--- a/BEDTools-Version-2.14.3/src/utils/genomeFile/genomeFile.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-/*****************************************************************************
-  genomeFile.cpp
-
-  (c) 2009 - Aaron Quinlan
-  Hall Laboratory
-  Department of Biochemistry and Molecular Genetics
-  University of Virginia
-  aaronquinlan@gmail.com
-
-  Licensed under the GNU General Public License 2.0 license.
-******************************************************************************/
-#include "lineFileUtilities.h"
-#include "genomeFile.h"
-
-
-GenomeFile::GenomeFile(const string &genomeFile) {
-    _genomeFile = genomeFile;
-    loadGenomeFileIntoMap();
-}
-
-GenomeFile::GenomeFile(const RefVector &genome) {
-    for (size_t i = 0; i < genome.size(); ++i) {
-        string chrom = genome[i].RefName;
-        int length = genome[i].RefLength;
-        
-        _chromSizes[chrom] = length;
-        _chromList.push_back(chrom);
-    }
-}
-
-// Destructor
-GenomeFile::~GenomeFile(void) {
-}
-
-
-void GenomeFile::loadGenomeFileIntoMap() {
-
-    string genomeLine;
-    int lineNum = 0;
-    vector<string> genomeFields;            // vector for a GENOME entry
-
-    // open the GENOME file for reading
-    ifstream genome(_genomeFile.c_str(), ios::in);
-    if ( !genome ) {
-        cerr << "Error: The requested genome file (" << _genomeFile << ") could not be opened. Exiting!" << endl;
-        exit (1);
-    }
-
-    while (getline(genome, genomeLine)) {
-
-        Tokenize(genomeLine,genomeFields);  // load the fields into the vector
-        lineNum++;
-
-        // ignore a blank line
-        if (genomeFields.size() > 0) {
-            if (genomeFields[0].find("#") == string::npos) {
-
-                // we need at least 2 columns
-                if (genomeFields.size() >= 2) {
-                    char *p2End;
-                    long c2;
-                    // make sure the second column is numeric.
-                    c2 = strtol(genomeFields[1].c_str(), &p2End, 10);
-
-                    // strtol  will set p2End to the start of the string if non-integral, base 10
-                    if (p2End != genomeFields[1].c_str()) {
-                        string chrom       = genomeFields[0];
-                        int size           = atoi(genomeFields[1].c_str());
-                        _chromSizes[chrom] = size;
-                        _chromList.push_back(chrom);
-                    }
-                }
-                else {
-                    cerr << "Less than the req'd two fields were encountered in the genome file (" << _genomeFile << ")";
-                    cerr << " at line " << lineNum << ".  Exiting." << endl;
-                    exit (1);
-                }
-            }
-        }
-        genomeFields.clear();
-    }
-}
-
-
-int GenomeFile::getChromSize(const string &chrom) {
-    chromToSizes::const_iterator chromIt = _chromSizes.find(chrom);
-    if (chromIt != _chromSizes.end())
-        return _chromSizes[chrom];
-    else
-        return -1;  // chrom not found.
-}
-
-vector<string> GenomeFile::getChromList() {
-    return _chromList;
-}
-
-int GenomeFile::getNumberOfChroms() {
-    return _chromList.size();
-}
-
-string GenomeFile::getGenomeFileName() {
-    return _genomeFile;
-}