public void count() throws IOException{
        TextFile tf = new TextFile("/Users/dashazhernakova/Documents/UMCG/hapmapData/tophat/1382_1_1/6.pairToBed_out.bed", false);
        tf.open();
        String[] fields;
        Map<String,ArrayList<String>> read_map = new HashMap<String, ArrayList<String>>();
        //first read
        fields = tf.readLineElems(TextFile.tab);
        String cur_read = fields[6];
        read_map.put(cur_read, new ArrayList<String>());
        ArrayList<String> cur_trList = read_map.get(cur_read);
        cur_trList.add(fields[13].replaceAll(":exon:[0-9]*", ""));
                            
        while ( (fields = tf.readLineElems(TextFile.tab)) != null){
            if (cur_read.equals("IL26_1382:1:12:857:252"))
                System.out.println("read");
            if (cur_read.equals(fields[6]))
                cur_trList.add(fields[13].replaceAll(":exon:[0-9]*", ""));
            else{
                //cur_trList = getCandidateTranscripts(cur_trList);
                if (getCandidateTranscripts(cur_trList) > 0)
                    System.out.println(" > 1: " + cur_read + " : " + fields[13]);
                cur_read = fields[6];
                if (cur_read.equals("IL26_1382:1:12:857:252"))
                    System.out.println("read");
                read_map.put(cur_read, new ArrayList<String>());
                cur_trList = read_map.get(cur_read);
                cur_trList.add(fields[13].replaceAll(":exon:[0-9]*", ""));
            }
                
            
        }
        
        tf.close();
    }