--- a/BEDTools-Version-2.14.3/src/shuffleBed/shuffleBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,244 +0,0 @@
-/*****************************************************************************
-  shuffleBed.cpp
-
-  (c) 2009 - Aaron Quinlan
-  Hall Laboratory
-  Department of Biochemistry and Molecular Genetics
-  University of Virginia
-  aaronquinlan@gmail.com
-
-  Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#include "lineFileUtilities.h"
-#include "shuffleBed.h"
-
-
-BedShuffle::BedShuffle(string &bedFile, string &genomeFile, string &excludeFile, string &includeFile, 
-                       bool haveSeed, bool haveExclude, bool haveInclude, bool sameChrom, 
-                       float overlapFraction, int seed) {
-
-    _bedFile         = bedFile;
-    _genomeFile      = genomeFile;
-    _excludeFile     = excludeFile;
-    _includeFile     = includeFile;
-    _sameChrom       = sameChrom;
-    _haveExclude     = haveExclude;
-    _haveInclude     = haveInclude;
-    _overlapFraction = overlapFraction;
-    _haveSeed        = haveSeed;
-
-
-    // use the supplied seed for the random
-    // number generation if given.  else,
-    // roll our own.
-    if (_haveSeed) {
-        _seed = seed;
-        srand(seed);
-    }
-    else {
-        // thanks to Rob Long for the tip.
-        _seed = (unsigned)time(0)+(unsigned)getpid();
-        srand(_seed);
-    }
-
-    _bed         = new BedFile(bedFile);
-    _genome      = new GenomeFile(genomeFile);
-    _chroms      = _genome->getChromList();
-    _numChroms   = _genome->getNumberOfChroms();
-
-    if (_haveExclude) {
-        _exclude = new BedFile(excludeFile);
-        _exclude->loadBedFileIntoMap();
-    }
-    
-    if (_haveInclude) {
-        _include = new BedFile(includeFile);
-        _include->loadBedFileIntoMapNoBin();
-        
-        _numIncludeChroms = 0;
-        masterBedMapNoBin::const_iterator it    = _include->bedMapNoBin.begin(); 
-        masterBedMapNoBin::const_iterator itEnd = _include->bedMapNoBin.end();
-        for(; it != itEnd; ++it) {
-            _includeChroms.push_back(it->first);
-            _numIncludeChroms++;
-        }
-    }
-
-    if (_haveExclude == true && _haveInclude == false)
-        ShuffleWithExclusions();
-    else if  (_haveExclude == false && _haveInclude == true)
-        ShuffleWithInclusions();
-    else
-        Shuffle();
-}
-
-
-BedShuffle::~BedShuffle(void) {
-
-}
-
-
-void BedShuffle::Shuffle() {
-
-    int lineNum = 0;
-    BED bedEntry, nullBed;     // used to store the current BED line from the BED file.
-    BedLineStatus bedStatus;
-
-    _bed->Open();
-    while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
-        if (bedStatus == BED_VALID) {
-            ChooseLocus(bedEntry);
-            _bed->reportBedNewLine(bedEntry);
-            bedEntry = nullBed;
-        }
-    }
-    _bed->Close();
-}
-
-
-
-void BedShuffle::ShuffleWithExclusions() {
-
-    int lineNum = 0;
-    BED bedEntry, nullBed;     // used to store the current BED line from the BED file.
-    BedLineStatus bedStatus;
-
-    _bed->Open();
-    while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
-        if (bedStatus == BED_VALID) {
-            // keep looking as long as the chosen
-            // locus happens to overlap with regions
-            // that the user wishes to exclude.
-            int  tries = 0;
-            bool haveOverlap = false;
-            do 
-            {
-                // choose a new locus
-                ChooseLocus(bedEntry);
-                haveOverlap = _exclude->FindOneOrMoreOverlapsPerBin(bedEntry.chrom, bedEntry.start, bedEntry.end,
-                                                                    bedEntry.strand, false, _overlapFraction);
-                tries++;
-            } while ((haveOverlap == true) && (tries <= MAX_TRIES));
-            
-
-            if (tries > MAX_TRIES) {
-                cerr << "Error, line " << lineNum << ": tried " << MAX_TRIES << " potential loci for entry, but could not avoid excluded regions.  Ignoring entry and moving on." << endl;
-            }
-            else {
-                _bed->reportBedNewLine(bedEntry);
-            }
-        }
-        bedEntry = nullBed;
-    }
-    _bed->Close();
-}
-
-
-void BedShuffle::ShuffleWithInclusions() {
-
-    int lineNum = 0;
-    BED bedEntry, nullBed;     // used to store the current BED line from the BED file.
