public static void main(String args[]) throws IOException, ParseException {
Options options = new Options();
options.addOption("u", "uniquehits", false, "only output hits with a single mapping");
options.addOption(
"s",
"nosuboptimal",
false,
"do not include hits whose score is not equal to the best score for the read");
CommandLineParser parser = new GnuParser();
CommandLine cl = parser.parse(options, args, false);
boolean uniqueOnly = cl.hasOption("uniquehits");
boolean filterSubOpt = cl.hasOption("nosuboptimal");
ArrayList<String[]> lines = new ArrayList<String[]>();
String line;
String lastRead = "";
BufferedReader reader = new BufferedReader(new InputStreamReader(System.in));
while ((line = reader.readLine()) != null) {
String pieces[] = line.split("\t");
if (!pieces[0].equals(lastRead)) {
printLines(lines, uniqueOnly, filterSubOpt);
lines.clear();
}
lines.add(pieces);
lastRead = pieces[0];
}
printLines(lines, uniqueOnly, filterSubOpt);
}
private boolean startLauncher(File dir) {
try {
Runtime rt = Runtime.getRuntime();
ArrayList<String> command = new ArrayList<String>();
command.add("java");
command.add("-jar");
command.add("Launcher.jar");
String[] cmdarray = command.toArray(new String[command.size()]);
Process proc = rt.exec(cmdarray, null, dir);
return true;
} catch (Exception ex) {
System.err.println("Unable to start the Launcher program.\n" + ex.getMessage());
return false;
}
}
public static void printLines(
ArrayList<String[]> lines, boolean uniqueOnly, boolean filterSubOpt) {
double numHits = 0;
ArrayList<String[]> linesToPrint;
// First count the number of (valid) hits
if (filterSubOpt && lines.size() > 1) {
linesToPrint = new ArrayList<String[]>();
int minMis = Integer.MAX_VALUE;
// Find minimum number of mismatchs
int[] mismatches = new int[lines.size()];
int i = 0;
for (String[] pieces : lines) {
int mis = 0;
if (pieces.length > 7 && pieces[7].length() > 1) mis = pieces[7].split(",").length;
mismatches[i] = mis;
if (mis < minMis) minMis = mis;
i++;
}
// Only add minimum mismatch hits
i = 0;
for (String[] pieces : lines) {
if (mismatches[i] == minMis) linesToPrint.add(pieces);
i++;
}
numHits = linesToPrint.size();
} else {
linesToPrint = lines;
numHits = lines.size();
}
// Now add the hits!
if (!uniqueOnly || linesToPrint.size() == 1) {
double weight = 1.0 / numHits;
for (String[] pieces : linesToPrint) {
if (readLength == -1) readLength = pieces[4].length();
Integer coord =
pieces[1].equals("+")
? Integer.valueOf(pieces[3])
: Integer.valueOf(pieces[3]) + readLength - 1;
coord += 1; // Bowtie default output is 0-based - we want 1-based.
System.out.println(
String.format(
"%s\t%s\t%s\t%d\t%f", pieces[2], coord, pieces[1], pieces[4].length(), weight));
}
}
}
public void run() {
started = true;
Thread.currentThread().setName("Q2-" + getInstanceId().toString());
try {
/*
* The following code determines whether a MBeanServer exists
* already. If so then the first one in the list is used.
* I have not yet find a way to interrogate the server for
* information other than MBeans so to pick a specific one
* would be difficult.
*/
ArrayList mbeanServerList = MBeanServerFactory.findMBeanServer(null);
if (mbeanServerList.isEmpty()) {
server = MBeanServerFactory.createMBeanServer(JMX_NAME);
} else {
server = (MBeanServer) mbeanServerList.get(0);
}
final ObjectName loaderName = new ObjectName(Q2_CLASS_LOADER);
try {
loader =
(QClassLoader)
java.security.AccessController.doPrivileged(
new java.security.PrivilegedAction() {
public Object run() {
return new QClassLoader(server, libDir, loaderName, mainClassLoader);
}
});
server.registerMBean(loader, loaderName);
loader = loader.scan(false);
} catch (Throwable t) {
if (log != null) log.error("initial-scan", t);
else t.printStackTrace();
}
factory = new QFactory(loaderName, this);
initSystemLogger();
addShutdownHook();
q2Thread = Thread.currentThread();
q2Thread.setContextClassLoader(loader);
if (cli != null) cli.start();
initConfigDecorator();
for (int i = 1; !shutdown; i++) {
try {
boolean forceNewClassLoader = scan();
QClassLoader oldClassLoader = loader;
loader = loader.scan(forceNewClassLoader);
if (loader != oldClassLoader) {
oldClassLoader = null; // We want't this to be null so it gets GCed.
System.gc(); // force a GC
log.info(
"new classloader ["
+ Integer.toString(loader.hashCode(), 16)
+ "] has been created");
}
deploy();
checkModified();
relax(SCAN_INTERVAL);
if (i % (3600000 / SCAN_INTERVAL) == 0) logVersion();
} catch (Throwable t) {
log.error("start", t);
relax();
}
}
undeploy();
try {
server.unregisterMBean(loaderName);
} catch (InstanceNotFoundException e) {
log.error(e);
}
if (decorator != null) {
decorator.uninitialize();
}
if (exit && !shuttingDown) System.exit(0);
} catch (Exception e) {
if (log != null) log.error(e);
else e.printStackTrace();
System.exit(1);
}
}