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;
    	
    }
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 ; }
Extract consensus sequences from a file in HML format.

@param inputHmlFile input HML file, if any