Method getReadLengths

src/rnabloom/RNABloom.java:917–956

(String path, int minLength, int sample)

    }
    
    public static int[] getReadLengths(String path, int minLength, int sample) throws FileFormatException, IOException{
        int[] lengths = new int[sample];
        int i = 0;
        
        if (FastqReader.isCorrectFormat(path)) {
            FastqRecord r = new FastqRecord();
            FastqReader fr = new FastqReader(path);
            for (; i< sample && fr.hasNext();) {
                fr.nextWithoutName(r);
                int len = r.seq.length();
                if (len < minLength) {
                    continue;
                }
                lengths[i] = len;
                ++i;
            }
            fr.close();
        }
        else if (FastaReader.isCorrectFormat(path)) {
            FastaReader fr = new FastaReader(path);
            for (; i< sample && fr.hasNext();) {
                int len = fr.next().length();
                if (len < minLength) {
                    continue;
                }
                lengths[i] = len;
                ++i;
            }
            fr.close();                
        }
        else {
            throw new FileFormatException("Incompatible file format for `" + path + "`");
        }
        
        if (i < sample) {
            return Arrays.copyOfRange(lengths, 0, i);
        }
        
        return lengths;
    }
    
    public static int getMaxReadLength(String path) throws FileFormatException, IOException{
        int max = -1;