public double next(int val) {
if (q.size() == this.max) {
total -= q.poll();
}
q.offer(val);
total += val;
return (double) total / q.size();
}
public int completed(R request) {
assert request.equals(requests.peek());
requests.poll();
int remaining = requests.size();
if (remaining != 0) coordinator.send(requests.peek());
return remaining;
}
@Override
public Boolean call() throws Exception {
long timeoutMillis = 5000;
try {
getServersFile();
getZkRunning();
while (true) {
while (!restartQueue.isEmpty()) {
LOG.debug("Restart queue size [" + restartQueue.size() + "]");
RestartHandler handler = restartQueue.poll();
Future<ScriptContext> runner = pool.submit(handler);
ScriptContext scriptContext = runner.get(); // blocking call
if (scriptContext.getExitCode() != 0) restartQueue.add(handler);
}
try {
Thread.sleep(timeoutMillis);
} catch (InterruptedException e) {
}
}
} catch (Exception e) {
e.printStackTrace();
LOG.error(e);
pool.shutdown();
throw e;
}
}
/**
* Returns the number of instances pending output
*
* @return the number of instances pending output
* @exception NullPointerException if no input structure has been defined
*/
public int numPendingOutput() {
if (m_OutputFormat == null) {
throw new NullPointerException("No output instance format defined");
}
return m_OutputQueue.size();
}
@Override
public void endWindow() {
if (currentWindowId > idempotentStorageManager.getLargestRecoveryWindow()) {
try {
idempotentStorageManager.save(currentWindowRecoveryState, operatorId, currentWindowId);
} catch (IOException e) {
throw new RuntimeException("saving recovery", e);
}
}
currentWindowRecoveryState.clear();
if (context != null) {
pendingFileCount.setValue(pendingFiles.size() + failedFiles.size() + unfinishedFiles.size());
if (currentFile != null) {
pendingFileCount.increment();
}
context.setCounters(fileCounters);
}
}
public void run() {
latch = new CountDownLatch(queue.size());
while (!queue.isEmpty()) {
final LineCounter counter = queue.remove();
new Thread(
new Runnable() {
public void run() {
execute(counter);
latch.countDown();
}
})
.start();
}
waitOnLatch();
}
int bfs(String[] terrain, int sr, int sc, int er, int ec) {
Queue<Node> nodes = new PriorityQueue<Node>();
boolean seen[][] = new boolean[n][m];
nodes.offer(new Node(sr, sc, 0));
while (nodes.size() > 0) {
Node top = nodes.poll();
int r = top.r;
int c = top.c;
int cost = top.cost;
if (r == er && c == ec) {
return cost;
}
if (seen[r][c]) {
continue;
}
seen[r][c] = true;
for (int i = 0; i < dx.length; i++) {
int nr = r + dx[i];
int nc = c + dy[i];
if (0 <= nr && nr < n && 0 <= nc && nc < m) {
char u = terrain[r].charAt(c);
char v = terrain[nr].charAt(nc);
if (u == 'X' || u == '$' || v == 'X' || v == '$') {
nodes.offer(new Node(nr, nc, cost + 2));
} else {
int uval = u - '0';
int vval = v - '0';
int dv = Math.abs(uval - vval);
if (dv <= 1) {
nodes.offer(new Node(nr, nc, cost + (dv == 0 ? 1 : 3)));
}
}
}
}
}
return -1;
}
public void levelOrder(TreeNode root) {
if (root == null) return;
Queue<TreeNode> queue = new LinkedList<TreeNode>();
queue.add(root);
HashMap<Integer, ArrayList<Integer>> map = new HashMap<Integer, ArrayList<Integer>>();
int i = 0;
while (true) {
int width = queue.size();
if (width == 0) break;
i = i + 1;
ArrayList<Integer> al = new ArrayList<Integer>();
while (width > 0) {
root = queue.poll();
al.add(root.n);
if (root.left != null) queue.add(root.left);
if (root.right != null) queue.add(root.right);
width = width - 1;
}
map.put(i, al);
}
}
public void insert(TreeNode node) {
if (root == null) {
root = node;
return;
}
Queue<TreeNode> queue = new LinkedList<TreeNode>();
queue.add(root);
while (queue.size() > 0) {
root = queue.poll();
if (root.left == null) {
root.left = node;
return;
} else {
queue.add(root.left);
}
if (root.right == null) {
root.right = node;
return;
} else {
queue.add(root.right);
}
}
}
public int getSize() {
return edits.size();
}
public static void main(String[] args) throws Exception {
if (args.length != 2) {
System.err.println("USAGE: java -jar SAMSort.jar <BWA PAIRED SAM file> <configFile>");
} else {
System.err.println("Running: java -jar SAMSort.jar " + args[0] + " " + args[1]);
// args[1]: conf file
Constants.loadConstants(args[1], false);
StringBuffer headers = new StringBuffer();
ArrayList<SAM> list = new ArrayList<SAM>();
BufferedReader br = new BufferedReader(new FileReader(args[0]));
int i = 0;
int count = 0;
String curline = null;
String curline2 = null;
SAM s1 = null;
SAM s2 = null;
boolean done = false;
// int cordantCount = 0;
// int discordantCount = 0;
int totalPairCount = 0;
int discordantPairCount = 0;
int singleEndMappedPairCount = 0;
int unmappedPairCount = 0;
BufferedWriter unmapped_bw = null;
BufferedWriter se_bw = null;
while (!done) {
curline = br.readLine();
if (curline == null) break;
else if (!curline.startsWith("@")) {
