public void process(String fName) throws FileNotFoundException, IOException{
        System.out.println("Starting to sum up reads for transcripts in " + fName);
        System.out.println("Writing output to " + fName.replace(".txt", "_out.txt"));
        BufferedReader exCounts=new BufferedReader(new FileReader(fName));
        BufferedWriter trCounts=new BufferedWriter(new FileWriter(fName.replace(".txt", "_out.txt")));
        String line="", curTranscr="", transcr="";
        float count;
        float curCount=0;
        while ((line = exCounts.readLine()) != null){
            String[] fields = line.split("\t");
            count = Float.valueOf(fields[1])*Float.valueOf(fields[4]);
            //count = Float.valueOf(fields[1]);
            transcr = fields[0].split(":")[0];
            if (transcr.equals(curTranscr))
                curCount += count;
            else{
                if (!curTranscr.isEmpty())
                    trCounts.write(curTranscr + "\t" + Float.toString(curCount)+"\n");
                curCount=count;
                curTranscr=transcr;
            }
        }
        trCounts.write(curTranscr + "\t" + Float.toString(curCount));

        trCounts.close();
        exCounts.close();
        
        //System.out.println("Finished summing up");
    }