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NCBI C++ ToolKit: src/objtools/format/sam_formatter.cpp Source File

StartAlignment(

);

AddRow(

& cigar);

fRead_Default = 0x0000,

fRead_Reverse = 0x0010

x_GetRefIdString(

)

;

x_GetTargetIdString(

)

;

.GetSeqIdString(

) :

.AsFastaString();

( !scope)

;

(seg_type !=

) {

clip_front, clip_back;

seq_data =

;

(!(*score)->IsSetId() || !(*score)->GetId().IsStr())

;

&

= (*score)->GetId().GetStr();

(AS.empty() &&

==

) {

(EV.empty() &&

==

) {

(BS.empty() &&

==

) {

(

.empty() &&

==

) {

=

(99.99, 100.0 * ((

)ni)/((

)

));

clip_front + cigar + clip_back +

+

AS + EV + NM +

+ BS

disc.

().SetDisc().Assign(aln_set);

(disc, query_id);

disc.

().SetDisc().Assign(aln_set);

(disc, query_row);

*

<<

;

*

<<

;

*

<<

;

*

<<

;

*

<<

;

*

<<

;

( !

)

;

*

<<

;

*

<< it->second <<

;

*

<< *it <<

;

(it->first ==

)

;

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

Base class for CIGAR formatters.

The base class for alignment formatters which use CIGAR format.

virtual void AddRow(const string &cigar)

set< CBioseq_Handle > m_KnownRefSeqs

virtual ~CSAM_CIGAR_Formatter(void)

string x_GetSeqIdString(const CSeq_id &id, TFlags flags) const

virtual void AdjustSeqIdType(CConstRef< CSeq_id > &id)

virtual void AddSegment(CNcbiOstream &cigar, char seg_type, TSeqPos seg_len)

CSAM_Formatter::CSAM_Headers THeaders

CSAM_Formatter::TLines TLines

virtual void StartRow(void)

string x_GetTargetIdString(void) const

CSAM_CIGAR_Formatter(THeaders &headers, TLines &body, const CSeq_align &aln, CScope &scope, TFlags flags)

string x_GetRefIdString(void) const

CSAM_Formatter::TFlags TFlags

virtual void StartAlignment(void)

TSeqPos GetAlignLength(bool include_gaps=true) const

Get the length of this alignment.

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

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

main entry point for tests

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

string m_Id

ID - program id.

CScope * GetScope(void) const

CSAM_Formatter(CNcbiOstream &out, CScope &scope, TFlags flags=fSAM_Default)

string m_CmdLine

CL - command line.

const TRange & GetTargetRange(void) const

list< pair< CSeq_id_Handle, string > > TData

void x_PrintGOTag(void) const

string m_Name

PN - program name.

int TFlags

bitwise OR of EFlags

int GetTargetSign(void) const

const TRange & GetRefRange(void) const

int GetRefSign(void) const

const CSeq_align & GetCurrentSeq_align(void) const

void x_PrintSOTag(void) const

void AddSequence(CSeq_id_Handle id, const string &line)

void FormatByTargetId(const CSeq_id &target_id)

const CSeq_id & GetRefId(void) const

string m_Version

VN - version.

CSAM_Formatter & Print(const CSeq_align &aln, const CSeq_id &query_id)

virtual void AddSegment(ostream &cigar, char seg_type, TSeqPos seg_len)

string m_Desc

DS - description.

void FormatByTargetRow(TNumrow target_row)

SProgramInfo m_ProgramInfo

const CSeq_id & GetTargetId(void) const

@ eSO_Unsorted

SO:unsorted.

@ eSO_QueryName

SO:queryname.

@ eSO_Coordinate

SO:coordinate.

@ eSO_User

User-provided string.

@ eGO_Reference

GO:reference.

@ eGO_User

User-provided string.

@ eGO_Query

GO:query (default)

@ fSAM_NumNucDiff

Generate NM tags.

@ fSAM_PercentageIdentity

Generate PI tags.

@ fSAM_SeqData

Print sequence data.

@ fSAM_ExpectationValue

Generate EV tags.

@ fSAM_AlignmentScore

Generate AS tags.

@ fSAM_ForceGISeqIds

Force using GI ids.

@ fSAM_PlainSeqIds

Drop type prefix in seq-ids.

@ fSAM_BitScore

Generate BS tags.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

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,...

@ eGetId_ForceAcc

return only an accession based seq-id

@ eGetId_ForceGi

return only a gi-based seq-id

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

position_type GetLength(void) const

position_type GetToOpen(void) const

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static string UInt8ToString(Uint8 value, TNumToStringFlags flags=0, int base=10)

Convert UInt8 to string.

TFrom GetFrom(void) const

Get the From member data.

vector< CRef< CScore > > TScore

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetType(TType value)

Assign a value to Type data member.

TInt GetInt(void) const

Get the variant data.

bool IsInt(void) const

Check if variant Int is selected.

const TValue & GetValue(void) const

Get the Value member data.

bool IsSetScore(void) const

for whole alignment Check if a value has been assigned to Score data member.

const TScore & GetScore(void) const

Get the Score member data.

TReal GetReal(void) const

Get the variant data.

@ eType_disc

discontinuous alignment

unsigned int

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

double value_type

The numeric datatype used by the parser.

static double GetFloatScore(const CScore &score)

static int GetIntScore(const CScore &score)

Flat formatter for Sequence Alignment/Map (SAM).

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