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    private final static boolean DEBUG = false;

    public static byte[] getBytes(final String alignment) {

        return alignment.replace("-","").getBytes();

    }

    private void assertNonUniques(final ReadThreadingGraph assembler, String ... nonUniques) {

        final Set<String> actual = new HashSet<>();

        assembler.buildGraphIfNecessary();

        for ( final Kmer kmer : assembler.getNonUniqueKmers() ) actual.add(kmer.baseString());

        final Set<String> expected = new HashSet<>(Arrays.asList(nonUniques));

        Assert.assertEquals(actual, expected);

    }

    @Test

    public void testSimpleHaplotypeRethreading() {

        final ReadThreadingGraph assembler = new ReadThreadingGraph(11);

        final String ref   = "CATGCACTTTAAAACTTGCCTTTTTAACAAGACTTCCAGATG";

        final String alt   = "CATGCACTTTAAAACTTGCCGTTTTAACAAGACTTCCAGATG";

        assembler.addSequence("anonymous", getBytes(ref), true);

        assembler.addSequence("anonymous", getBytes(alt), false);

        assembler.buildGraphIfNecessary();

        Assert.assertNotEquals(ref.length() - 11 + 1,assembler.vertexSet().size(),"the number of vertex in the graph is the same as if there was no alternative sequence");

        Assert.assertEquals(ref.length() - 11 + 1 + 11,assembler.vertexSet().size(),"the number of vertex in the graph is not the same as if there is an alternative sequence");

        MultiDeBruijnVertex startAlt = assembler.findKmer(new Kmer(alt.getBytes(),20,11));

        Assert.assertNotNull(startAlt);

    }

    @Test(enabled = ! DEBUG)

    public void testNonUniqueMiddle() {

        final ReadThreadingGraph assembler = new ReadThreadingGraph(3);

        final String ref   = "GACACACAGTCA";

        final String read1 = "GACAC---GTCA";

        final String read2 =   "CAC---GTCA";

        assembler.addSequence(getBytes(ref), true);

        assembler.addSequence(getBytes(read1), false);

        assembler.addSequence(getBytes(read2), false);

        assertNonUniques(assembler, "ACA", "CAC");

    }

    @Test(enabled = ! DEBUG)

    public void testReadsCreateNonUnique() {

        final ReadThreadingGraph assembler = new ReadThreadingGraph(3);

        final String ref   = "GCAC--GTCA"; // CAC is unique

        final String read1 = "GCACACGTCA"; // makes CAC non unique because it has a duplication

        final String read2 =    "CACGTCA"; // shouldn't be allowed to match CAC as start

        assembler.addSequence(getBytes(ref), true);

        assembler.addSequence(getBytes(read1), false);

        assembler.addSequence(getBytes(read2), false);

        assertNonUniques(assembler, "CAC");

        //assertSingleBubble(assembler, ref, "CAAAATCGGG");

    }

    @Test(enabled = ! DEBUG)

         public void testCountingOfStartEdges() {

        final ReadThreadingGraph assembler = new ReadThreadingGraph(3);

        final String ref   = "NNNGTCAAA"; // ref has some bases before start

        final String read1 =    "GTCAAA"; // starts at first non N base

        assembler.addSequence(getBytes(ref), true);

        assembler.addSequence(getBytes(read1), false);

        assembler.buildGraphIfNecessary();

        for ( final MultiSampleEdge edge : assembler.edgeSet() ) {

            final MultiDeBruijnVertex source = assembler.getEdgeSource(edge);

            final MultiDeBruijnVertex target = assembler.getEdgeTarget(edge);

            final boolean headerVertex = source.getSuffix() == 'N' || target.getSuffix() == 'N';

            if ( headerVertex ) {

                Assert.assertEquals(edge.getMultiplicity(), 1, "Bases in the unique reference header should have multiplicity of 1");

            } else {

                Assert.assertEquals(edge.getMultiplicity(), 2, "Should have multiplicity of 2 for any edge outside the ref header but got " + edge + " " + source + " -> " + target);

