public BedFile(File bedFile){
		this.fileName = bedFile.getName();
		
		//Upload the bed File
		try {
			BufferedReader br = new BufferedReader(new FileReader(bedFile));
			
			String line;
				int id = 0;
				while((line = br.readLine()) != null){
					String[] chunks = line.split("\\s");
					
					String token = chunks[0];
					int chromo = -1;
						if(token.equalsIgnoreCase("chrM")){
							chromo = Definitions.chromosomeM;
						}else if(token.equalsIgnoreCase("chrX")){
							chromo = Definitions.chromosomeX;
						}else if(token.equalsIgnoreCase("chrY")){
							chromo = Definitions.chromosomeY;
						}else{
							chromo = Integer.parseInt(token.substring(token.indexOf('r') + 1));	
						}
						

						int start = Integer.parseInt(chunks[1]);
						int stop = Integer.parseInt(chunks[2]);
						
						String restOfLine = "";
						for(int i = 3; i < chunks.length; i++){
							
							restOfLine += chunks[i];
							if(i != chunks.length - 1){
								restOfLine += "\t";
							}//if
						}//for
						
						this.add(new BedFileLine(id, chromo, start, stop, restOfLine, bedFile));

					id++;
				}//while
		
		} catch (FileNotFoundException e) {
			System.out.println("Unable to setup this bed file.  Error uploading file.");
			inError = true;
		} catch (IOException e) {	
			System.out.println("Unable to read this bed file.  Error uploading file.");
			inError = true;
		}

	}//bedFile