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Public Member Functions | Public Attributes | Private Member Functions | Private Attributes

BedFile Class Reference

Collaboration diagram for BedFile:
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List of all members.

Public Member Functions

 BedFile (string &)
void Close (void)
void countHits (const BED &a, bool forceStrand)
void countListHits (const BED &a, int index, bool forceStrand)
void countSplitHits (const vector< BED > &bedBlock, bool forceStrand)
bool FindOneOrMoreOverlapsPerBin (string chrom, CHRPOS start, CHRPOS end, string strand, bool forceStrand, float overlapFraction=0.0)
bool FindOneOrMoreReciprocalOverlapsPerBin (string chrom, CHRPOS start, CHRPOS end, string strand, bool forceStrand, float overlapFraction=0.0)
void FindOverlapsPerBin (string chrom, CHRPOS start, CHRPOS end, string strand, vector< BED > &hits, bool forceStrand)
BedLineStatus GetNextBed (BED &bed, int &lineNum)
void loadBedCovFileIntoMap ()
void loadBedCovListFileIntoMap ()
void loadBedFileIntoMap ()
void loadBedFileIntoMapNoBin ()
void Open (void)
template<typename T >
void reportBedNewLine (const T &bed)
template<typename T >
void reportBedRangeNewLine (const T &bed, CHRPOS start, CHRPOS end)
template<typename T >
void reportBedRangeTab (const T &bed, CHRPOS start, CHRPOS end)
template<typename T >
void reportBedTab (const T &bed)
void reportNullBedNewLine ()
void reportNullBedTab ()

Public Attributes

masterBedCovListMap bedCovListMap
masterBedCovMap bedCovMap
string bedFile
masterBedMap bedMap
masterBedMapNoBin bedMapNoBin
unsigned int bedType
bool isZeroBased

Private Member Functions

template<typename T >
bool parseBedLine (T &bed, const vector< string > &lineVector, int lineNum, unsigned int numFields)
template<typename T >
bool parseGffLine (T &bed, const vector< string > &lineVector, int lineNum, unsigned int numFields)
template<typename T >
BedLineStatus parseLine (T &bed, const vector< string > &lineVector, int &lineNum)
template<typename T >
bool parseVcfLine (T &bed, const vector< string > &lineVector, int lineNum, unsigned int numFields)
void setBedType (int colNums)
void setFileType (FileType type)
void setGff (bool isGff)
void setVcf (bool isVcf)
void setZeroBased (bool zeroBased)

Private Attributes

istream * _bedStream
FileType _fileType
bool _isGff
bool _isVcf
bool _typeIsKnown

Detailed Description

Definition at line 392 of file bedFile.h.


The documentation for this class was generated from the following files:

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