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Public Types | Public Member Functions | Public Attributes

BamTools::BamReader::BamReaderPrivate Struct Reference

Collaboration diagram for BamTools::BamReader::BamReaderPrivate:
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List of all members.

Public Types

enum  RegionState { BEFORE_REGION = 0, WITHIN_REGION, AFTER_REGION }

Public Member Functions

 BamReaderPrivate (BamReader *parent)
bool BuildCharData (BamAlignment &bAlignment)
void ClearIndex (void)
void Close (void)
bool CreateIndex (bool useDefaultIndex)
bool GetNextAlignment (BamAlignment &bAlignment)
bool GetNextAlignmentCore (BamAlignment &bAlignment)
int GetReferenceID (const string &refName) const
RegionState IsOverlap (BamAlignment &bAlignment)
bool Jump (int refID, int position=0)
void LoadHeaderData (void)
bool LoadIndex (void)
bool LoadNextAlignment (BamAlignment &bAlignment)
void LoadReferenceData (void)
bool Open (const string &filename, const string &indexFilename="")
bool Rewind (void)
bool SetRegion (const BamRegion &region)

Public Attributes

int64_t AlignmentsBeginOffset
const char * CIGAR_LOOKUP
int CurrentLeft
int CurrentRefID
const char * DNA_LOOKUP
string Filename
string HeaderText
string IndexFilename
bool IsBigEndian
bool IsIndexLoaded
bool IsLeftBoundSpecified
bool IsRegionSpecified
bool IsRightBoundSpecified
BgzfData mBGZF
BamIndexNewIndex
BamReaderParent
RefVector References
BamRegion Region

Detailed Description

Definition at line 28 of file BamReader.cpp.


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

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