Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bamread_8hpp_source.html below:

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

AlignAccessMgr;

AlignAccessRefSeqEnumerator;

AlignAccessAlignmentEnumerator;

(

& rep_path,

& vol_path);

GetDefaultRepPath(

);

GetDefaultVolPath(

);

AddRepPath(

& rep_path);

AddVolPath(

& vol_path);

FindAccPath(

& acc, EMissing mising);

FindAccPath(acc, eMissing_Throw);

FindAccPath(acc, eMissing_Empty);

m_AlignAccessMgr;

& db_name,

EUseAPI use_api = eUseDefaultAPI);

& db_name,

& idx_name,

EUseAPI use_api = eUseDefaultAPI);

UseRawIndex(

use_api);

m_IdMapper.reset(idmapper, ownership);

m_IdMapper.get();

.size() == 2 &&

[0] == name[0] &&

[1] == name[1];

m_IncludedAlignTags;

GetShortSeq_id(

&

,

external =

)

;

GetRefSeqLength(

&

)

;

GetHeaderText(

)

;

SPileupValues;

m_IntronMode != eNoCountIntron;

cc_acgt.

()->cc;

( m_SplitACGTLen <

) {

cc_split_acgt[k].

();

cc_match.

();

cc_gap.

();

cc_intron.

();

( ; pos < end; ++pos ) {

( callback && ref_pos >= m_RefFrom+FLUSH_SIZE && 2*ref_pos >= m_RefFrom+m_RefToOpen ) {

advance_current_beg(ref_pos, callback);

( ref_end <= m_RefFrom ) {

( ref_pos < m_RefFrom ) {

( ref_end > m_RefStop ) {

( ref_end > m_RefToOpen ) {

advance_current_end(ref_end);

( ref_end <= m_RefFrom ) {

( ref_pos < m_RefFrom ) {

read_pos += m_RefFrom - ref_pos;

( ref_end > m_RefStop ) {

( ref_end > m_RefToOpen ) {

advance_current_end(ref_end);

( trim_ref_range(ref_pos, ref_end) ) {

add_match_graph_range(ref_pos - m_RefFrom,

ref_end - m_RefFrom);

( trim_ref_range(ref_pos, ref_end) ) {

add_gap_graph_range(ref_pos - m_RefFrom,

ref_end - m_RefFrom);

( count_introns() && trim_ref_range(ref_pos, ref_end) ) {

add_intron_graph_range(ref_pos - m_RefFrom,

ref_end - m_RefFrom);

( trim_ref_range(ref_pos, ref_end, read_pos) ) {

add_bases_graph_range(ref_pos - m_RefFrom,

( trim_ref_range(ref_pos, ref_end, read_pos) ) {

add_bases_graph_range_raw(ref_pos - m_RefFrom,

max_count[

];

& ref_id,

(

& mgr,

& db_name,

& idx_name);

: m_Size(0), m_Capacity(0)

(

* p = m_Buffer.get() ) {

( capacity() < min_capacity ) {

x_reserve(min_capacity);

m_Buffer.get();

m_Buffer[pos];

m_Buffer.get();

x_reserve(

min_capacity);

.write(

.data(),

.size());

m_DB->GetIdMapper();

(*TGetString)(

AlignAccessRefSeqEnumerator *

,

*

,

bsize,

*

);

x_AllocBuffers(

);

x_InvalidateBuffers(

);

x_CheckValid(

)

;

*

, TGetString func)

;

:

<const BAMAlignment>

GetRefSeqIndex(

)

;

GetFlags(

)

;

* file_pos =

);

& ref_id,

ESearchMode search_mode = eSearchByOverlap,

* file_pos =

);

& ref_id,

ESearchMode search_mode = eSearchByOverlap,

* file_pos =

);

m_DB->GetIdMapper();

m_SpotIdDetector = spot_id_detector;

m_SpotIdDetector.GetNCPointerOrNull();

m_RawImpl? &m_RawImpl.GetNCObject().m_Iter: 0;

GetRefSeqIndex(

)

;

GetRefSeqPos(

)

;

GetNextRefSeqIndex()

;

GetNextRefSeqPos()

;

GetShortSequenceLength(

)

;

GetCIGARPos(

)

;

GetCIGARRefSize(

)

;

GetCIGARShortSize(

)

;

GetRawCIGAROpsCount()

;

GetRawCIGAR(vector<Uint4>& raw_cigar)

