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    private GenomeLocParser genomeLocParser;

    private IndexedFastaSequenceFile seq;

    private SAMFileHeader header;

    @BeforeClass

    public void setup() throws FileNotFoundException {

        seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));

        genomeLocParser = new GenomeLocParser(seq);

        header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());

    }

    @DataProvider(name = "AssembleIntervalsData")

    public Object[][] makeAssembleIntervalsData() {

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

        final String contig = "20";

        final int start = 10000000;

        final int end   = 10100000;

        final int windowSize = 100;

        final int stepSize = 200;

        final int nReadsToUse = 5;

        for ( int startI = start; startI < end; startI += stepSize) {

            final int endI = startI + windowSize;

            final GenomeLoc refLoc = genomeLocParser.createGenomeLoc(contig, startI, endI);

            tests.add(new Object[]{new ReadThreadingAssembler(), refLoc, nReadsToUse});

        }

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

    }

    @DataProvider(name = "AssembleIntervalsWithVariantData")

    public Object[][] makeAssembleIntervalsWithVariantData() {

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

        final String contig = "20";

        final int start = 10000000;

        final int end   = 10001000;

        final int windowSize = 100;

        final int stepSize = 200;

        final int variantStepSize = 1;

        final int nReadsToUse = 5;

        for ( int startI = start; startI < end; startI += stepSize) {

            final int endI = startI + windowSize;

            final GenomeLoc refLoc = genomeLocParser.createGenomeLoc(contig, startI, endI);

            for ( int variantStart = windowSize / 2 - 10; variantStart < windowSize / 2 + 10; variantStart += variantStepSize ) {

                tests.add(new Object[]{new ReadThreadingAssembler(), refLoc, nReadsToUse, variantStart});

            }

        }

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

    }

    @Test(dataProvider = "AssembleIntervalsData")

    public void testAssembleRef(final ReadThreadingAssembler assembler, final GenomeLoc loc, final int nReadsToUse) {

        final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();

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

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

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

            final byte[] quals = Utils.dupBytes((byte) 30, refBases.length);

            final String cigar = refBases.length + "M";

            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, loc.getContig(), loc.getContigIndex(), loc.getStart(), bases, quals, cigar);

            reads.add(read);

        }

        // TODO -- generalize to all assemblers

        final Haplotype refHaplotype = new Haplotype(refBases, true);

        final List<Haplotype> haplotypes = assemble(assembler, refBases, loc, reads);

        Assert.assertEquals(haplotypes, Collections.singletonList(refHaplotype));

    }

    @Test(dataProvider = "AssembleIntervalsWithVariantData")

    public void testAssembleRefAndSNP(final ReadThreadingAssembler assembler, final GenomeLoc loc, final int nReadsToUse, final int variantSite) {

        final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();

        final Allele refBase = Allele.create(refBases[variantSite], true);

        final Allele altBase = Allele.create((byte)(refBase.getBases()[0] == 'A' ? 'C' : 'A'), false);

        final VariantContextBuilder vcb = new VariantContextBuilder("x", loc.getContig(), variantSite, variantSite, Arrays.asList(refBase, altBase));

        testAssemblyWithVariant(assembler, refBases, loc, nReadsToUse, vcb.make());

    }

    @Test(dataProvider = "AssembleIntervalsWithVariantData")

    public void testAssembleRefAndDeletion(final ReadThreadingAssembler assembler, final GenomeLoc loc, final int nReadsToUse, final int variantSite) {

        final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();

        for ( int deletionLength = 1; deletionLength < 10; deletionLength++ ) {

            final Allele refBase = Allele.create(new String(refBases).substring(variantSite, variantSite + deletionLength + 1), true);

            final Allele altBase = Allele.create(refBase.getBases()[0], false);

            final VariantContextBuilder vcb = new VariantContextBuilder("x", loc.getContig(), variantSite, variantSite + deletionLength, Arrays.asList(refBase, altBase));

            testAssemblyWithVariant(assembler, refBases, loc, nReadsToUse, vcb.make());

        }

    }

    @Test(dataProvider = "AssembleIntervalsWithVariantData")

    public void testAssembleRefAndInsertion(final ReadThreadingAssembler assembler, final GenomeLoc loc, final int nReadsToUse, final int variantSite) {

        final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();

        for ( int insertionLength = 1; insertionLength < 10; insertionLength++ ) {

            final Allele refBase = Allele.create(refBases[variantSite], false);

            final Allele altBase = Allele.create(new String(refBases).substring(variantSite, variantSite + insertionLength + 1), true);

            final VariantContextBuilder vcb = new VariantContextBuilder("x", loc.getContig(), variantSite, variantSite + insertionLength, Arrays.asList(refBase, altBase));

            testAssemblyWithVariant(assembler, refBases, loc, nReadsToUse, vcb.make());

