public static HashMap<String, Integer> getCountMap(List<File> fastaFiles) throws Exception
	{
		HashMap<String, Integer> map = new HashMap<String, Integer>();
		
		for( File f : fastaFiles)
		{
			BufferedReader reader = new BufferedReader(new FileReader(f));
			
			String nextLine = reader.readLine();
			
			while ( nextLine != null ) 
			{
				String header = nextLine;
				header = new StringTokenizer(header).nextToken();
				if( header.startsWith(">"))
					header = header.substring(1);
				
				if( map.keySet().contains(header) )
					throw new Exception("Duplicate key " + header);
				
				nextLine = reader.readLine();
				
				int count = 0;
				
				while ( nextLine != null && ! nextLine.startsWith(">") ) 
				{
					count+=	stripWhiteSpace( nextLine ).length();
					nextLine = reader.readLine();
				}
				
				map.put(header, count);
			}
			
			reader.close();
			
		}
		
		return map;
	}