;

IsSetStrand(

)

;

GetMapQuality(

)

;

IsPaired(

)

;

IsFirstInPair(

)

;

IsSecondInPair(

)

;

IsSecondary(

)

;

GetFlags(

)

;

(*TGetString)(

AlignAccessAlignmentEnumerator *

,

*

,

bsize,

*

);

(*TGetString2)(

AlignAccessAlignmentEnumerator *

,

*

,

bsize,

*

);

x_CheckValid(

)

;

*

, TGetString func)

;

*

, TGetString2 func)

;

x_GetCIGAR(

)

;

x_HasAmbiguousMatch()

;

x_GetStrand(

)

;

AlignAccessAlignmentEnumerator* ptr);

x_InvalidateBuffers();

x_HasAmbiguousMatch()

;

* file_pos =

);

& ref_label,

* file_pos =

);

& ref_label,

* file_pos =

);

x_InvalidateBuffers();

eStrand_not_read = -2,

->m_Iter.GetCIGAROpsCount();

->m_Iter.GetCIGAROp(index);

CNcbiOstream & operator<<(CNcbiOstream &out, const CBamString &str)

SPECIALIZE_BAM_REF_TRAITS(AlignAccessMgr, const)

ISpotIdDetector interface is used to detect spot id in case of incorrect flag combination.

virtual void AddSpotId(string &short_id, const CBamAlignIterator *iter)=0

ISpotIdDetector * GetSpotIdDetector(void) const

CIRef< ISpotIdDetector > m_SpotIdDetector

CRef< CSeq_annot > GetSeq_annot(void) const

AutoPtr< SCreateCache > m_CreateCache

DECLARE_OPERATOR_BOOL(m_AADBImpl||m_RawImpl)

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

CRef< SRawImpl > m_RawImpl

Uint2 GetRawCIGAROpsCount() const

CRef< CObject_id > TObjectIdCache

void x_MapId(CSeq_id &id) const

CBamRawAlignIterator * GetRawIndexIteratorPtr() const

IIdMapper * GetIdMapper(void) const

void SetSpotIdDetector(ISpotIdDetector *spot_id_detector)

EBamFlagsAvailability m_BamFlagsAvailability

CRef< CSeq_id > m_ShortSeq_id

bool UsesRawIndex() const

CRef< SAADBImpl > m_AADBImpl

bool UsesAlignAccessDB() const

Uint4 GetRawCIGAROp(Uint2 index) const

CRef< CSeq_id > m_RefSeq_id

CRef< CSeq_entry > GetMatchEntry(void) const

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

virtual void AddValuesTail(TSeqPos count, const SPileupValues &values)=0

virtual ~ICollectPileupCallback()

virtual void AddZerosBy16(TSeqPos count)=0

virtual bool AcceptAlign(const CBamAlignIterator &ait)

virtual void AddValuesBy16(TSeqPos count, const SPileupValues &values)=0

AutoPtr< TRefSeqLengths > m_RefSeqLengths

DECLARE_OPERATOR_BOOL(m_AADB||m_RawDB)

bool UsesAlignAccessDB() const

size_t CollectPileup(SPileupValues &values, const string &ref_id, CRange< TSeqPos > graph_range, ICollectPileupCallback *callback=0, SPileupValues::EIntronMode intron_mode=SPileupValues::eNoCountIntron, TSeqPos gap_to_intron_threshold=kInvalidSeqPos) const

bool UsesRawIndex() const

TTagList m_IncludedAlignTags

AutoPtr< IIdMapper > m_IdMapper

void SetIdMapper(IIdMapper *idmapper, EOwnership ownership)

const string & GetDbName(void) const

vector< STagInfo > TTagList

unordered_map< string, CRef< CSeq_id > > TRefSeqIds

AutoPtr< TRefSeqIds > m_RefSeqIds

IIdMapper * GetIdMapper(void) const

const TTagList & GetIncludedAlignTags() const

const string & GetIndexName(void) const

CRef< CObjectFor< CBamRawDb > > m_RawDB

unordered_map< string, TSeqPos > TRefSeqLengths

const CBamRef< const AlignAccessMgr > & GetAlignAccessMgr() const

const CBamVFSManager & GetVFSManager() const

CBamRef< const AlignAccessMgr > m_AlignAccessMgr

CRef< CObjectFor< CBamRawDb > > m_RawDB

DECLARE_OPERATOR_BOOL(m_AADBImpl||m_RawDB)

CRef< CSeq_id > m_CachedRefSeq_id

IIdMapper * GetIdMapper(void) const

CRef< SAADBImpl > m_AADBImpl

void reserve(size_t min_capacity)

char operator[](size_t pos) const

void operator=(const CBamString &)

AutoArray< char > m_Buffer

const char * data() const

CBamString(const CBamString &)

Reallocable memory buffer (no memory copy overhead) Mimics vector<>, without the overhead of explicit...

const value_type * data() const

@ eBadFormat

Invalid SRZ accession format.

