Method NTCardHistogram

src/rnabloom/util/NTCardHistogram.java:35–64

(String path)

    public long[] counts = new long[MAX_MULTIPLICITY];
    
    public NTCardHistogram(String path) throws FileNotFoundException, IOException {
        boolean f0Found = false;
        BufferedReader br = getTextFileReader(path);
        String line;
        long sum = 0;
        while ((line = br.readLine()) != null) {
            if (line.length() > 0) {
                String[] cols = line.split("\t");
                if (f0Found) {
                    long count = Long.parseLong(cols[1]);
                    counts[Integer.parseInt(cols[0]) - 1] = count;
                    sum += count;
                }
                else if (cols[0].equals("F1")) {
                    numKmers = Long.parseLong(cols[1]);
                }
                else if (cols[0].equals("F0")) {
                    numUniqueKmers = Long.parseLong(cols[1]); 
                    f0Found = true;
                    if ((numUniqueKmers < 1 && numKmers > 0) ||
                            numKmers < numUniqueKmers) {
                        break;
                    }
                }
            }
        }
        
        numUniqueOverrepresentedKmers = numUniqueKmers - sum;
        br.close();
    }
    
    public long getNumSingletons() {
        return counts[0];