public static void main(String args[]) {
CmdLineParser parser = new CmdLineParser();
CmdLineParser.Option inFile = parser.addStringOption('f', "file");
CmdLineParser.Option outFile = parser.addStringOption('o', "output");
CmdLineParser.Option window = parser.addIntegerOption('w', "window");
CmdLineParser.Option step = parser.addIntegerOption('s', "step");
try {
parser.parse(args);
} catch (CmdLineParser.OptionException e) {
System.err.println(e.getMessage());
printUsage();
System.exit(2);
}
windowSize = (Integer) parser.getOptionValue(window, 5);
windowStep = (Integer) parser.getOptionValue(step, 1);
SequenceGC sequence = new SequenceGC();
String inPath = (String) parser.getOptionValue(inFile);
String outPath = (String) parser.getOptionValue(outFile);
if (!(inPath == null)) sequence.ProcessPath(inPath, outPath);
else printUsage();
}
/** Main client entry point for stand-alone operation. */
public static void main(String[] args) {
BasicConfigurator.configure(new ConsoleAppender(new PatternLayout("%d [%-25t] %-5p: %m%n")));
CmdLineParser parser = new CmdLineParser();
CmdLineParser.Option help = parser.addBooleanOption('h', "help");
CmdLineParser.Option output = parser.addStringOption('o', "output");
CmdLineParser.Option iface = parser.addStringOption('i', "iface");
try {
parser.parse(args);
} catch (CmdLineParser.OptionException oe) {
System.err.println(oe.getMessage());
usage(System.err);
System.exit(1);
}
// Display help and exit if requested
if (Boolean.TRUE.equals(parser.getOptionValue(help))) {
usage(System.out);
System.exit(0);
}
String outputValue = (String) parser.getOptionValue(output, DEFAULT_OUTPUT_DIRECTORY);
String ifaceValue = (String) parser.getOptionValue(iface);
String[] otherArgs = parser.getRemainingArgs();
if (otherArgs.length != 1) {
usage(System.err);
System.exit(1);
}
try {
Client c = new Client(getIPv4Address(ifaceValue));
SharedTorrent torrent =
SharedTorrent.fromFile(new File(otherArgs[0]), new File(outputValue), false);
c.addTorrent(torrent);
// Set a shutdown hook that will stop the sharing/seeding and send
// a STOPPED announce request.
Runtime.getRuntime().addShutdownHook(new Thread(new ClientShutdown(c, null)));
c.share();
if (ClientState.ERROR.equals(torrent.getClientState())) {
System.exit(1);
}
} catch (Exception e) {
logger.error("Fatal error: {}", e.getMessage(), e);
System.exit(2);
}
}
/** @param args */
public static void main(String[] args) {
CmdLineParser parser = new CmdLineParser();
CmdLineParser.Option server = parser.addBooleanOption("server");
CmdLineParser.Option list = parser.addBooleanOption("list");
CmdLineParser.Option download = parser.addBooleanOption("download");
CmdLineParser.Option multidownload = parser.addBooleanOption("multidownload");
CmdLineParser.Option upload = parser.addBooleanOption("upload");
CmdLineParser.Option port = parser.addIntegerOption('p', "port");
CmdLineParser.Option dir = parser.addStringOption('d', "dir");
CmdLineParser.Option hostname = parser.addStringOption('h', "hostname");
CmdLineParser.Option file = parser.addStringOption('f', "file");
try {
parser.parse(args);
} catch (CmdLineParser.OptionException e) {
LOGGER.info(e.getMessage());
printUsage();
System.exit(2);
}
Boolean serverValue = (Boolean) parser.getOptionValue(server, new Boolean(false));
Boolean listValue = (Boolean) parser.getOptionValue(list, new Boolean(false));
Boolean downloadValue = (Boolean) parser.getOptionValue(download, new Boolean(false));
Boolean uploadValue = (Boolean) parser.getOptionValue(upload, new Boolean(false));
Boolean multidownloadValue = (Boolean) parser.getOptionValue(multidownload, new Boolean(false));
Integer portValue =
(Integer) parser.getOptionValue(port, new Integer(FtperSettings.INSTANCE.getServerPort()));
if (serverValue.booleanValue()) {
String current = new File(".").getAbsolutePath();
String dirValue =