            }

        }

    }

    @Test(enabled = !DEBUG)

    public void testCountingOfStartEdgesWithMultiplePrefixes() {

        final ReadThreadingGraph assembler = new ReadThreadingGraph(3);

        assembler.increaseCountsThroughBranches = true;

        final String ref   = "NNNGTCAXX"; // ref has some bases before start

        final String alt1  = "NNNCTCAXX"; // alt1 has SNP right after N

        final String read  =     "TCAXX"; // starts right after SNP, but merges right before branch

        assembler.addSequence(getBytes(ref), true);

        assembler.addSequence(getBytes(alt1), false);

        assembler.addSequence(getBytes(read), false);

        assembler.buildGraphIfNecessary();

        assembler.printGraph(new File("test.dot"), 0);

        final List<String> oneCountVertices = Arrays.asList("NNN", "NNG", "NNC", "NGT", "NCT");

        final List<String> threeCountVertices = Arrays.asList("CAX", "AXX");

        for ( final MultiSampleEdge edge : assembler.edgeSet() ) {

            final MultiDeBruijnVertex source = assembler.getEdgeSource(edge);

            final MultiDeBruijnVertex target = assembler.getEdgeTarget(edge);

            final int expected = oneCountVertices.contains(target.getSequenceString()) ? 1 : (threeCountVertices.contains(target.getSequenceString()) ? 3 : 2);

            Assert.assertEquals(edge.getMultiplicity(), expected, "Bases at edge " + edge + " from " + source + " to " + target + " has bad multiplicity");

        }

    }

    @Test(enabled = !DEBUG)

    public void testCyclesInGraph() {

        // b37 20:12655200-12655850

        final String ref = "CAATTGTCATAGAGAGTGACAAATGTTTCAAAAGCTTATTGACCCCAAGGTGCAGCGGTGCACATTAGAGGGCACCTAAGACAGCCTACAGGGGTCAGAAAAGATGTCTCAGAGGGACTCACACCTGAGCTGAGTTGTGAAGGAAGAGCAGGATAGAATGAGCCAAAGATAAAGACTCCAGGCAAAAGCAAATGAGCCTGAGGGAAACTGGAGCCAAGGCAAGAGCAGCAGAAAAGAGCAAAGCCAGCCGGTGGTCAAGGTGGGCTACTGTGTATGCAGAATGAGGAAGCTGGCCAAGTAGACATGTTTCAGATGATGAACATCCTGTATACTAGATGCATTGGAACTTTTTTCATCCCCTCAACTCCACCAAGCCTCTGTCCACTCTTGGTACCTCTCTCCAAGTAGACATATTTCAGATCATGAACATCCTGTGTACTAGATGCATTGGAAATTTTTTCATCCCCTCAACTCCACCCAGCCTCTGTCCACACTTGGTACCTCTCTCTATTCATATCTCTGGCCTCAAGGAGGGTATTTGGCATTAGTAAATAAATTCCAGAGATACTAAAGTCAGATTTTCTAAGACTGGGTGAATGACTCCATGGAAGAAGTGAAAAAGAGGAAGTTGTAATAGGGAGACCTCTTCGG";

        // SNP at 20:12655528 creates a cycle for small kmers

        final String alt = "CAATTGTCATAGAGAGTGACAAATGTTTCAAAAGCTTATTGACCCCAAGGTGCAGCGGTGCACATTAGAGGGCACCTAAGACAGCCTACAGGGGTCAGAAAAGATGTCTCAGAGGGACTCACACCTGAGCTGAGTTGTGAAGGAAGAGCAGGATAGAATGAGCCAAAGATAAAGACTCCAGGCAAAAGCAAATGAGCCTGAGGGAAACTGGAGCCAAGGCAAGAGCAGCAGAAAAGAGCAAAGCCAGCCGGTGGTCAAGGTGGGCTACTGTGTATGCAGAATGAGGAAGCTGGCCAAGTAGACATGTTTCAGATGATGAACATCCTGTGTACTAGATGCATTGGAACTTTTTTCATCCCCTCAACTCCACCAAGCCTCTGTCCACTCTTGGTACCTCTCTCCAAGTAGACATATTTCAGATCATGAACATCCTGTGTACTAGATGCATTGGAAATTTTTTCATCCCCTCAACTCCACCCAGCCTCTGTCCACACTTGGTACCTCTCTCTATTCATATCTCTGGCCTCAAGGAGGGTATTTGGCATTAGTAAATAAATTCCAGAGATACTAAAGTCAGATTTTCTAAGACTGGGTGAATGACTCCATGGAAGAAGTGAAAAAGAGGAAGTTGTAATAGGGAGACCTCTTCGG";

        final List<GATKSAMRecord> reads = new ArrayList<>();

        for ( int index = 0; index < alt.length() - 100; index += 20 )

            reads.add(ArtificialSAMUtils.createArtificialRead(Arrays.copyOfRange(alt.getBytes(), index, index + 100), Utils.dupBytes((byte) 30, 100), 100 + "M"));

