public void update(Long pos, Object readpos, HashMap<Long, ArrayList<String>> map) {
// USE BUECKTS
ReadPos rp = (ReadPos) readpos;
Long Buck = new Long(((Long) pos).longValue() / BUCKET_SIZE);
ArrayList<String> reads = map.get(Buck);
if (reads == null) {
reads = new ArrayList<String>();
}
// also add read START and END to the list
String spos = rp.toString();
if (!reads.contains(spos)) {
reads.add(spos);
// p("Adding rp "+spos+" to bucket "+Buck);
}
map.put(Buck, reads);
}
