Method extractSimplePaths

src/rnabloom/olc/Layout.java:3349–3462

(String outFastaPath)

    }
    
    public void extractSimplePaths(String outFastaPath) throws IOException {
        HashSet<String> containedSet = populateGraphFromOverlaps();
        
        Timer timer = new Timer();
        
        if (!containedSet.isEmpty()) {
            printMessage("contained reads: " + NumberFormat.getInstance().format(containedSet.size()));
        }
        
        Set<String> vertexSet = graph.vertexSet();
        if (!vertexSet.isEmpty()) {
            int numDovetailReads = vertexSet.size();
            if (!stranded) {
                numDovetailReads /= 2;
            }
            printMessage("dovetail reads:  " + NumberFormat.getInstance().format(numDovetailReads));
        }
        
        Set<OverlapEdge> edgeSet = graph.edgeSet();
        
        if (edgeSet.size() > 1) {
            //printGraph();
            printMessage("G: |V|=" + NumberFormat.getInstance().format(vertexSet.size()) + " |E|=" + NumberFormat.getInstance().format(edgeSet.size()));
            
            ArrayDeque<String> removedVertexes = removeRedundantNodes();
            if (stranded) {
                for (String vid : removedVertexes) {
                    containedSet.add(getVertexName(vid));
                }
            }
            else {
                for (String vid : removedVertexes) {
                    if (!graph.containsVertex(getReverseComplementID(vid))) {
                        containedSet.add(getVertexName(vid));
                    }
                }
            }
            
            removeTransitiveEdges();
            
            //printGraph();
            printMessage("G: |V|=" + NumberFormat.getInstance().format(vertexSet.size()) + " |E|=" + NumberFormat.getInstance().format(edgeSet.size()));
            writeGraph(this.seqFastaPath + ".dot.gz");
        }
        
        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 + '+') || (!stranded && vertexSet.contains(name + '-'))) {
                dovetailReadSeqs.put(name, new BitSequence(nameSeq[1]));
            }
            else if (!containedSet.contains(name)) {