BamTools::BamAlignment Struct Reference

Detailed description

Definition at line 52 of file BamAux.h.

#include <BamAux.h>

Public Types
enum	{   PAIRED = 1, PROPER_PAIR = 2, UNMAPPED = 4, MATE_UNMAPPED = 8,   REVERSE = 16, MATE_REVERSE = 32, READ_1 = 64, READ_2 = 128,   SECONDARY = 256, QC_FAILED = 512, DUPLICATE = 1024 }

Public Methods
bool	IsDuplicate (void) const
bool	IsFailedQC (void) const
bool	IsFirstMate (void) const
bool	IsMapped (void) const
bool	IsMateMapped (void) const
bool	IsMateReverseStrand (void) const
bool	IsPaired (void) const
bool	IsPrimaryAlignment (void) const
bool	IsProperPair (void) const
bool	IsReverseStrand (void) const
bool	IsSecondMate (void) const
bool	GetReadGroup (std::string &readGroup) const
bool	GetEditDistance (uint8_t &editDistance) const
template<typename T >
bool	GetTag (const char *tagName, T &tagVal) const
const char *	GetTag (const char *tagName) const

Public Members
std::string	Name
int32_t	Length
std::string	QueryBases
std::string	AlignedBases
std::string	Qualities
std::string	TagData
int32_t	RefID
int32_t	Position
uint16_t	Bin
uint16_t	MapQuality
uint32_t	AlignmentFlag
std::vector< CigarOp >	CigarData
std::vector< RefEdit >	DeltaData
int32_t	MateRefID
int32_t	MatePosition
int32_t	InsertSize

Member Enumeration Documentation

anonymous enum

Enumerator
PAIRED
PROPER_PAIR
UNMAPPED
MATE_UNMAPPED
REVERSE
MATE_REVERSE
READ_1
READ_2
SECONDARY
QC_FAILED
DUPLICATE

Definition at line 403 of file BamAux.h.

Member Function Documentation

bool BamTools::BamAlignment::GetEditDistance ( uint8_t &  editDistance) const

inline

Definition at line 98 of file BamAux.h.

bool BamTools::BamAlignment::GetReadGroup ( std::string &  readGroup) const

inline

Definition at line 82 of file BamAux.h.

template<typename T >

bool BamTools::BamAlignment::GetTag ( const char *  tagName, T &  tagVal  ) const

inline

Definition at line 102 of file BamAux.h.

const char* BamTools::BamAlignment::GetTag ( const char *  tagName) const

inline

Definition at line 146 of file BamAux.h.

bool BamTools::BamAlignment::IsDuplicate ( void  ) const

inline

Definition at line 57 of file BamAux.h.

bool BamTools::BamAlignment::IsFailedQC ( void  ) const

inline

Definition at line 59 of file BamAux.h.

bool BamTools::BamAlignment::IsFirstMate ( void  ) const

inline

Definition at line 61 of file BamAux.h.

bool BamTools::BamAlignment::IsMapped ( void  ) const

inline

Definition at line 63 of file BamAux.h.

bool BamTools::BamAlignment::IsMateMapped ( void  ) const

inline

Definition at line 65 of file BamAux.h.

bool BamTools::BamAlignment::IsMateReverseStrand ( void  ) const

inline

Definition at line 67 of file BamAux.h.

bool BamTools::BamAlignment::IsPaired ( void  ) const

inline

Definition at line 69 of file BamAux.h.

bool BamTools::BamAlignment::IsPrimaryAlignment ( void  ) const

inline

Definition at line 71 of file BamAux.h.

bool BamTools::BamAlignment::IsProperPair ( void  ) const

inline

Definition at line 73 of file BamAux.h.

bool BamTools::BamAlignment::IsReverseStrand ( void  ) const

inline

Definition at line 75 of file BamAux.h.

bool BamTools::BamAlignment::IsSecondMate ( void  ) const

inline

Definition at line 77 of file BamAux.h.

Member Data Documentation

std::string BamTools::BamAlignment::AlignedBases

Definition at line 388 of file BamAux.h.

uint32_t BamTools::BamAlignment::AlignmentFlag

Definition at line 395 of file BamAux.h.

uint16_t BamTools::BamAlignment::Bin

Definition at line 393 of file BamAux.h.

std::vector<CigarOp> BamTools::BamAlignment::CigarData

Definition at line 396 of file BamAux.h.

std::vector<RefEdit> BamTools::BamAlignment::DeltaData

Definition at line 397 of file BamAux.h.

int32_t BamTools::BamAlignment::InsertSize

Definition at line 400 of file BamAux.h.

int32_t BamTools::BamAlignment::Length

Definition at line 386 of file BamAux.h.

uint16_t BamTools::BamAlignment::MapQuality

Definition at line 394 of file BamAux.h.

int32_t BamTools::BamAlignment::MatePosition

Definition at line 399 of file BamAux.h.

int32_t BamTools::BamAlignment::MateRefID

Definition at line 398 of file BamAux.h.

std::string BamTools::BamAlignment::Name

Definition at line 385 of file BamAux.h.

int32_t BamTools::BamAlignment::Position

Definition at line 392 of file BamAux.h.

std::string BamTools::BamAlignment::Qualities

Definition at line 389 of file BamAux.h.

std::string BamTools::BamAlignment::QueryBases

Definition at line 387 of file BamAux.h.

int32_t BamTools::BamAlignment::RefID

Definition at line 391 of file BamAux.h.

std::string BamTools::BamAlignment::TagData

Definition at line 390 of file BamAux.h.

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The documentation for this struct was generated from the following file:

• E:/git/nvbio/contrib/bamtools/BamAux.h