NCBI_EXCEPTION_DEFAULT(CSrzException, CException)

vector< string > m_VolPath

vector< string > m_RepPath

string FindAccPathNoThrow(const string &acc)

string FindAccPath(const string &acc)

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.

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

main entry point for tests

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

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

CException & operator=(const CException &)

Private assignment operator to prohibit assignment.

virtual void x_Init(const CDiagCompileInfo &info, const string &message, const CException *prev_exception, EDiagSev severity)

Helper method for initializing exception data.

EErrCode

Error types that an application can generate.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

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

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

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned integer

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

enum ENcbiOwnership EOwnership

Ownership relations between objects.

#define NCBI_BAMREAD_EXPORT

static const char label[]

ENa_strand

strand of nucleic acid

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

Defines NCBI C++ exception handling.

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

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static int GetDebugLevel()

CConstRef< CBamDb::SAADBImpl > m_DB

CBamRef< AlignAccessAlignmentEnumerator > m_Iter

CBamString m_ShortSequence

CRef< CObjectFor< CBamRawDb > > m_RawDB

CBamString m_ShortSequence

CBamRawAlignIterator m_Iter

CBamRef< const AlignAccessDB > m_DB

void add_match_graph_pos(TSeqPos pos)

TCount get_max_count(int type) const

void add_gap_graph_range(TSeqPos pos, TSeqPos end)

void advance_current_end(TSeqPos ref_end)

void add_gap_ref_range(TSeqPos ref_pos, TSeqPos ref_end)

void add_bases_ref_range_raw(TSeqPos ref_pos, TSeqPos ref_end, const CTempString &read, TSeqPos read_pos)

void add_match_ref_range(TSeqPos ref_pos, TSeqPos ref_end)

void decode_intron(TSeqPos len)

void add_bases_ref_range(TSeqPos ref_pos, TSeqPos ref_end, const CTempString &read, TSeqPos read_pos)

bool trim_ref_range(TSeqPos &ref_pos, TSeqPos &ref_end, TSeqPos &read_pos)

SPileupValues(CRange< TSeqPos > ref_range, EIntronMode intron_mode=eNoCountIntron)

void add_bases_graph_range_raw(TSeqPos pos, TSeqPos end, CTempString read, TSeqPos read_pos)

const TCount * get_intron_counts() const

CSimpleBufferT< TCount > cc_gap

void add_intron_graph_range(TSeqPos pos, TSeqPos end)

void update_max_counts(TSeqPos len)

CSimpleBufferT< TCount > cc_intron

bool trim_ref_range(TSeqPos &ref_pos, TSeqPos &ref_end)

void add_bases_graph_range(TSeqPos pos, TSeqPos end, CTempString read, TSeqPos read_pos)

const TCount * get_match_counts() const

void add_intron_ref_range(TSeqPos ref_pos, TSeqPos ref_end)

CSimpleBufferT< TCount > cc_match

void finalize(ICollectPileupCallback *callback)

CSimpleBufferT< SCountACGT > cc_acgt

void initialize(CRange< TSeqPos > ref_range, EIntronMode intron_mode=eNoCountIntron)

const TCount * get_acgt_counts() const

void add_match_graph_range(TSeqPos pos, TSeqPos end)

void advance_current_beg(TSeqPos ref_pos, ICollectPileupCallback *callback)

const TCount * get_split_acgt_counts(int k, TSeqPos len) const

void decode_gap(TSeqPos len)

void update_current_ref_start(TSeqPos ref_pos, ICollectPileupCallback *callback)

const TCount * get_gap_counts() const

void make_split_acgt(TSeqPos len)

bool count_introns() const

bool operator==(CTempString n) const

CRef< CObject_id > id_cache

CBamString m_RefSeqIdBuffer

CBamRef< AlignAccessRefSeqEnumerator > m_Iter

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4