--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/maskFastaFromBed/maskFastaFromBed.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,155 @@
+/*****************************************************************************
+  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;
+    }
+}
+