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Public Member Functions | Private Member Functions | Private Attributes

BedGenomeCoverage Class Reference

Collaboration diagram for BedGenomeCoverage:
Collaboration graph

List of all members.

Public Member Functions

 BedGenomeCoverage (string bedFile, string genomeFile, bool eachBase, bool startSites, bool bedGraph, bool bedGraphAll, int max, bool bamInput, bool obeySplits, bool filterByStrand, string requestedStrand)

Private Member Functions

void AddBlockedCoverage (const vector< BED > &bedBlocks)
void AddCoverage (int start, int end)
void CoverageBam (string bamFile)
void CoverageBed ()
void PrintFinalCoverage ()
void ReportChromCoverage (const vector< DEPTH > &, const int &chromSize, const string &chrom, chromHistMap &)
void ReportChromCoverageBedGraph (const vector< DEPTH > &chromCov, const int &chromSize, const string &chrom)
void ReportGenomeCoverage (chromHistMap &chromDepthHist)
void ResetChromCoverage ()
void StartNewChrom (const string &chrom)

Private Attributes

bool _bamInput
string _bedFile
bool _bedGraph
bool _bedGraphAll
chromDepthMap _chromCov
vector< DEPTH_currChromCoverage
chromHistMap _currChromDepthHist
string _currChromName
int _currChromSize
bool _eachBase
bool _filterByStrand
string _genomeFile
int _max
bool _obeySplits
string _requestedStrand
bool _startSites
set< string > _visitedChromosomes

Detailed Description

Definition at line 39 of file genomeCoverageBed.h.

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

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