-    BedLineStatus bedStatus;
-
-    _bed->Open();
-    while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
-        if (bedStatus == BED_VALID) {
-            // choose a new locus
-            ChooseLocusFromInclusionFile(bedEntry);
-            _bed->reportBedNewLine(bedEntry);
-        }
-        bedEntry = nullBed;
-    }
-    _bed->Close();
-}
-
-
-void BedShuffle::ChooseLocus(BED &bedEntry) {
-
-    string chrom = bedEntry.chrom;
-    CHRPOS start    = bedEntry.start;
-    CHRPOS end      = bedEntry.end;
-    CHRPOS length   = end - start;
-
-    string randomChrom;
-    CHRPOS randomStart;
-    CHRPOS chromSize;
-
-    if (_sameChrom == false) {
-        randomChrom    = _chroms[rand() % _numChroms];
-        chromSize      = _genome->getChromSize(randomChrom);
-        randomStart    = rand() % chromSize;
-        bedEntry.chrom = randomChrom;
-        bedEntry.start = randomStart;
-        bedEntry.end   = randomStart + length;
-    }
-    else {
-        chromSize      = _genome->getChromSize(chrom);
-        randomStart    = rand() % chromSize;
-        bedEntry.start = randomStart;
-        bedEntry.end   = randomStart + length;
-    }
-
-    // ensure that the chosen location doesn't go past
-    // the length of the chromosome. if so, keep looking
-    // for a new spot.
-    while (bedEntry.end > chromSize) {
-        if (_sameChrom == false) {
-            randomChrom    = _chroms[rand() % _numChroms];
-            chromSize      = _genome->getChromSize(randomChrom);
-            randomStart    = rand() % chromSize;
-            bedEntry.chrom = randomChrom;
-            bedEntry.start = randomStart;
-            bedEntry.end   = randomStart + length;
-        }
-        else {
-            chromSize      = _genome->getChromSize(chrom);
-            randomStart    = rand() % chromSize;
-            bedEntry.start = randomStart;
-            bedEntry.end   = randomStart + length;
-        }
-    }
-}
-
-
-void BedShuffle::ChooseLocusFromInclusionFile(BED &bedEntry) {
-
-    string chrom    = bedEntry.chrom;
-    CHRPOS length   = bedEntry.end - bedEntry.start;
-
-    string randomChrom;
-    CHRPOS randomStart;
-    BED includeInterval;
-    
-    if (_sameChrom == false) {
-
-        // grab a random chromosome from the inclusion file.
-        randomChrom            = _includeChroms[rand() % _numIncludeChroms];
-        // get the number of inclusion intervals for that chrom
-        size_t size            =  _include->bedMapNoBin[randomChrom].size();
-        // grab a random interval on the chosen chromosome.
-        size_t interval        = rand() % size;
-        // retreive a ranom -incl interval on the selected chrom
-        includeInterval        = _include->bedMapNoBin[randomChrom][interval];
-
-        bedEntry.chrom = randomChrom;        
-    }
-    else {
-        // get the number of inclusion intervals for the original chrom
-        size_t size =  _include->bedMapNoBin[chrom].size();
-        // grab a random interval on the chosen chromosome.
-        includeInterval       = _include->bedMapNoBin[chrom][rand() % size];
-    }
-    
-    randomStart    = includeInterval.start + rand() % (includeInterval.size());
-    bedEntry.start = randomStart;
-    bedEntry.end   = randomStart + length;
-    
-    // use recursion to ensure that the chosen location 
-    // doesn't go past the end of the chrom
-    if (bedEntry.end > ((size_t) _genome->getChromSize(chrom))) {
-        //bedEntry.end = _genome->getChromSize(chrom);
-        ChooseLocusFromInclusionFile(bedEntry);
-    }
-}
-