const

TRefInfoMapBySeq_id m_RefMapBySeq_id

TSeqPos GetRowSize(void) const

void SetShortReadId(string &str, TVDBRowId id1, INSDC_coord_one id2) const

const CVDBTable & AlnTable(bool is_secondary)

CCSraDb_Impl(CVDBMgr &mgr, const string &csra_path, IIdMapper *ref_id_mapper, ERefIdType ref_id_type, const string &sra_id_part)

CRef< CSeq_id > MakeShortReadId(TVDBRowId id1, INSDC_coord_one id2) const

friend struct SSeqTableCursor

CRef< SAlnTableCursor > Aln(bool is_secondary)

void OpenAlnTable(bool is_secondary)

TSeqPos GetRowSize(void) const

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

Uint8 GetEstimatedNumberOfAlignments(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

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

size_t GetRowAlignCount(TVDBRowId row) const

const CBioseq::TId & GetRefSeq_ids(void) const

const vector< TSeqPos > & GetAlnOverStarts(void) const

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

CRef< CSeq_graph > GetCoverageGraph(void) const

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

const CCSraDb_Impl::SRefInfo & GetInfo(void) const

list< CRef< CSeq_literal > > TLiterals

TSeqPos GetAlnOverToOpen(TRange range) const

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

CCSraRefSeqIterator(void)

TSeqPos GetSeqLength(void) const

CRef< CSeq_id > GetRefSeq_id(void) const

bool IsCircular(void) const

CCSraDb_Impl & GetDb(void) const

CRef< CSeq_annot > GetCoverageAnnot(void) const

void x_Init(const CCSraDb &csra_db, EClipType clip_type)

bool x_ValidRead(void) const

~CCSraShortReadIterator(void)

TOpenRange GetReadRange(EClipType clip_type=eDefaultClip) const

COpenRange< TSeqPos > TOpenRange

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

CCSraShortReadIterator(void)

void x_GetMaxReadId(void)

void SetLastSpotId(TVDBRowId spot_id)

bool IsTechnicalRead(void) const

bool Select(TVDBRowId spot_id)

CCSraAlignIterator GetAlignIter() const

CTempString GetSpotGroup(void) const

bool x_Settle(bool single_spot=false)

bool m_IncludeTechnicalReads

CTempString GetName(void) const

CTempString GetReadData(EClipType clip_type=eDefaultClip) const

TVDBRowId GetShortId1(void) const

CRef< CSeq_id > GetShortSeq_id(void) const

TSeqPos GetClipQualityLength(void) const

TSeqPos GetClipQualityLeft(void) const

CCSraShortReadIterator & operator=(const CCSraShortReadIterator &iter)

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

bool HasClippingInfo(void) const

bool IsSetName(void) const

CCSraDb_Impl & GetDb(void) const

CRef< CSeq_graph > GetQualityGraph(void) const

CRef< CSeq_graph > x_GetQualityGraph(TOpenRange range) const

CCSraRefSeqIterator GetRefSeqIter(TSeqPos *ref_pos_ptr=NULL) const

INSDC_read_filter GetReadFilter(void) const

CRef< CCSraDb_Impl::SSeqTableCursor > m_Seq

CTempString x_GetReadData(TOpenRange range) const

uint32_t GetShortId2(void) const

uint32_t GetMateCount(void) const

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

@ eDataError

VDB data is incorrect.

@ eNotFoundTable

DB table not found.

const string & GetParam(void) const

virtual TErrCode GetErrCode(void) const

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

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

const TValue * data() const

static bool IsPlainAccession(const string &acc_or_path)

General IdMapper interface.

virtual void MapObject(CSerialObject &)=0

Map all embedded IDs in a given object at once.

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

const_iterator lower_bound(const key_type &key) const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

The NCBI C++ standard methods for dealing with std::string.

