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    private final static Logger logger = Logger.getLogger(ReadThreadingAssembler.class);

    private final static int DEFAULT_NUM_PATHS_PER_GRAPH = 128;

    private final static int GGA_MODE_ARTIFICIAL_COUNTS = 1000;

    private final static int KMER_SIZE_ITERATION_INCREASE = 10;

    private final static int MAX_KMER_ITERATIONS_TO_ATTEMPT = 6;

    /** The min and max kmer sizes to try when building the graph. */

    private final List<Integer> kmerSizes;

    private final boolean dontIncreaseKmerSizesForCycles;

    private final boolean allowNonUniqueKmersInRef;

    private final int numPruningSamples;

    protected boolean removePathsNotConnectedToRef = true;

    private boolean justReturnRawGraph = false;

    /** for testing only */

    public ReadThreadingAssembler() {

        this(DEFAULT_NUM_PATHS_PER_GRAPH, Arrays.asList(25));

    }

    public ReadThreadingAssembler(final int maxAllowedPathsForReadThreadingAssembler, final List<Integer> kmerSizes, final boolean dontIncreaseKmerSizesForCycles, final boolean allowNonUniqueKmersInRef, final int numPruningSamples) {

        super(maxAllowedPathsForReadThreadingAssembler);

        this.kmerSizes = kmerSizes;

        this.dontIncreaseKmerSizesForCycles = dontIncreaseKmerSizesForCycles;

        this.allowNonUniqueKmersInRef = allowNonUniqueKmersInRef;

        this.numPruningSamples = numPruningSamples;

    }

    protected ReadThreadingAssembler(final int maxAllowedPathsForReadThreadingAssembler, final List<Integer> kmerSizes) {

        this(maxAllowedPathsForReadThreadingAssembler, kmerSizes, true, true, 1);

    }

    /** for testing purposes */

    protected void setJustReturnRawGraph(boolean justReturnRawGraph) {

        this.justReturnRawGraph = justReturnRawGraph;

    }

    private void addResult(final List<AssemblyResult> results, final AssemblyResult maybeNullResult) {

        if ( maybeNullResult != null )

            results.add(maybeNullResult);

    }

    @Override

    public List<AssemblyResult> assemble(final List<GATKSAMRecord> reads, final Haplotype refHaplotype, final List<Haplotype> givenHaplotypes) {

        final List<AssemblyResult> results = new LinkedList<>();

        // first, try using the requested kmer sizes

        for ( final int kmerSize : kmerSizes ) {

            addResult(results, createGraph(reads, refHaplotype, kmerSize, givenHaplotypes, dontIncreaseKmerSizesForCycles, allowNonUniqueKmersInRef));

        }

        // if none of those worked, iterate over larger sizes if allowed to do so

        if ( results.isEmpty() && !dontIncreaseKmerSizesForCycles ) {

            int kmerSize = MathUtils.arrayMaxInt(kmerSizes) + KMER_SIZE_ITERATION_INCREASE;

            int numIterations = 1;

            while ( results.isEmpty() && numIterations <= MAX_KMER_ITERATIONS_TO_ATTEMPT ) {

                // on the last attempt we will allow low complexity graphs

                final boolean lastAttempt = numIterations == MAX_KMER_ITERATIONS_TO_ATTEMPT;

                addResult(results, createGraph(reads, refHaplotype, kmerSize, givenHaplotypes, lastAttempt, lastAttempt));

                kmerSize += KMER_SIZE_ITERATION_INCREASE;

                numIterations++;

            }

        }

        return results;

    }

    /**

     * Creates the sequence graph for the given kmerSize

     *

     * @param reads            reads to use

     * @param refHaplotype     reference haplotype

     * @param kmerSize         kmer size

     * @param activeAlleleHaplotypes the GGA haplotypes to inject into the graph

     * @param allowLowComplexityGraphs if true, do not check for low-complexity graphs

     * @param allowNonUniqueKmersInRef if true, do not fail if the reference has non-unique kmers

     * @return sequence graph or null if one could not be created (e.g. because it contains cycles or too many paths or is low complexity)

     */

    protected AssemblyResult createGraph(final List<GATKSAMRecord> reads,

                                         final Haplotype refHaplotype,

                                         final int kmerSize,

                                         final List<Haplotype> activeAlleleHaplotypes,

                                         final boolean allowLowComplexityGraphs,

                                         final boolean allowNonUniqueKmersInRef) {

        if ( refHaplotype.length() < kmerSize ) {

            // happens in cases where the assembled region is just too small

            return new AssemblyResult(AssemblyResult.Status.FAILED, null);

