code: static HashMap<String, BlastResults> readBlast(final int alleleCutoff, final File inputBlastFile) throws IOException{
      	
          BufferedReader reader = null;
          HashMap<String, BlastResults> blast = new HashMap<String, BlastResults>();
          
          try {
              reader = new BufferedReader(new FileReader(inputBlastFile));
  
              for (HighScoringPair hsp : HspReader.read(reader)) {
  
              	//id	allele 
              	List<String> BlastnParts = Splitter.on("\t").splitToList(hsp.toString());
              	String sequenceId        = BlastnParts.get(0);
              	String allele            = BlastnParts.get(1);
              
                 BlastResults blastResults    = blast.get(sequenceId);
                 if(blastResults == null){
              	   blastResults  = new BlastResults(alleleCutoff);
                 	   blast.put(sequenceId, blastResults);
                 }
                 
                 blastResults.addTyping(allele);
              }
              
          }finally {
              try {
              	reader.close();
              }
              catch (Exception e) {
              	 e.printStackTrace();
              	 System.exit(1);
              }
          }
      
          
          return blast;
      	
      }
docs: Extract consensus sequences from a file in HML format.
  
  @param inputHmlFile input HML file, if any