(String) parser.getOptionValue(dir, current.substring(0, current.length() - 1));
LOGGER.info("Creating ftper server at port {} with root in {}", portValue, dirValue);
FtperSettings.INSTANCE.setServerPort(portValue.intValue());
FtperSettings.INSTANCE.setServerMode(serverValue.booleanValue());
FtperSettings.INSTANCE.setServerRoot(dirValue);
FtperServer serverInstance = new FtperServer();
serverInstance.start();
} else {
FtperSettings.INSTANCE.setServerMode(serverValue.booleanValue());
String hostnameValue = (String) parser.getOptionValue(hostname);
String fileValue = (String) parser.getOptionValue(file);
String[] otherArgs = parser.getRemainingArgs();
if (listValue.booleanValue()) {
String dirValue = (String) parser.getOptionValue(dir, "");
ListClient client = new ListClient();
client.init(hostnameValue, portValue.intValue(), dirValue);
} else if (downloadValue.booleanValue()
&& hostnameValue != null
&& otherArgs.length % 2 == 0
&& otherArgs.length >= 2) {
SingleModeClient client = new SingleModeClient();
Map<String, String> uploads = new HashMap<String, String>();
Map<String, String> downloads = new HashMap<String, String>();
for (int i = 0; i + 1 < otherArgs.length; i = i + 2) {
LOGGER.info("Requested transfer of {} as {}", otherArgs[i], otherArgs[i + 1]);
downloads.put(otherArgs[i], otherArgs[i + 1]);
}
client.init(hostnameValue, portValue.intValue(), uploads, downloads);
} else if (uploadValue.booleanValue()
&& hostnameValue != null
&& otherArgs.length % 2 == 0
&& otherArgs.length >= 2) {
SingleModeClient client = new SingleModeClient();
Map<String, String> uploads = new HashMap<String, String>();
Map<String, String> downloads = new HashMap<String, String>();
for (int i = 0; i + 1 < otherArgs.length; i = i + 2) {
LOGGER.info("Requested transfer of {} to {}", otherArgs[i + 1], otherArgs[i]);
uploads.put(otherArgs[i + 1], otherArgs[i]);
}
client.init(hostnameValue, portValue.intValue(), uploads, downloads);
} else if (multidownloadValue.booleanValue()
&& fileValue != null
&& otherArgs.length % 2 == 0
&& otherArgs.length >= 2) {
MultiModeClient client = new MultiModeClient();
Map<String, String> requests = new HashMap<String, String>();
for (int i = 0; i + 1 < otherArgs.length; i = i + 2) {
LOGGER.info(
"Requested transfer of {} to {}",
otherArgs[i + 1] + " at " + otherArgs[i],
fileValue);
requests.put(otherArgs[i], otherArgs[i + 1]);
}
client.init(fileValue, requests);
} else {
printUsage();
System.exit(2);
}
}
}
void run(String[] argv) {
if (argv.length == 0) {
System.out.println(usageString());
System.out.println("Error: No arguments provided");
return;
}
String command = argv[0].toLowerCase();
if (command.equals(CMD_HELP)) {
if (argv.length > 1) {
System.out.println(usageString(argv[1]));
} else {
System.out.println(usageString());
}
return;
}
if (command.equals(CMD_GUI)) {
launchGUI();
Runtime.getRuntime().halt(0);
}
// Do "version" now, its the only command with no arguments
if (command.equals(CMD_VERSION)) {
System.out.println(getVersionString());
return;
}
CmdLineParser parser = initParser(command);
// Parse optional arguments (switches, etc)
try {
parser.parse(argv);
} catch (CmdLineParser.OptionException e) {
System.err.println(e.getMessage());
System.out.println("Enter igvtools help " + command + " for help on this command");
return;
}
String tmpDirName = null;
if (tmpDirOption != null) {
tmpDirName = (String) parser.getOptionValue(tmpDirOption, null);
}
int maxRecords = MAX_RECORDS_IN_RAM;
if (maxRecordsOption != null) {
maxRecords = (Integer) parser.getOptionValue(maxRecordsOption, MAX_RECORDS_IN_RAM);
}
String[] nonOptionArgs = parser.getRemainingArgs();
try {
String basic_syntax =
"Error in syntax. Enter igvtools help " + command + " for usage instructions.";
// All remaining commands require an input file, and most need the file extension. Do that
// here.