        }

    }

    private void testAssemblyWithVariant(final ReadThreadingAssembler assembler, final byte[] refBases, final GenomeLoc loc, final int nReadsToUse, final VariantContext site) {

        final String preRef = new String(refBases).substring(0, site.getStart());

        final String postRef = new String(refBases).substring(site.getEnd() + 1, refBases.length);

        final byte[] altBases = (preRef + site.getAlternateAllele(0).getBaseString() + postRef).getBytes();

//        logger.warn("alt " + new String(altBases));

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

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

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

            final byte[] quals = Utils.dupBytes((byte) 30, altBases.length);

            final String cigar = altBases.length + "M";

            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, loc.getContig(), loc.getContigIndex(), loc.getStart(), bases, quals, cigar);

            reads.add(read);

        }

        final Haplotype refHaplotype = new Haplotype(refBases, true);

        final Haplotype altHaplotype = new Haplotype(altBases, false);

        final List<Haplotype> haplotypes = assemble(assembler, refBases, loc, reads);

        Assert.assertEquals(haplotypes, Arrays.asList(refHaplotype, altHaplotype));

    }

    private List<Haplotype> assemble(final ReadThreadingAssembler assembler, final byte[] refBases, final GenomeLoc loc, final List<GATKSAMRecord> reads) {

        final Haplotype refHaplotype = new Haplotype(refBases, true);

        final Cigar c = new Cigar();

        c.add(new CigarElement(refHaplotype.getBases().length, CigarOperator.M));

        refHaplotype.setCigar(c);

        final ActiveRegion activeRegion = new ActiveRegion(loc, null, true, genomeLocParser, 0);

        activeRegion.addAll(reads);

        final AssemblyResultSet assemblyResultSet =  assembler.runLocalAssembly(activeRegion, refHaplotype, refBases, loc, Collections.<VariantContext>emptyList(), null);

        return assemblyResultSet.getHaplotypeList();

    }

    @DataProvider(name = "SimpleAssemblyTestData")

    public Object[][] makeSimpleAssemblyTestData() {

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

        final String contig  = "20";

        final int start      = 10000000;

        final int windowSize = 200;

        final int end        = start + windowSize;

        final int excludeVariantsWithinXbp = 25; // TODO -- decrease to zero when the edge calling problem is fixed

        final String ref = new String(seq.getSubsequenceAt(contig, start, end).getBases());

        final GenomeLoc refLoc = genomeLocParser.createGenomeLoc(contig, start, end);

            for ( int snpPos = 0; snpPos < windowSize; snpPos++) {

                if ( snpPos > excludeVariantsWithinXbp && (windowSize - snpPos) >= excludeVariantsWithinXbp ) {

                    final byte[] altBases = ref.getBytes();

                    altBases[snpPos] = altBases[snpPos] == 'A' ? (byte)'C' : (byte)'A';

                    final String alt = new String(altBases);

                    tests.add(new Object[]{"SNP at " + snpPos, new ReadThreadingAssembler(), refLoc, ref, alt});

                }

            }

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

    }

    @Test(dataProvider = "SimpleAssemblyTestData")

    public void testSimpleAssembly(final String name, final ReadThreadingAssembler assembler, final GenomeLoc loc, final String ref, final String alt) {

        final byte[] refBases = ref.getBytes();

        final byte[] altBases = alt.getBytes();

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

        for ( int i = 0; i < 20; i++ ) {

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

            final byte[] quals = Utils.dupBytes((byte) 30, altBases.length);

            final String cigar = altBases.length + "M";

            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, loc.getContig(), loc.getContigIndex(), loc.getStart(), bases, quals, cigar);

            reads.add(read);

        }

        final Haplotype refHaplotype = new Haplotype(refBases, true);

        final Haplotype altHaplotype = new Haplotype(altBases, false);

        final List<Haplotype> haplotypes = assemble(assembler, refBases, loc, reads);

        Assert.assertTrue(haplotypes.size() > 0, "Failed to find ref haplotype");

        Assert.assertEquals(haplotypes.get(0), refHaplotype);

        Assert.assertEquals(haplotypes.size(), 2, "Failed to find single alt haplotype");

        Assert.assertEquals(haplotypes.get(1), altHaplotype);

    }

}