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Public Member Functions | Private Member Functions | Private Attributes

BedIntersectPE Class Reference

Collaboration diagram for BedIntersectPE:
Collaboration graph
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List of all members.

Public Member Functions

 BedIntersectPE (string bedAFilePE, string bedBFile, float overlapFraction, string searchType, bool forceStrand, bool bamInput, bool bamOutput, bool uncompressedBam, bool useEditDistance)
void DetermineBedPEInput ()
bool FindOneOrMoreOverlaps (const BEDPE &, const string &type)
bool FindOneOrMoreSpanningOverlaps (const BEDPE &a, const string &type)
void FindOverlaps (const BEDPE &, vector< BED > &hits1, vector< BED > &hits2, const string &type)
void FindSpanningOverlaps (const BEDPE &a, vector< BED > &hits, const string &type)
void IntersectBamPE (string bamFile)
void IntersectBedPE ()

Private Member Functions

void ConvertBamToBedPE (const BamAlignment &bam1, const BamAlignment &bam2, const RefVector &refs, BEDPE &a)
void ProcessBamBlock (const BamAlignment &bam1, const BamAlignment &bam2, const RefVector &refs, BamWriter &writer)

Private Attributes

bool _bamInput
bool _bamOutput
BedFilePE_bedA
string _bedAFilePE
BedFile_bedB
string _bedBFile
bool _forceStrand
bool _isUncompressedBam
float _overlapFraction
string _searchType
bool _useEditDistance

Detailed Description

Definition at line 40 of file pairToBed.h.


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

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