ExtractBlast implements Callable<Integer> { 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; } ExtractBlast(final File inputBlastFile, 
    		            final File inputFastqFile, 
    		            final File outputFile,
    		            final int alleleCutoff, 
    		            final String imgtDbVersion); @Override Integer call(); static void main(final String[] args);  }
@Test public void testReadFasta() throws Exception { copyResource("1000-0000-0.fa", inputFastqFile); assertNotNull(inputFastqFile); Map<String, String> fasta = readFasta(inputFastqFile); assertNotNull(fasta); assertNotNull(fasta.get("0|Ref151|32552989|1||1|0")); }