NCBI_PARAM_DEF(bool, CSRA, READ_FILTER_IN_ALIGN_EXT, true)

#define RC_NO_MORE_ALIGNMENTS

NCBI_PARAM_DECL(bool, CSRA, EXPLICIT_MATE_INFO)

static bool s_GetPathInId(void)

static bool s_GetReadFilterInAlignExt(void)

static bool s_GetClipByQuality(void)

NCBI_DEFINE_ERR_SUBCODE_X(2)

static bool s_GetCigarInAlignExt(void)

NCBI_PARAM_DEF_EX(bool, CSRA, EXPLICIT_MATE_INFO, false, eParam_NoThread, CSRA_EXPLICIT_MATE_INFO)

static bool s_GetIncludeTechnicalReads(void)

static bool s_GetExplicitMateInfoParam(void)

uint8_t INSDC_read_filter

bool Empty(const CNcbiOstrstream &src)

static const struct name_t names[]

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.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#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 NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#define NCBI_THROW_FMT(exception_class, err_code, message)

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

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.

static void SplitPath(const string &path, string *dir=0, string *base=0, string *ext=0)

Split a path string into its basic components.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

const string AsFastaString(void) const

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

TObjectType & GetNCObject(void) const

Get object.

#define NCBI_PARAM_TYPE(section, name)

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

@ eParam_NoThread

Do not use per-thread values.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

position_type GetLength(void) const

position_type GetToOpen(void) const

position_type GetFrom(void) const

static TThisType GetEmpty(void)

static TThisType GetWhole(void)

const_iterator end() const

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

CTempString literal(const char(&str)[Size])

Templatized initialization from a string literal.

const char * data(void) const

Return a pointer to the array represented.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

size_type size(void) const

Return the length of the represented array.

TFrom GetFrom(void) const

Get the From member data.

const TStr & GetStr(void) const

Get the variant data.

void SetTag(TTag &value)

Assign a value to Tag data member.

const TData & GetData(void) const

Get the Data member data.

TData & SetData(void)

Assign a value to Data data member.

void SetLabel(TLabel &value)

Assign a value to Label data member.

TStr & SetStr(void)

Select the variant.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetDb(const TDb &value)

Assign a value to Db data member.

TLens & SetLens(void)

Assign a value to Lens data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

vector< ENa_strand > TStrands

vector< TSignedSeqPos > TStarts

void SetType(TType value)

Assign a value to Type data member.

vector< CRef< CSeq_id > > TIds

TExt & SetExt(void)

Assign a value to Ext data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

TIds & SetIds(void)

Assign a value to Ids data member.

@ eType_diags

unbroken, but not ordered, diagonals

void SetTo(TTo value)

Assign a value to To data member.

TGeneral & SetGeneral(void)

Select the variant.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

bool IsLocal(void) const

Check if variant Local is selected.

void SetStrand(TStrand value)

Assign a value to Strand data member.

@ e_General

for other databases

void SetMin(TMin value)

Assign a value to Min data member.

void SetTitle(const TTitle &value)

Assign a value to Title data member.

void SetNumval(TNumval value)

Assign a value to Numval data member.

void SetComp(TComp value)

Assign a value to Comp data member.

TValues & SetValues(void)

Assign a value to Values data member.

void SetGraph(TGraph &value)

Assign a value to Graph data member.

void SetMax(TMax value)

Assign a value to Max data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

void SetAxis(TAxis value)

Assign a value to Axis data member.

TSeq & SetSeq(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

TTitle & SetTitle(void)

Select the variant.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

void SetExt(TExt &value)

Assign a value to Ext data member.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

TName & SetName(void)

Select the variant.

TUser & SetUser(void)

Select the variant.

list< CRef< CSeq_id > > TId

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetTopology(TTopology value)

Assign a value to Topology data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

void SetRepr(TRepr value)

Assign a value to Repr data member.

void SetLength(TLength value)

Assign a value to Length data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void SetMol(TMol value)

Assign a value to Mol data member.

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ eMol_na

just a nucleic acid

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

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

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::SIZE size

const struct ncbi::grid::netcache::search::fields::KEY key

string s_Value(TValue value)

const GenericPointer< typename T::ValueType > T2 value

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

#define row(bind, expected)

TObjectIdCache m_ObjectIdMISMATCH

TObjectIdCache m_ObjectIdRefPos

CRef< CUser_object > m_SecondaryIndicator

CRef< CUser_object > m_ReadFilterIndicator[4]

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

DECLARE_VDB_COLUMN_AS(char, HAS_REF_OFFSET)

DECLARE_VDB_COLUMN_AS(bool, REF_ORIENTATION)

DECLARE_VDB_COLUMN_AS_STRING(RAW_READ)

DECLARE_VDB_COLUMN_AS(char, HAS_MISMATCH)

DECLARE_VDB_COLUMN_AS(Uint1, REF_OFFSET_TYPE)