validateArgsLength(nonOptionArgs, 2, "Error: No input file provided");
String ifile = nonOptionArgs[1];
boolean isList = ifile.indexOf(",") > 0;
if (!isList && !FileUtils.resourceExists(ifile)) {
throw new PreprocessingException("File not found: " + ifile);
}
String typeString = null;
if (typeOption != null) {
typeString = (String) parser.getOptionValue(typeOption);
}
if (typeString == null || typeString.length() == 0) {
typeString = Preprocessor.getExtension(ifile).toLowerCase();
} else {
typeString = typeString.toLowerCase();
}
if (command.equals(CMD_COUNT) || command.equals(CMD_TILE) || command.equals(CMD_TOTDF)) {
// Parse out options common to both count and tile
validateArgsLength(nonOptionArgs, 4, basic_syntax);
int maxZoomValue = (Integer) parser.getOptionValue(maxZoomOption, MAX_ZOOM);
String ofile = nonOptionArgs[2];
String genomeId = nonOptionArgs[3];
boolean isGCT = typeString.endsWith("gct") || typeString.equals("mage-tab");
String wfsString = (String) parser.getOptionValue(windowFunctions);
Collection<WindowFunction> wfList = parseWFS(wfsString, isGCT);
if (command.equals(CMD_COUNT)) {
String trackLine = null;
String color = (String) parser.getOptionValue(colorOption);
if (color != null) {
trackLine = "track color=\"" + color + "\"";
}
int extFactorValue = (Integer) parser.getOptionValue(extFactorOption, EXT_FACTOR);
int countFlags = parseCountFlags(parser);
String queryString = (String) parser.getOptionValue(queryStringOpt);
int minMapQuality = (Integer) parser.getOptionValue(minMapQualityOpt, 0);
int windowSizeValue = (Integer) parser.getOptionValue(windowSizeOption, WINDOW_SIZE);
doCount(
ifile,
ofile,
genomeId,
maxZoomValue,
wfList,
windowSizeValue,
extFactorValue,
trackLine,
queryString,
minMapQuality,
countFlags);
} else {
String probeFile = (String) parser.getOptionValue(probeFileOption, PROBE_FILE);
toTDF(
typeString,
ifile,
ofile,
probeFile,
genomeId,
maxZoomValue,
wfList,
tmpDirName,
maxRecords);
}
} else if (command.equals(CMD_SORT)) {
validateArgsLength(nonOptionArgs, 3, basic_syntax);
String ofile = nonOptionArgs[2];
doSort(ifile, ofile, tmpDirName, maxRecords);
} else if (command.equals(CMD_INDEX)) {
int indexType = (Integer) parser.getOptionValue(indexTypeOption, LINEAR_INDEX);
int defaultBinSize = indexType == LINEAR_INDEX ? LINEAR_BIN_SIZE : INTERVAL_SIZE;
int binSize = (Integer) parser.getOptionValue(binSizeOption, defaultBinSize);
String outputDir = (String) parser.getOptionValue(outputDirOption, null);
doIndex(ifile, typeString, outputDir, indexType, binSize);
} else if (command.equals(CMD_FORMATEXP)) {
validateArgsLength(nonOptionArgs, 3, basic_syntax);
File inputFile = new File(nonOptionArgs[1]);
File outputFile = new File(nonOptionArgs[2]);
(new ExpressionFormatter()).convert(inputFile, outputFile);
} else if (command.equals("wibtowig")) {
validateArgsLength(
nonOptionArgs,
4,
"Error in syntax. Expected: " + command + " [options] txtfile wibfile wigfile");
File txtFile = new File(nonOptionArgs[1]);
File wibFile = new File(nonOptionArgs[2]);
File wigFile = new File(nonOptionArgs[3]);
String trackLine = nonOptionArgs.length > 4 ? nonOptionArgs[4] : null;
doWIBtoWIG(txtFile, wibFile, wigFile, trackLine);
} else if (command.equals("splitgff")) {
validateArgsLength(
nonOptionArgs,
3,
"Error in syntax. Expected: " + command + " [options] inputfile outputdir");
String outputDirectory = nonOptionArgs[2];
GFFParser.splitFileByType(ifile, outputDirectory);
} else if (command.toLowerCase().equals("gcttoigv")) {
validateArgsLength(nonOptionArgs, 4, basic_syntax + " genomeId");
String ofile = nonOptionArgs[2];
// Output files must have .igv extension
if (!ofile.endsWith(".igv")) {
ofile = ofile + ".igv";
}
String genomeId = nonOptionArgs[3];
Genome genome = loadGenome(genomeId, true);
if (genome == null) {
throw new PreprocessingException("Genome could not be loaded: " + genomeId);
}
String probeFile = (String) parser.getOptionValue(probeFileOption, PROBE_FILE);
doGCTtoIGV(typeString, ifile, new File(ofile), probeFile, maxRecords, tmpDirName, genome);
} else if (command.toLowerCase().equals("tdftobedgraph")) {
validateArgsLength(nonOptionArgs, 3, basic_syntax);
String ofile = nonOptionArgs[2];
TDFUtils.tdfToBedgraph(ifile, ofile);
} else if (command.equals("wigtobed")) {
validateArgsLength(
