--- a/BEDTools-Version-2.14.3/src/maskFastaFromBed/maskFastaFromBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
-/*****************************************************************************
-  maskFastaFromBed.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 "maskFastaFromBed.h"
-
-
-MaskFastaFromBed::MaskFastaFromBed(const string &fastaInFile,  const string &bedFile, 
-                                   const string &fastaOutFile, bool softMask, char maskChar) {
-    _softMask     = softMask;
-    _fastaInFile  = fastaInFile;
-    _bedFile      = bedFile;
-    _fastaOutFile = fastaOutFile;
-    _maskChar     = maskChar;
-    _bed          = new BedFile(_bedFile);
-
-    _bed->loadBedFileIntoMapNoBin();
-    // start masking.
-    MaskFasta();
-}
-
-
-MaskFastaFromBed::~MaskFastaFromBed(void) {
-}
-
-
-//******************************************************************************
-// Mask the Fasta file based on the coordinates in the BED file.
-//******************************************************************************
-void MaskFastaFromBed::MaskFasta() {
-
-    /* Make sure that we can open all of the files successfully*/
-
-    // open the fasta database for reading
-    ifstream fa(_fastaInFile.c_str(), ios::in);
-    if ( !fa ) {
-        cerr << "Error: The requested fasta file (" << _fastaInFile << ") could not be opened. Exiting!" << endl;
-        exit (1);
-    }
-
-    // open the fasta database for reading
-    ofstream faOut(_fastaOutFile.c_str(), ios::out);
-    if ( !faOut ) {
-        cerr << "Error: The requested fasta output file (" << _fastaOutFile << ") could not be opened. Exiting!" << endl;
-        exit (1);
-    }
-
-
-    /* Read the fastaDb chromosome by chromosome*/
-    string fastaInLine;
-    string currChrom;
-    string currDNA = "";
-    currDNA.reserve(500000000);
-    int fastaWidth = -1;
-    bool widthSet  = false;
-    int start, end, length;
-    string replacement;
-
-    while (getline(fa,fastaInLine)) {
-
-        if (fastaInLine.find(">",0) != 0 ) {
-            if (widthSet == false) {
-                fastaWidth = fastaInLine.size();
-                widthSet = true;
-            }
-            currDNA += fastaInLine;
-        }
-        else {
-            if (currDNA.size() > 0) {
-
-                vector<BED> bedList = _bed->bedMapNoBin[currChrom];
-
-                /*
-                    loop through each BED entry for this chrom and
-                    mask the requested sequence in the FASTA file.
-                */
-                for (unsigned int i = 0; i < bedList.size(); i++) {
-                    start = bedList[i].start;
-                    end = bedList[i].end;
-                    length = end - start;
-
-                    /*
-                       (1) if soft masking, extract the sequence, lowercase it,
-                           then put it back
-                       (2) otherwise replace with Ns
-                    */
-                    if (_softMask) {
-                        replacement = currDNA.substr(start, length);
-                        toLowerCase(replacement);
-                        currDNA.replace(start, length, replacement);
-                    }
-                    else {
-                        string hardmask(length, _maskChar);
-                        currDNA.replace(start, length, hardmask);
-                    }
-                }
-                // write the masked chrom to the output file
-                PrettyPrintChrom(faOut, currChrom, currDNA, fastaWidth);
-            }
-
-            // reset for the next chromosome.
-            currChrom = fastaInLine.substr(1, fastaInLine.find_first_of(" ")-1);
-            currDNA = "";
-        }
-    }
-
-    // process the last chromosome.
-    // exact same logic as in the main loop.
-    if (currDNA.size() > 0) {
-
-        vector<BED> bedList = _bed->bedMapNoBin[currChrom];
-
-        for (unsigned int i = 0; i < bedList.size(); i++) {
-            start = bedList[i].start;
-            end = bedList[i].end;
-            length = end - start;
-
-            if (_softMask) {
-                replacement = currDNA.substr(start, length);
-                toLowerCase(replacement);
-                currDNA.replace(start, length, replacement);
-            }
-            else {
-                string hardmask(length, _maskChar);
-                currDNA.replace(start, length, hardmask);
-            }
-        }
-        PrettyPrintChrom(faOut, currChrom, currDNA, fastaWidth);
-    }
-
-    // closed for business.
-    fa.close();
-    faOut.close();
-}
-
-
-void MaskFastaFromBed::PrettyPrintChrom(ofstream &out, string chrom, const string &sequence, int width) {
-
-    int seqLength = sequence.size();
-
-    out << ">" << chrom << endl;
-    for(int i = 0; i < seqLength; i += width)  {
-        if (i + width < seqLength) out << sequence.substr(i, width) << endl;
-        else out << sequence.substr(i, seqLength-i) << endl;
-    }
-}
-