public static void main(String[] args) throws Exception
	{
		File topDir = new File(ConfigReader.getVanderbiltDir() + File.separator + 
				"krakenOut");
		
		for( int x=0; x < KRAKEN_LEVELS.length; x++)
		{
			HashMap<String, HashMap<String, Integer>> map = 
						new HashMap<String, HashMap<String,Integer>>();
			
			System.out.println(KRAKEN_LEVELS[x]);
			for(String s : topDir.list())
				if( s.startsWith("standardReport_for_Sample_") && s.indexOf("16S") == -1)
				{
					//System.out.println("NON 16S " + s);
					addToMap(new File(topDir.getAbsolutePath() + File.separator + s),
							map, KRAKEN_LEVELS[x]);
	
				}
					
			File outFile = new File(ConfigReader.getVanderbiltDir() + File.separator + 
					"spreadsheets" + File.separator + 
					"kraken_" + RDP_LEVELS[x] +"_taxaAsColumns.txt");
			PivotOTUs.writeResults(map, outFile.getAbsolutePath());
			
			OtuWrapper wrapper = new OtuWrapper(outFile);
			wrapper.writeNormalizedLoggedDataToFile(ConfigReader.getVanderbiltDir() 
					+ File.separator + 
					"spreadsheets" + File.separator + 
					"kraken_" + RDP_LEVELS[x] +"_taxaAsColumnsLogNorm.txt");
		}
		
		for( int x=0; x < KRAKEN_LEVELS.length; x++)
		{
			HashMap<String, HashMap<String, Integer>> map = 
						new HashMap<String, HashMap<String,Integer>>();
			
			System.out.println(KRAKEN_LEVELS[x]);
			for(String s : topDir.list())
			{
				//System.out.println(s);
				if( s.startsWith("standardReport_for_") && s.indexOf("16S") != -1)
				{
					//System.out.println("For 16S " + s);
					addToMap(new File(topDir.getAbsolutePath() + File.separator + s),
							map, KRAKEN_LEVELS[x]);
	
				}
			}
				
					
			File outFile = new File(ConfigReader.getVanderbiltDir() + File.separator + 
					"spreadsheets" + File.separator + 
					"kraken_" + RDP_LEVELS[x] +"_taxaAsColumnsFor16S.txt");
			PivotOTUs.writeResults(map, outFile.getAbsolutePath());
			
			OtuWrapper wrapper = new OtuWrapper(outFile);
			wrapper.writeNormalizedLoggedDataToFile(ConfigReader.getVanderbiltDir() 
					+ File.separator + 
					"spreadsheets" + File.separator + 
					"kraken_" + RDP_LEVELS[x] +"_taxaAsColumnsLogNormFor16S.txt");
		}
	}