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Viewing changes to src/shuffleBed/shuffleBed.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/shuffleBed/shuffleBed.h
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  Licenced under the GNU General Public License 2.0 license.
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******************************************************************************/
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#include "bedFile.h"
 
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#include "bedFilePE.h"
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#include "genomeFile.h"
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#include <vector>
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public:
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    // constructor
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    BedShuffle(string &bedFile, string &genomeFile, string &excludeFile, string &includeFile, 
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                           bool haveSeed, bool haveExclude, bool haveInclude, bool sameChrom, 
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                           float overlapFraction, int seed, bool chooseChrom);
 
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    BedShuffle(string &bedFile, string &genomeFile, 
 
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               string &excludeFile, string &includeFile, 
 
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               bool haveSeed, bool haveExclude, 
 
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               bool haveInclude, bool sameChrom, 
 
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               float overlapFraction, int seed, 
 
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               bool chooseChrom, bool isBedpe);
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    // destructor
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    ~BedShuffle(void);
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    bool _haveInclude;
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    bool _haveSeed;
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    bool _chooseChrom;
 
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    bool _isBedpe;
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    // The BED file from which to compute coverage.
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    BedFile *_bed;
 
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    BedFilePE *_bedpe;
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    BedFile *_exclude;
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    BedFile *_include;
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    void ChooseLocus(BED &);
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    void ChooseLocusFromInclusionFile(BED &);
 
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    void ChoosePairedLocus(BEDPE &b);
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};