DECLARE_VDB_COLUMN_AS_STRING(MISMATCH)

DECLARE_VDB_COLUMN_AS(int32_t, REF_OFFSET)

DECLARE_VDB_COLUMN_AS(INSDC_coord_zero, REF_POS)

DECLARE_VDB_COLUMN_AS(INSDC_coord_len, SPOT_LEN)

SAlnTableCursor(const CVDBTable &table, bool is_secondary)

DECLARE_VDB_COLUMN_AS(TVDBRowId, MATE_ALIGN_ID)

DECLARE_VDB_COLUMN_AS_STRING(MISMATCH_READ)

DECLARE_VDB_COLUMN_AS(INSDC_coord_len, REF_LEN)

DECLARE_VDB_COLUMN_AS_STRING(REF_SEQ_ID)

DECLARE_VDB_COLUMN_AS_STRING(CIGAR_SHORT)

DECLARE_VDB_COLUMN_AS_STRING(CIGAR_LONG)

DECLARE_VDB_COLUMN_AS_STRING(NAME)

DECLARE_VDB_COLUMN_AS_STRING(REF_NAME)

DECLARE_VDB_COLUMN_AS(INSDC_read_filter, READ_FILTER)

DECLARE_VDB_COLUMN_AS_STRING(SPOT_GROUP)

DECLARE_VDB_COLUMN_AS(INSDC_coord_one, SEQ_READ_ID)

DECLARE_VDB_COLUMN_AS(INSDC_quality_phred, QUALITY)

DECLARE_VDB_COLUMN_AS(int32_t, MAPQ)

DECLARE_VDB_COLUMN_AS(TVDBRowId, SEQ_SPOT_ID)

DECLARE_VDB_COLUMN_AS_STRING(SEQ_ID)

DECLARE_VDB_COLUMN_AS(Uint1, CGRAPH_HIGH)

DECLARE_VDB_COLUMN_AS(row_range_t, NAME_RANGE)

SRefTableCursor(const CVDBTable &table)

DECLARE_VDB_COLUMN_AS_STRING(READ)

DECLARE_VDB_COLUMN_AS(TVDBRowId, SECONDARY_ALIGNMENT_IDS)

DECLARE_VDB_COLUMN_AS(INSDC_coord_len, SEQ_LEN)

DECLARE_VDB_COLUMN_AS(INSDC_coord_zero, OVERLAP_REF_POS)

DECLARE_VDB_COLUMN_AS(bool, CIRCULAR)

DECLARE_VDB_COLUMN_AS_STRING(NAME)

pair< TVDBRowId, TVDBRowId > row_range_t

DECLARE_VDB_COLUMN_AS(INSDC_coord_len, MAX_SEQ_LEN)

DECLARE_VDB_COLUMN_AS(TVDBRowId, PRIMARY_ALIGNMENT_IDS)

DECLARE_VDB_COLUMN_AS_STRING(READ)

DECLARE_VDB_COLUMN_AS(INSDC_coord_zero, TRIM_START)

DECLARE_VDB_COLUMN_AS(INSDC_coord_len, READ_LEN)

DECLARE_VDB_COLUMN_AS(INSDC_coord_zero, READ_START)

DECLARE_VDB_COLUMN_AS_STRING(NAME)

DECLARE_VDB_COLUMN_AS(TVDBRowId, PRIMARY_ALIGNMENT_ID)

DECLARE_VDB_COLUMN_AS(INSDC_quality_phred, QUALITY)

DECLARE_VDB_COLUMN_AS(INSDC_coord_len, TRIM_LEN)

DECLARE_VDB_COLUMN_AS(INSDC_read_filter, READ_FILTER)

DECLARE_VDB_COLUMN_AS_STRING(SPOT_GROUP)

DECLARE_VDB_COLUMN_AS(INSDC_read_type, READ_TYPE)

SSeqTableCursor(const CVDBTable &table, bool is_CSRA)

#define INIT_VDB_COLUMN(name)

#define INIT_OPTIONAL_VDB_COLUMN_BACKUP(name, backup_name)

#define INIT_VDB_COLUMN_BACKUP(name, backup_name)

pair< TVDBRowId, TVDBRowCount > TVDBRowIdRange

#define INIT_OPTIONAL_VDB_COLUMN(name)

#define INIT_CONDITIONAL_VDB_COLUMN(name, condition)

uint8_t INSDC_quality_phred

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