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NCBI C++ ToolKit: include/objtools/format/sam_formatter.hpp Source File

fSAM_AlignmentScore = 1 << 0,

fSAM_ExpectationValue = 1 << 1,

fSAM_NumNucDiff = 1 << 2,

fSAM_PercentageIdentity = 1 << 3,

fSAM_BitScore = 1 << 4,

fSAM_PlainSeqIds = 1 << 5,

fSAM_SeqData = 1 << 6,

fSAM_ForceGISeqIds = 1 << 7,

fSAM_Default = fSAM_AlignmentScore |

fSAM_ExpectationValue |

fSAM_PercentageIdentity |

: m_Id(id), m_Version(ver), m_CmdLine(

) {}

m_SO_Value = so_value;

m_GO_Value = go_value;

x_PrintSOTag(

)

;

x_PrintGOTag(

)

;

list<pair<CSeq_id_Handle, string> >

;

static CRef< CScope > m_Scope

void Print(const CCompactSAMApplication::AlignInfo &ai)

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

main entry point for tests

void UnsetFlag(EFlags flag)

void SetGroupOrder(EGroupOrder go, const string &go_value=kEmptyStr)

Set GO tag value.

string m_Id

ID - program id.

string m_CmdLine

CL - command line.

SProgramInfo(const string &id=kEmptyStr, const string &ver=kEmptyStr, const string &cmd=kEmptyStr)

void SetOutputStream(CNcbiOstream &out)

list< pair< CSeq_id_Handle, string > > TData

string m_Name

PN - program name.

void SetFlags(TFlags flags)

int TFlags

bitwise OR of EFlags

SProgramInfo & SetProgram(void)

const SProgramInfo & GetProgram(void) const

void SetScope(CScope &scope)

void SetProgram(const SProgramInfo &pg)

string m_Version

VN - version.

void SetFlag(EFlags flag)

void SetSortOrder(ESortOrder so, const string &so_value=kEmptyStr)

Set SO tag value.

string m_Desc

DS - description.

SProgramInfo m_ProgramInfo

@ eSO_Skip

Do not print SO tag (default)

@ eSO_Unsorted

SO:unsorted.

@ eSO_QueryName

SO:queryname.

@ eSO_Coordinate

SO:coordinate.

@ eGO_Reference

GO:reference.

@ eGO_Query

GO:query (default)

@ eGO_Skip

Do not print GO tag.

void Reset(void)

Reset reference object.

#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.

#define NCBI_FORMAT_EXPORT

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

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