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Viewing changes to src/multiBamCov/multiBamCov.h

  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2012-11-04 17:59:41 UTC
  • mfrom: (1.1.9)
  • Revision ID: package-import@ubuntu.com-20121104175941-hahqzy1w8uy650z0
Tags: 2.17.0-1
bb9012e Imported Upstream version 2.16.2.
9006b23 Imported Upstream version 2.17.0.
9112569 Documented BEDTools license as a whole.
325689c Removed Pre-Depends: dpkg (>= 1.15.6).
a781b14 Conforms with Policy 3.9.4.
84b1167 Use Debhelper 9. 
0bf572d Distribute the test suite.
422cd34 Bash completion for BEDTools.

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src/multiBamCov/multiBamCov.h
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#include "bedFile.h"
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#include "api/BamMultiReader.h"
 
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#include "BlockedIntervals.h"
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using namespace BamTools;
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    // constructor
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    MultiCovBam(const vector<string> &bam_files, const string bed_file, 
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                int minQual, bool properOnly, 
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                bool keepDuplicates, bool keepFailedQC);
 
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                bool keepDuplicates, bool keepFailedQC,
 
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                bool obeySplits, bool sameStrand,
 
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                bool diffStrand, float overlapFraction,
 
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                bool reciprocal);
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    // destructor
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    ~MultiCovBam(void);
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    bool _properOnly;
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    bool _keepDuplicates;
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    bool _keepFailedQC;
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    bool _obeySplits;
 
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    bool _sameStrand;
 
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    bool _diffStrand;
 
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    float _overlapFraction;
 
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    bool _reciprocal;
 
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    map<string, int> bamFileMap;
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    bool FindBlockedOverlaps(const BED &a, const vector<BED> &a_blocks, 
 
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        const BED &hit);
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    void LoadBamFileMap(void);
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    void ReportCounts(const vector<int> &counts);
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};