Method layoutStrandedBackbones

src/rnabloom/olc/Layout.java:4221–4302

(String outFastaPath)

    }
    
    private boolean layoutStrandedBackbones(String outFastaPath) throws IOException {
        HashSet<String> containedSet = populateGraphFromOverlaps();
        
        if (!containedSet.isEmpty()) {
            printMessage("contained reads: " + NumberFormat.getInstance().format(containedSet.size()));
        }
        
        Set<String> vertexSet = graph.vertexSet();
        if (!vertexSet.isEmpty()) {
            printMessage("dovetail reads:  " + NumberFormat.getInstance().format(vertexSet.size()));
        }
        
        int numEdges = graph.edgeSet().size();        
        if (numEdges > 1) {
            printMessage("G: |V|=" + NumberFormat.getInstance().format(graph.vertexSet().size()) + " |E|=" + NumberFormat.getInstance().format(numEdges));
            
//            ArrayDeque<String> redundantNodeNames = removeRedundantNodes();
//            for (String n : redundantNodeNames) {
//                containedSet.add(getVertexName(n));
//            }
//            numEdges = graph.edgeSet().size();
//            System.out.println("G: |V|=" + NumberFormat.getInstance().format(graph.vertexSet().size()) + " |E|=" + NumberFormat.getInstance().format(numEdges));           
            
            resolveJunctions();
            numEdges = graph.edgeSet().size();
            printMessage("G: |V|=" + NumberFormat.getInstance().format(graph.vertexSet().size()) + " |E|=" + NumberFormat.getInstance().format(numEdges));
        }
        
        // extract read sequences
        HashMap<String, BitSequence> dovetailReadSeqs = new HashMap<>(vertexSet.size());
        FastaReader fr = new FastaReader(seqFastaPath);
        FastaWriter fw = new FastaWriter(outFastaPath, false);
        long seqID = 0;
        long originalNumSeq = 0;
        while (fr.hasNext()) {
            ++originalNumSeq;
            String[] nameSeq = fr.nextWithName();
            String name = nameSeq[0];
            if (vertexSet.contains(name + '+')) {
                String seq = nameSeq[1];
                dovetailReadSeqs.put(name, new BitSequence(seq));
            }
            else if (!containedSet.contains(name)) {
                // this sequence either contains shorter sequences or it has no overlaps with others
                fw.write(Long.toString(++seqID), nameSeq[1]);
            }
        }
        fr.close();
        
        // layout unambiguous paths
        HashSet<String> visitedReadNames = new HashSet<>(vertexSet.size());
        for (String n : vertexSet) {
            if (!visitedReadNames.contains(getVertexName(n))) {                
                ArrayDeque<String> path = getUnambiguousLeftExtension(n);
                path.add(n);
                if (!graph.containsEdge(n, path.getFirst())) {
                    // detect cycles
                    path.addAll(getUnambiguousRightExtension(n));