private void createOutput(){
		double maxLog2Score = 0;
		double minLog2Score = 0;

		//Determine maximum and minimum score
		for(BedLine bl: bedLines){
			if(bl.getLog2() > maxLog2Score){
				maxLog2Score = bl.getLog2();
			}
			if(bl.getLog2() < minLog2Score){
				minLog2Score = bl.getLog2();
			}
		}

		//Set each lines color based on its proportion to the maximum/minimum score.
		for(BedLine bl: bedLines){
			if(bl.getLog2() > 0){
				bl.setColor(0, (int)((bl.getLog2() / maxLog2Score) * 255), 0);
			}else{
				bl.setColor((int)((bl.getLog2() / minLog2Score) * 255), 0, 0);
			}
		}

		//Writing to HDD related variables
		StringBuffer sb;
		BufferedWriter out;


		try {
			sb = new StringBuffer();
			out = new BufferedWriter(new FileWriter(outputDir + inputFile.substring(inputFile.lastIndexOf('/')) + ".bed"));
			
			//This information is necessary for colors to be displayed in the UCSC browser
			sb.append("track itemRgb='On'" + "\n");
			//Write each bed line to the string buffer
			for(BedLine bl: bedLines){
				sb.append(bl.toString() + "\n");
			}
			
			
			//Write the string buffer to the file.
			out.write(sb.toString());
			//Flush and close the stream to ensure all data was written to disk.
			out.flush();
			out.close();
			
			
			
			
		} catch (IOException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}//Catch
		
		
	}//createOutput