        }

        if ( !allowNonUniqueKmersInRef && !ReadThreadingGraph.determineNonUniqueKmers(new SequenceForKmers("ref", refHaplotype.getBases(), 0, refHaplotype.getBases().length, 1, true), kmerSize).isEmpty() ) {

            if ( debug ) logger.info("Not using kmer size of " + kmerSize + " in read threading assembler because reference contains non-unique kmers");

            return null;

        }

        final ReadThreadingGraph rtgraph = new ReadThreadingGraph(kmerSize, debugGraphTransformations, minBaseQualityToUseInAssembly, numPruningSamples);

        rtgraph.setThreadingStartOnlyAtExistingVertex(!recoverDanglingBranches);

        // add the reference sequence to the graph

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

        // add the artificial GGA haplotypes to the graph

        int hapCount = 0;

        for ( final Haplotype h : activeAlleleHaplotypes ) {

            rtgraph.addSequence("activeAllele" + hapCount++, h.getBases(), GGA_MODE_ARTIFICIAL_COUNTS, false);

        }

        // Next pull kmers out of every read and throw them on the graph

        for( final GATKSAMRecord read : reads ) {

            rtgraph.addRead(read);

        }

        // actually build the read threading graph

        rtgraph.buildGraphIfNecessary();

        // sanity check: make sure there are no cycles in the graph

        if ( rtgraph.hasCycles() ) {

            if ( debug ) logger.info("Not using kmer size of " + kmerSize + " in read threading assembler because it contains a cycle");

            return null;

        }

        // sanity check: make sure the graph had enough complexity with the given kmer

        if ( ! allowLowComplexityGraphs && rtgraph.isLowComplexity() ) {

            if ( debug ) logger.info("Not using kmer size of " + kmerSize + " in read threading assembler because it does not produce a graph with enough complexity");

            return null;

        }

        printDebugGraphTransform(rtgraph, new File("" + refHaplotype.getGenomeLocation() + "-sequenceGraph." + kmerSize + ".0.0.raw_readthreading_graph.dot"));

        // go through and prune all of the chains where all edges have <= pruneFactor.  This must occur

        // before recoverDanglingTails in the graph, so that we don't spend a ton of time recovering

        // tails that we'll ultimately just trim away anyway, as the dangling tail edges have weight of 1

        rtgraph.pruneLowWeightChains(pruneFactor);

        // look at all chains in the graph that terminate in a non-ref node (dangling sources and sinks) and see if

        // we can recover them by merging some N bases from the chain back into the reference

        if ( recoverDanglingBranches ) {

            rtgraph.recoverDanglingTails(pruneFactor, minDanglingBranchLength);

            rtgraph.recoverDanglingHeads(pruneFactor, minDanglingBranchLength);

        }

        // remove all heading and trailing paths

        if ( removePathsNotConnectedToRef ) rtgraph.removePathsNotConnectedToRef();

        printDebugGraphTransform(rtgraph, new File("" + refHaplotype.getGenomeLocation() + "-sequenceGraph." + kmerSize + ".0.1.cleaned_readthreading_graph.dot"));

        final SeqGraph initialSeqGraph = rtgraph.convertToSequenceGraph();

        if (debugGraphTransformations) initialSeqGraph.printGraph(new File("" + refHaplotype.getGenomeLocation() + "-sequenceGraph." + kmerSize + ".0.1.initial_seqgraph.dot"),10000);

        // if the unit tests don't want us to cleanup the graph, just return the raw sequence graph

        if ( justReturnRawGraph ) return new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, initialSeqGraph);

        if (debug) logger.info("Using kmer size of " + rtgraph.getKmerSize() + " in read threading assembler");

        printDebugGraphTransform(initialSeqGraph, new File( "" + refHaplotype.getGenomeLocation() + "-sequenceGraph." + kmerSize + ".0.2.initial_seqgraph.dot"));

        initialSeqGraph.cleanNonRefPaths(); // TODO -- I don't this is possible by construction

        final AssemblyResult cleaned = cleanupSeqGraph(initialSeqGraph);

        final AssemblyResult.Status status = cleaned.getStatus();

        final AssemblyResult result = new AssemblyResult(status, cleaned.getGraph());

        result.setThreadingGraph(rtgraph);

        return result;

    }

    @Override

    public String toString() {

        return "ReadThreadingAssembler{" +

                "kmerSizes=" + kmerSizes +

                '}';

    }

}