private static void addKmersToGenes(List<GeneHolder> geneHolderList) throws Exception
	{
		HashMap<String, FastaSequence> fastaMap = FastaSequence.getFirstTokenSequenceMap(
				ConfigReader.getBioLockJDir() + File.separator + "resistantAnnotation" + 
						File.separator +"refGenome" + File.separator 
						+ "klebsiella_pneumoniae_chs_11.0.scaffolds.fasta");
		
		int index=0;
		for(GeneHolder gh: geneHolderList)
		{
			System.out.println(index++ + " " + geneHolderList.size());
			FastaSequence fs = fastaMap.get(gh.chr);
			String seq = fs.getSequence();
			List<Long> backEncodes = new ArrayList<Long>();
			
			for( RangeHolder rh : gh.rangeList )
			{
				for( int x=rh.start - 1; x +  CoinFlipTest.KMER_SIZE <= rh.stop ; x++)
				{
					String nucl = seq.substring(x, x + CoinFlipTest.KMER_SIZE);
					
					Long encode = Encode.makeLong(nucl);
					
					if( encode != null)
					{
						gh.includedKmers.add(encode);
						gh.positions.add(x);
					}
						
					nucl = Translate.safeReverseTranscribe(nucl);
					encode = Encode.makeLong(nucl);
					
					if( encode != null)
						backEncodes.add(encode);					
				}
			}
			
			gh.includedKmers.addAll(backEncodes);
			
			for( int x=0; x < gh.includedKmers.size(); x++)
			{
				gh.pValues.add(null);
				gh.ratioConserved.add(null);
				gh.positions.add(null);
			}
		}
	}