        // test that there are cycles detected for small kmer

        final ReadThreadingGraph rtgraph25 = new ReadThreadingGraph(25);

        rtgraph25.addSequence("ref", ref.getBytes(), true);

        for ( final GATKSAMRecord read : reads )

            rtgraph25.addRead(read);

        rtgraph25.buildGraphIfNecessary();

        Assert.assertTrue(rtgraph25.hasCycles());

        // test that there are no cycles detected for large kmer

        final ReadThreadingGraph rtgraph75 = new ReadThreadingGraph(75);

        rtgraph75.addSequence("ref", ref.getBytes(), true);

        for ( final GATKSAMRecord read : reads )

            rtgraph75.addRead(read);

        rtgraph75.buildGraphIfNecessary();

        Assert.assertFalse(rtgraph75.hasCycles());

    }

    @Test(enabled = !DEBUG)

    public void testNsInReadsAreNotUsedForGraph() {

        final int length = 100;

        final byte[] ref = Utils.dupBytes((byte)'A', length);

        final ReadThreadingGraph rtgraph = new ReadThreadingGraph(25);

        rtgraph.addSequence("ref", ref, true);

        // add reads with Ns at any position

        for ( int i = 0; i < length; i++ ) {

            final byte[] bases = ref.clone();

            bases[i] = 'N';

            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, Utils.dupBytes((byte) 30, length), length + "M");

            rtgraph.addRead(read);

        }

        rtgraph.buildGraphIfNecessary();

        final SeqGraph graph = rtgraph.convertToSequenceGraph();

        Assert.assertEquals(new KBestHaplotypeFinder(graph, graph.getReferenceSourceVertex(), graph.getReferenceSinkVertex()).size(), 1);

    }

//    @DataProvider(name = "KmerSizeData")

//    public Object[][] makeKmerSizeDataProvider() {

//        List<Object[]> tests = new ArrayList<Object[]>();

//

//        // this functionality can be adapted to provide input data for whatever you might want in your data

//        tests.add(new Object[]{3, 3, 3, Arrays.asList("ACG"), Arrays.asList()});

//        tests.add(new Object[]{3, 4, 3, Arrays.asList("CAGACG"), Arrays.asList()});

//

//        tests.add(new Object[]{3, 3, 3, Arrays.asList("AAAAC"), Arrays.asList("AAA")});

//        tests.add(new Object[]{3, 4, 4, Arrays.asList("AAAAC"), Arrays.asList()});

//        tests.add(new Object[]{3, 5, 4, Arrays.asList("AAAAC"), Arrays.asList()});

//        tests.add(new Object[]{3, 4, 3, Arrays.asList("CAAA"), Arrays.asList()});

//        tests.add(new Object[]{3, 4, 4, Arrays.asList("CAAAA"), Arrays.asList()});

//        tests.add(new Object[]{3, 5, 4, Arrays.asList("CAAAA"), Arrays.asList()});

//        tests.add(new Object[]{3, 5, 5, Arrays.asList("ACGAAAAACG"), Arrays.asList()});

//

//        for ( int maxSize = 3; maxSize < 20; maxSize++ ) {

//            for ( int dupSize = 3; dupSize < 20; dupSize++ ) {

//                final int expectedSize = Math.min(maxSize, dupSize);

//                final String dup = Utils.dupString("C", dupSize);

//                final List<String> nonUnique = dupSize > maxSize ? Arrays.asList(Utils.dupString("C", maxSize)) : Collections.<String>emptyList();

//                tests.add(new Object[]{3, maxSize, expectedSize, Arrays.asList("ACGT", "A" + dup + "GT"), nonUnique});

//                tests.add(new Object[]{3, maxSize, expectedSize, Arrays.asList("A" + dup + "GT", "ACGT"), nonUnique});

//            }

//        }

//

//        return tests.toArray(new Object[][]{});

//    }

//

//    /**

//     * Example testng test using MyDataProvider

//     */

//    @Test(dataProvider = "KmerSizeData")

//    public void testDynamicKmerSizing(final int min, final int max, final int expectKmer, final List<String> seqs, final List<String> expectedNonUniques) {

//        final ReadThreadingGraph assembler = new ReadThreadingGraph(min, max);

//        for ( String seq : seqs ) assembler.addSequence(seq.getBytes(), false);

//        assembler.buildGraphIfNecessary();

//        Assert.assertEquals(assembler.getKmerSize(), expectKmer);

//        assertNonUniques(assembler, expectedNonUniques.toArray(new String[]{}));

//    }