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BamTools::BamAlignment Struct Reference

Collaboration diagram for BamTools::BamAlignment:
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List of all members.

Classes

struct  BamAlignmentSupportData

Public Member Functions

bool AddTag (const std::string &tag, const std::string &type, const std::string &value)
bool AddTag (const std::string &tag, const std::string &type, const uint32_t &value)
bool AddTag (const std::string &tag, const std::string &type, const int32_t &value)
bool AddTag (const std::string &tag, const std::string &type, const float &value)
 BamAlignment (const BamAlignment &other)
bool EditTag (const std::string &tag, const std::string &type, const int32_t &value)
bool EditTag (const std::string &tag, const std::string &type, const float &value)
bool EditTag (const std::string &tag, const std::string &type, const std::string &value)
bool EditTag (const std::string &tag, const std::string &type, const uint32_t &value)
bool GetEditDistance (uint32_t &editDistance) const
int GetEndPosition (bool usePadded=false) const
bool GetReadGroup (std::string &readGroup) const
bool GetTag (const std::string &tag, std::string &destination) const
bool GetTag (const std::string &tag, uint32_t &destination) const
bool GetTag (const std::string &tag, int32_t &destination) const
bool GetTag (const std::string &tag, float &destination) const
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 RemoveTag (const std::string &tag)
void SetIsDuplicate (bool ok)
void SetIsFailedQC (bool ok)
void SetIsFirstMate (bool ok)
void SetIsMateReverseStrand (bool ok)
void SetIsMateUnmapped (bool ok)
void SetIsPaired (bool ok)
void SetIsProperPair (bool ok)
void SetIsReverseStrand (bool ok)
void SetIsSecondaryAlignment (bool ok)
void SetIsSecondMate (bool ok)
void SetIsUnmapped (bool ok)

Public Attributes

std::string AlignedBases
uint32_t AlignmentFlag
uint16_t Bin
std::vector< CigarOpCigarData
int32_t InsertSize
int32_t Length
uint16_t MapQuality
int32_t MatePosition
int32_t MateRefID
std::string Name
int32_t Position
std::string Qualities
std::string QueryBases
int32_t RefID
BamAlignmentSupportData SupportData
std::string TagData

Private 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
}

Static Private Member Functions

static bool FindTag (const std::string &tag, char *&pTagData, const unsigned int &tagDataLength, unsigned int &numBytesParsed)
static bool SkipToNextTag (const char storageType, char *&pTagData, unsigned int &numBytesParsed)

Friends

class BamReader
class BamWriter

Detailed Description

Definition at line 68 of file BamAux.h.


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

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