code: static Map<String, String> readFasta(final File inputFastqFile) throws IOException, NoSuchElementException, BioException{
      	
      	BufferedReader reader = null;
      	HashMap<String, String> fasta = new HashMap<String, String>();
          
      	try{
      		 reader = reader(inputFastqFile);
      		 for (SequenceIterator sequences = SeqIOTools.readFastaDNA(reader); sequences.hasNext(); ) 
      		{
                   Sequence sequence = sequences.nextSequence();
                   String sequenceId = sequence.getName();
                   String fastaSeq   = sequence.seqString();
                   fasta.put(sequenceId, fastaSeq);
               }
      		
      	}finally {
              try {
              	reader.close();
              }
              catch (Exception e) {
              	 e.printStackTrace();
              	 System.exit(1);
              }
          }
      
          
          return fasta;
      	
      }
docs: Extract consensus sequences from a file in HML format.
  
  @param inputHmlFile input HML file, if any