s1 = new SAM(curline);
// skip secondary. Load until primary
while (s1.isSecondary()) {
curline = br.readLine();
if (curline == null) {
done = true;
break;
}
s1 = new SAM(curline);
}
if (done) break;
curline2 = br.readLine();
s2 = new SAM(curline2);
// skip secondary. Load until primary
while (s2.isSecondary()) {
curline = br.readLine();
if (curline == null) {
done = true;
break;
}
s2 = new SAM(curline);
}
if (done) break;
totalPairCount++;
// only collect discordant
SAMPair tmppair = new SAMPair(s1, s2);
if (tmppair.isDiscordant()) {
discordantPairCount++;
list.add(s1);
list.add(s2);
s1 = null;
s2 = null;
if (list.size() == 200000) {
Collections.sort(list);
BufferedWriter bw = new BufferedWriter(new FileWriter(args[0] + ".part_" + i));
for (SAM s : list) {
bw.write(s.getSamline() + "\n");
}
bw.close();
bw = null;
i++;
list = new ArrayList<SAM>();
}
} else if (!tmppair.isBothUnmapped()) { // single-end mapped
if (se_bw == null) {
se_bw = new BufferedWriter(new FileWriter(args[0] + ".singleEndMapped"));
se_bw.write(headers.toString());
}
singleEndMappedPairCount++;
se_bw.write(s1.getSamline() + "\n");
se_bw.write(s2.getSamline() + "\n");
s1 = null;
s2 = null;
} else { // both unmapped
if (unmapped_bw == null) {
unmapped_bw = new BufferedWriter(new FileWriter(args[0] + ".unmapped"));
unmapped_bw.write(headers.toString());
}
unmappedPairCount++;
unmapped_bw.write(s1.getSamline() + "\n");
unmapped_bw.write(s2.getSamline() + "\n");
s1 = null;
s2 = null;
}
} else {
headers.append(curline + "\n");
}
}
br.close();
br = null;
if (se_bw != null) se_bw.close();
if (unmapped_bw != null) unmapped_bw.close();
if (list.size() > 0) {
Collections.sort(list);
BufferedWriter bw = new BufferedWriter(new FileWriter(args[0] + ".part_" + i));
// System.err.println(count + "\t" + set.size());
for (SAM s : list) {
bw.write(s.getSamline() + "\n");
}
bw.close();
bw = null;
i++;
list = null;
}
Map<SAM, Queue<SAM>> map = new TreeMap<SAM, Queue<SAM>>();
// Set<SAM> set = new TreeSet<SAM>();
// System.err.println("openning " + i + " files");
BufferedReader[] brArr = new BufferedReader[i];
for (int j = 0; j < i; j++) {
brArr[j] = new BufferedReader(new FileReader(args[0] + ".part_" + j));
String tmpline = brArr[j].readLine();
SAM tmp = new SAM(tmpline, j);
if (!map.containsKey(tmp)) map.put(tmp, new LinkedList<SAM>());
else {
// System.err.println("here");
map.get(tmp).add(tmp); // brArr[j].pushBack(tmpline);
}
// System.err.println(map.get(tmp).size());
}
// System.err.println(map.size());
BufferedWriter bw = new BufferedWriter(new FileWriter(args[0] + ".discordant.midsorted"));
bw.write(headers.toString());
SAM s = null;
// int counter = 0;
Queue<SAM> q = null;
while (!map.isEmpty()) {
s = map.keySet().iterator().next();
q = map.get(s);
// map.remove(s);
bw.write(s.getSamline());
bw.write("\n");
if (q.size() == 0) {
map.remove(s);
int tmpIndex = s.getIndex();
String tmpline = brArr[tmpIndex].readLine();
if (tmpline != null) {
s = new SAM(tmpline, tmpIndex);
if (!map.containsKey(s)) {
// System.err.print("put b4: " + map.size());
map.put(s, new LinkedList<SAM>());
// System.err.println("\ta4: " + map.size());
} else {
// System.err.print("here2: ");
map.get(s).add(s);
// System.err.println(map.size());
}
} // else{
// System.err.println("reader[" + tmpIndex + "] : NULL");
// }
} else {
// System.err.print("B4 Q size: " + q.size() + " map size: " + map.size() );
map.remove(s);
map.put(q.remove(), q);
// System.err.println("\tA4 Q size: " + q.size() + " map size: " + map.size() );
int tmpIndex = s.getIndex();
String tmpline = brArr[tmpIndex].readLine();
if (tmpline != null) {
s = new SAM(tmpline, tmpIndex);
if (!map.containsKey(s)) {
// System.err.print("put b4: " + map.size());
map.put(s, new LinkedList<SAM>());
// System.err.println("\ta4: " + map.size());
} else {
// System.err.print("here2: ");
map.get(s).add(s);
// System.err.println(map.size());
}
} // else{
// System.err.println("reader[" + tmpIndex + "] : NULL");
// }
}
// counter++;
}
// System.err.println(counter);
bw.close();
for (int j = 0; j < brArr.length; j++) {
brArr[j].close();
new File(args[0] + ".part_" + j).delete();
}
// int totalPairCount = 0;
// int discordantPairCount = 0;
System.out.println("------ DONE WITH REMOVAL OF CONCORDANT & UNMAPPED PAIRS ---------");
System.out.println("------ Processed a total of\t" + totalPairCount + " read-pairs");
System.out.println(
"------ Retained a total of\t"
+ discordantPairCount
+ " read-pairs writtend out to "
+ args[0]
+ ".discordant.midsorted");
System.out.println(
"------ Single-end mapped :\t"
+ singleEndMappedPairCount
+ " read-pairs written out to "
+ args[0]
+ ".singleEndMapped");
System.out.println(
"------ Unmapped (both ends) : \t"
+ unmappedPairCount
+ " read-pairs written out to "
+ args[0]
+ ".unmapped");
}
}
public int jobsLeft() {
return jobs.size();
}
