public void test_02() {
		readFile("tests/indexer_test_01.fastq");

		// Sort all references
		String latest = "";
		Collections.sort(references, seqIndex);

		// Check that is was sorted correctly
		for( Long ref : references ) {
			DnaAndQualitySequence seq = seqIndex.get(SequenceReference.getSeqIdx(ref));
			int start = SequenceReference.getStart(ref);
			Math.min(seq.length() - start, latest.length());
			String subseq = seq.getSequence().substring(start);

			if( subseq.compareTo(latest) < 0 ) throw new RuntimeException("References out of order!\n\t" + SequenceReference.getSeqIdx(ref) + ":" + SequenceReference.getStart(ref) + "\t" + ref + "\t" + subseq + "\n\tLatest: " + latest);
			latest = subseq;
		}
	}