--- a/BEDTools-Version-2.14.3/src/utils/chromsweep/chromsweep.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,180 +0,0 @@
-/*****************************************************************************
-  chromsweep.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 "chromsweep.h"
-#include <queue>
-
-bool after(const BED &a, const BED &b);
-void report_hits(const BED &curr_qy, const vector<BED> &hits);
-vector<BED> scan_cache(const BED &curr_qy, BedLineStatus qy_status, const vector<BED> &db_cache, vector<BED> &hits);
-
-
-/*
-    // constructor using existing BedFile pointers
-*/
-ChromSweep::ChromSweep(BedFile *bedA, BedFile *bedB, bool sameStrand, bool diffStrand)
-: _bedA(bedA)
-, _bedB(bedB)
-, _sameStrand(sameStrand)
-, _diffStrand(diffStrand)
-{
-    // prime the results pump.
-    _qy_lineNum = 0;
-    _db_lineNum = 0;
-    
-    _hits.reserve(1000);
-    _cache.reserve(1000);
-    
-    _bedA->Open();
-    _bedB->Open();
-    _qy_status = _bedA->GetNextBed(_curr_qy, _qy_lineNum);
-    _db_status = _bedB->GetNextBed(_curr_db, _db_lineNum);
-}
-
-/*
-    Constructor with filenames
-*/
-ChromSweep::ChromSweep(string &bedAFile, string &bedBFile) 
-{
-    // prime the results pump.
-    _qy_lineNum = 0;
-    _db_lineNum = 0;
-    
-    _hits.reserve(100000);
-    _cache.reserve(100000);
-    
-    _bedA = new BedFile(bedAFile);
-    _bedB = new BedFile(bedBFile);
-    
-    _bedA->Open();
-    _bedB->Open();
-    
-    _qy_status = _bedA->GetNextBed(_curr_qy, _qy_lineNum);
-    _db_status = _bedB->GetNextBed(_curr_db, _db_lineNum);
-}
-
-
-/*
-    Destructor
-*/
-ChromSweep::~ChromSweep(void) {
-}
-
-
-void ChromSweep::ScanCache() {
-    if (_qy_status != BED_INVALID) {
-        vector<BED>::iterator c = _cache.begin();
-        while (c != _cache.end())
-        {
-            if ((_curr_qy.chrom == c->chrom) && !(after(_curr_qy, *c))) {
-                if (IsValidHit(_curr_qy, *c)) {
-                    _hits.push_back(*c);
-                }
-                ++c;
-            }
-            else {
-                c = _cache.erase(c);
-            }
-        }
-    }
-}
-
-
-bool ChromSweep::ChromChange()
-{
-    // the files are on the same chrom
-    if ((_curr_qy.chrom == _curr_db.chrom) || (_db_status == BED_INVALID) || (_qy_status == BED_INVALID)) {
-        return false;
-    }
-    // the query is ahead of the database. fast-forward the database to catch-up.
-    else if (_curr_qy.chrom > _curr_db.chrom) {
-        while (!_bedB->Empty() && _curr_db.chrom < _curr_qy.chrom)
-        {
-            _db_status = _bedB->GetNextBed(_curr_db, _db_lineNum);
-        }
-        _cache.clear();
-        return false;
-    }
-    // the database is ahead of the query.
-    else {
-        // 1. scan the cache for remaining hits on the query's current chrom.
-        if (_curr_qy.chrom == _curr_chrom)
-        {
-            ScanCache();
-            _results.push(make_pair(_curr_qy, _hits));
-            _hits.clear();
-        }
-        // 2. fast-forward until we catch up and report 0 hits until we do.
-        else if (_curr_qy.chrom < _curr_db.chrom)
-        {
-            _results.push(make_pair(_curr_qy, _no_hits));
-            _cache.clear();
-        }
-        _qy_status = _bedA->GetNextBed(_curr_qy, _qy_lineNum);
-        _curr_chrom = _curr_qy.chrom;
-        return true;
-    }
-}
-
-bool ChromSweep::IsValidHit(const BED &query, const BED &db) {
-    // do we have an overlap in the DB?
-    if (overlaps(query.start, query.end, db.start, db.end) > 0) {
-        // Now test for necessary strandedness.
-        bool strands_are_same = (query.strand == db.strand);
-        if ( (_sameStrand == false && _diffStrand == false)
-             ||
-             (_sameStrand == true && strands_are_same == true)
-             ||
-             (_diffStrand == true && strands_are_same == false)
-           )
-        {
-            return true;
-        }
-    }
-    return false;
-}
-
-
-bool ChromSweep::Next(pair<BED, vector<BED> > &next) {
-    if (!_bedA->Empty()) {
-        // have we changed chromosomes?
-        if (ChromChange() == false) {
-            // scan the database cache for hits
-            ScanCache();
-            // advance the db until we are ahead of the query. update hits and cache as necessary
-            while (!_bedB->Empty() && _curr_qy.chrom == _curr_db.chrom && !(after(_curr_db, _curr_qy)))
-            {
-                if (IsValidHit(_curr_qy, _curr_db)) {
-                    _hits.push_back(_curr_db);
-                }
-                _cache.push_back(_curr_db);
-                _db_status = _bedB->GetNextBed(_curr_db, _db_lineNum);
-            }
-            // add the hits for this query to the pump
-            _results.push(make_pair(_curr_qy, _hits));
-            // reset for the next query
-            _hits.clear();
-            _curr_qy = _nullBed;
-            _qy_status = _bedA->GetNextBed(_curr_qy, _qy_lineNum);
-            _curr_chrom = _curr_qy.chrom;
-        }
-    }
-    // report the next set if hits if there are still overlaps in the pump
-    if (!_results.empty()) {
-        next = _results.front();
-        _results.pop();
-        return true;
-    }
-    // otherwise, the party is over.
-    else {return false;}
-}
-