public void getAllTranscripts() throws FileNotFoundException, IOException{

	System.out.println("Getting all transcripts from " + annotationFname);
        TextFile in = new TextFile(annotationFname, false);
        allTranscr = new ArrayList();
        String line = in.readLine();
        int len = 0, cnt = 0;
        String[] spl;
        if (! normalizeByLength){
            while ((line = in.readLine()) != null){
                allTranscr.add(line.split("\t")[1]);
                cnt++;
            }
        }
        else{
            trLengths = new HashMap<String, Integer>();
            while ((line = in.readLine()) != null){
                spl = line.split("\t");
                allTranscr.add(spl[1]);
                len = Integer.parseInt(spl[5]) - Integer.parseInt(spl[4]);
                trLengths.put(spl[1], len);
                cnt++;
            }
        }
        in.close();
        System.out.println(cnt + " transcripts / genes read.\n");
    }