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);
}
private void updateLine(HashMap<Long, ArrayList<String>> map, String line) {
int tab = line.indexOf("\t");
if (tab < 1) {
warn("err or in readloc, no tab on line " + nrrows + ":" + line);
} else {
String a = line.substring(0, tab).trim();
Long pos = Long.parseLong(a);
// bunch of reads...
line = line.substring(tab + 1).trim();
ArrayList<String> readposlist = StringTools.parseList(line, "\t");
for (String rpline : readposlist) {
ReadPos rp = ReadPos.fromString(rpline);
if (rp != null) update(pos, rp, map);
}
}
}
