--- a/BEDTools-Version-2.14.3/src/fastaFromBed/fastaFromBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,141 +0,0 @@
-/*****************************************************************************
-  fastaFromBed.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 "fastaFromBed.h"
-
-
-Bed2Fa::Bed2Fa(bool useName, const string &dbFile, const string &bedFile,
-    const string &fastaOutFile, bool useFasta, bool useStrand) {
-
-    _useName      = useName;
-    _dbFile       = dbFile;
-    _bedFile      = bedFile;
-    _fastaOutFile = fastaOutFile;
-    _useFasta     = useFasta;
-    _useStrand    = useStrand;
-
-    _bed = new BedFile(_bedFile);
-
-    // Figure out what the output file should be.
-    if (fastaOutFile == "stdout") {
-        _faOut = &cout;
-    }
-    else {
-        // Make sure we can open the file.
-        ofstream fa(fastaOutFile.c_str(), ios::out);
-        if ( !fa ) {
-            cerr << "Error: The requested fasta output file (" << fastaOutFile << ") could not be opened. Exiting!" << endl;
-            exit (1);
-        }
-        else {
-            fa.close();
-            _faOut = new ofstream(fastaOutFile.c_str(), ios::out);
-        }
-    }
-
-    // Extract the requested intervals from the FASTA input file.
-    ExtractDNA();
-}
-
-
-Bed2Fa::~Bed2Fa(void) {
-}
-
-
-//******************************************************************************
-// ReportDNA
-//******************************************************************************
-void Bed2Fa::ReportDNA(const BED &bed, string &dna) {
-
-    // revcomp if necessary.  Thanks to Thomas Doktor.
-    if ((_useStrand == true) && (bed.strand == "-"))
-        reverseComplement(dna);
-
-    if (!(_useName)) {
-        if (_useFasta == true) {
-            if (_useStrand == true)
-                *_faOut << ">" << bed.chrom << ":" << bed.start << "-" << bed.end   << "(" << bed.strand << ")" << endl << dna << endl;
-            else
-                *_faOut << ">" << bed.chrom << ":" << bed.start << "-" << bed.end << endl << dna << endl;
-        }
-        else {
-            if (_useStrand == true)
-                *_faOut << bed.chrom << ":" << bed.start << "-" << bed.end << "(" << bed.strand << ")" << "\t" << dna << endl;
-            else
-                *_faOut << bed.chrom << ":" << bed.start << "-" << bed.end << "\t" << dna << endl;
-        }
-    }
-    else {
-        if (_useFasta == true)
-            *_faOut << ">" << bed.name << endl << dna << endl;
-        else
-            *_faOut << bed.name << "\t" << dna << endl;
-    }
-}
-
-
-
-//******************************************************************************
-// ExtractDNA
-//******************************************************************************
-void Bed2Fa::ExtractDNA() {
-
-    /* Make sure that we can oen all of the files successfully*/
-
-    // open the fasta database for reading
-    ifstream faDb(_dbFile.c_str(), ios::in);
-    if ( !faDb ) {
-        cerr << "Error: The requested fasta database file (" << _dbFile << ") could not be opened. Exiting!" << endl;
-        exit (1);
-    }
-
-    // open and memory-map genome file
-    FastaReference *fr = new FastaReference;
-    bool memmap = true;
-    fr->open(_dbFile, memmap);
-
-    BED bed, nullBed;
-    int lineNum = 0;
-    BedLineStatus bedStatus;
-    string sequence;
-
-    _bed->Open();
-    while ((bedStatus = _bed->GetNextBed(bed, lineNum)) != BED_INVALID) {
-        if (bedStatus == BED_VALID) {
-            // make sure we are extracting >= 1 bp
-            if (bed.zeroLength == false) {
-                size_t seqLength = fr->sequenceLength(bed.chrom);
-                // make sure this feature will not exceed the end of the chromosome.
-                if ( (bed.start <= seqLength) && (bed.end <= seqLength) ) 
-                {
-                    int length = bed.end - bed.start;
-                    sequence = fr->getSubSequence(bed.chrom, bed.start, length);
-                    ReportDNA(bed, sequence);
-                }
-                else
-                {
-                    cerr << "Feature (" << bed.chrom << ":" << bed.start << "-" << bed.end << ") beyond the length of "
-                        << bed.chrom << " size (" << seqLength << " bp).  Skipping." << endl;
-                }
-            }
-            // handle zeroLength 
-            else {
-                cerr << "Feature (" << bed.chrom << ":" << bed.start+1 << "-" << bed.end-1 << ") has length = 0, Skipping." << endl;
-            }
-            bed = nullBed;
-        }
-    }
-    _bed->Close();
-}
-
-
-