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BamTools::BamReader::BamReaderPrivate Struct Reference

Detailed description

Definition at line 26 of file BamReader.cpp.

Public Methods

 BamReaderPrivate (void)
 ~BamReaderPrivate (void)
void Close (void)
bool Jump (int refID, int position=0)
void Open (const string &filename, const string &indexFilename="")
bool Rewind (void)
bool GetNextAlignment (BamAlignment &bAlignment)
const string GetHeaderText (void) const
const int GetReferenceCount (void) const
const RefVector GetReferenceData (void) const
const int GetReferenceID (const string &refName) const
bool CreateIndex (void)
int BinsFromRegion (int refID, int left, uint16_t[MAX_BIN])
int CalculateAlignmentEnd (const int &position, const std::vector< CigarOp > &cigarData)
int64_t GetOffset (int refID, int left)
bool IsOverlap (BamAlignment &bAlignment)
void LoadHeaderData (void)
bool LoadNextAlignment (BamAlignment &bAlignment)
void LoadReferenceData (void)
bool BuildIndex (void)
void ClearIndex (void)
void InsertBinEntry (BamBinMap &binMap, const uint32_t &saveBin, const uint64_t &saveOffset, const uint64_t &lastOffset)
void InsertLinearOffset (LinearOffsetVector &offsets, const BamAlignment &bAlignment, const uint64_t &lastOffset)
bool LoadIndex (void)
void MergeChunks (void)
void Roundup32 (int &value)
bool WriteIndex (void)

Public Members

BgzfData mBGZF
string HeaderText
BamIndex Index
RefVector References
bool IsIndexLoaded
int64_t AlignmentsBeginOffset
string Filename
string IndexFilename
bool IsRegionSpecified
int CurrentRefID
int CurrentLeft
const char * DNA_LOOKUP
const char * CIGAR_LOOKUP

Constructor & Destructor Documentation

BamTools::BamReader::BamReaderPrivate::BamReaderPrivate ( void  )

Definition at line 158 of file BamReader.cpp.

BamTools::BamReader::BamReaderPrivate::~BamReaderPrivate ( void  )

Definition at line 169 of file BamReader.cpp.

Member Function Documentation

int BamTools::BamReader::BamReaderPrivate::BinsFromRegion ( int  refID,
int  left,
uint16_t  list[MAX_BIN] 

Definition at line 174 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::BuildIndex ( void  )

Definition at line 197 of file BamReader.cpp.

int BamTools::BamReader::BamReaderPrivate::CalculateAlignmentEnd ( const int &  position,
const std::vector< CigarOp > &  cigarData 

Definition at line 327 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::ClearIndex ( void  )

Definition at line 346 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::Close ( void  )

Definition at line 351 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::CreateIndex ( void  )

Definition at line 359 of file BamReader.cpp.

const string BamTools::BamReader::BamReaderPrivate::GetHeaderText ( void  ) const
bool BamTools::BamReader::BamReaderPrivate::GetNextAlignment ( BamAlignment bAlignment)

Definition at line 389 of file BamReader.cpp.

int64_t BamTools::BamReader::BamReaderPrivate::GetOffset ( int  refID,
int  left 

Definition at line 412 of file BamReader.cpp.

const int BamTools::BamReader::BamReaderPrivate::GetReferenceCount ( void  ) const
const RefVector BamTools::BamReader::BamReaderPrivate::GetReferenceData ( void  ) const
const int BamTools::BamReader::BamReaderPrivate::GetReferenceID ( const string &  refName) const

Definition at line 374 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::InsertBinEntry ( BamBinMap binMap,
const uint32_t saveBin,
const uint64_t saveOffset,
const uint64_t lastOffset 

Definition at line 457 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::InsertLinearOffset ( LinearOffsetVector offsets,
const BamAlignment bAlignment,
const uint64_t lastOffset 

Definition at line 483 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::IsOverlap ( BamAlignment bAlignment)

Definition at line 508 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::Jump ( int  refID,
int  position = 0 

Definition at line 521 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::LoadHeaderData ( void  )

Definition at line 546 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::LoadIndex ( void  )

Definition at line 574 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::LoadNextAlignment ( BamAlignment bAlignment)

Definition at line 686 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::LoadReferenceData ( void  )

Definition at line 819 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::MergeChunks ( void  )

Definition at line 853 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::Open ( const string &  filename,
const string &  indexFilename = "" 

Definition at line 910 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::Rewind ( void  )

Definition at line 930 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::Roundup32 ( int &  value)

Definition at line 949 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::WriteIndex ( void  )

Definition at line 960 of file BamReader.cpp.

Member Data Documentation

int64_t BamTools::BamReader::BamReaderPrivate::AlignmentsBeginOffset

Definition at line 38 of file BamReader.cpp.

const char* BamTools::BamReader::BamReaderPrivate::CIGAR_LOOKUP

Definition at line 49 of file BamReader.cpp.

int BamTools::BamReader::BamReaderPrivate::CurrentLeft

Definition at line 45 of file BamReader.cpp.

int BamTools::BamReader::BamReaderPrivate::CurrentRefID

Definition at line 44 of file BamReader.cpp.

const char* BamTools::BamReader::BamReaderPrivate::DNA_LOOKUP

Definition at line 48 of file BamReader.cpp.

string BamTools::BamReader::BamReaderPrivate::Filename

Definition at line 39 of file BamReader.cpp.

string BamTools::BamReader::BamReaderPrivate::HeaderText

Definition at line 34 of file BamReader.cpp.

BamIndex BamTools::BamReader::BamReaderPrivate::Index

Definition at line 35 of file BamReader.cpp.

string BamTools::BamReader::BamReaderPrivate::IndexFilename

Definition at line 40 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::IsIndexLoaded

Definition at line 37 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::IsRegionSpecified

Definition at line 43 of file BamReader.cpp.

BgzfData BamTools::BamReader::BamReaderPrivate::mBGZF

Definition at line 33 of file BamReader.cpp.

RefVector BamTools::BamReader::BamReaderPrivate::References

Definition at line 36 of file BamReader.cpp.

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