public static void main(String[] args) throws Exception
	{
		HashSet<String> set = getMatchingSequences();
		System.out.println(set);
		System.out.println(set.size());
		
		BufferedReader reader = new BufferedReader(new InputStreamReader( 
				new GZIPInputStream( new FileInputStream( ConfigReader.getVanderbiltDir() + 
						File.separator + "MSHRM1" + File.separator + "lane1_Undetermined_L001_R1_001.fastq.gz"))));
		
		int numChecked=0;
		int numMatched=0;
		for(FastQ fq = FastQ.readOneOrNull(reader); fq != null; fq = FastQ.readOneOrNull(reader))
		{
			numChecked++;
			
			String aSeq = fq.getSequence().trim();
			String backSeq = Translate.safeReverseTranscribe(fq.getSequence().trim());
			
			boolean match = false;
			for(String s : set)
			{
				if( aSeq.startsWith(s) || aSeq.endsWith(s)  || backSeq.startsWith(s) || backSeq.endsWith(s))
					match = true;
			}
			
			if( match)
				numMatched++;
			
			if(numChecked % 100000 ==0)
				System.out.println(numChecked + " " + numMatched);
		}
	}