nonOptionArgs, 2, "Error in syntax. Expected: " + command + " [options] inputfile");
String inputFile = nonOptionArgs[1];
float hetThreshold = 0.17f;
if (nonOptionArgs.length > 2) {
hetThreshold = Float.parseFloat(nonOptionArgs[2]);
}
float homThreshold = 0.55f;
if (nonOptionArgs.length > 3) {
homThreshold = Float.parseFloat(nonOptionArgs[3]);
}
WigToBed.run(inputFile, hetThreshold, homThreshold);
} else if (command.equals("vcftobed")) {
validateArgsLength(nonOptionArgs, 3, basic_syntax);
String inputFile = nonOptionArgs[1];
String outputFile = nonOptionArgs[2];
VCFtoBed.convert(inputFile, outputFile);
} else if (command.equals("sumwigs")) {
sumWigs(nonOptionArgs[1], nonOptionArgs[2]);
} else if (command.equals("densitiestobedgraph")) {
validateArgsLength(
nonOptionArgs,
3,
"Error in syntax. Expected: " + command + " [options] inputdir outputdir");
File inputDir = new File(nonOptionArgs[1]);
File outputDir = new File(nonOptionArgs[2]);
if (inputDir.isDirectory() && outputDir.isDirectory()) {
DensitiesToBedGraph.convert(inputDir, outputDir);
} else if (inputDir.isFile() && outputDir.isFile()) {
DensitiesToBedGraph.convert(inputDir, outputDir);
}
} else if (command.equals(CMD_BAMTOBED)) {
validateArgsLength(nonOptionArgs, 3, basic_syntax);
String ofile = nonOptionArgs[2];
Boolean pairOption = (Boolean) parser.getOptionValue(pairedCoverageOpt, false);
BamToBed.convert(new File(ifile), new File(ofile), pairOption);
} else if (command.equalsIgnoreCase("genGenomeList")) {
// Generate a genomes.txt list file based on a directory
// TODO Probably a better place for this. Users won't generally use it
File inDir = new File(ifile);
GenomeManager manager = GenomeManager.getInstance();
manager.generateGenomeList(inDir, nonOptionArgs[2], nonOptionArgs[3]);
} else {
throw new PreprocessingException("Unknown command: " + argv[EXT_FACTOR]);
}
} catch (PreprocessingException e) {
System.err.println(e.getMessage());
} catch (IOException e) {
throw new PreprocessingException("Unexpected IO error: ", e);
}
}
public static void main(String[] args) {
CmdLineParser parser = new CmdLineParser();
CmdLineParser.Option help = parser.addBooleanOption('h', "help");
CmdLineParser.Option urdfFile = parser.addStringOption('u', "urdf");
CmdLineParser.Option groupsFile = parser.addStringOption('g', "groups");
CmdLineParser.Option srdlFile = parser.addStringOption('s', "srdl");
CmdLineParser.Option targetUri = parser.addStringOption('i', "uri");
CmdLineParser.Option capsList = parser.addStringOption('c', "caps");
System.out.println();
try {
parser.parse(args);
} catch (CmdLineParser.OptionException e) {
System.out.println("[ERROR]\t" + e.getMessage());
printUsage();
System.exit(2);
}
boolean showUsage = (Boolean) parser.getOptionValue(help, Boolean.FALSE);
String urdfValue = (String) parser.getOptionValue(urdfFile);
String groupsValue = (String) parser.getOptionValue(groupsFile);
String srdlValue = (String) parser.getOptionValue(srdlFile);
String uriValue = (String) parser.getOptionValue(targetUri);
String capsValue = (String) parser.getOptionValue(capsList);
ArrayList<Capability> caps = new ArrayList<Capability>();
String[] otherArgs = parser.getRemainingArgs();
for (String s : otherArgs) {
System.out.println("[INFO]\tIgnoring other argument '" + s + "'");
}
if (!showUsage) {
if (urdfValue == null || urdfValue.length() == 0) {
System.out.println("[ERROR]\tNo URDF file specified (-u / --urdf)");
showUsage = true;
}
if (srdlValue == null || srdlValue.length() == 0) {
System.out.println("[ERROR]\tNo target SRDL file specified (-s / --srdl)");
showUsage = true;
}
if (uriValue == null || uriValue.length() == 0) {
System.out.println("[ERROR]\tNo URI specified to use for SRDL description (-i / --uri)");
showUsage = true;
} else {
if (!uriValue.endsWith("#")) {
uriValue += "#";
}
}
if (capsValue == null) {
System.out.println("[WARN]\tNo SRDL capabilities specified (-c / --caps)");
} else {
StringTokenizer t = new StringTokenizer(capsValue, ",");
while (t.hasMoreTokens()) {
String token = t.nextToken().trim();
Capability c = null;
try {
c = Capability.valueOf(token);
} catch (Exception e) {
System.out.println("[ERROR]\tUnknown SRDL capability '" + token + "'");
showUsage = true;
}
if (c != null) {
caps.add(c);
}
}
}
}
if (showUsage) {
printUsage();
System.exit(2);
}
URDF2SRDL ui = new URDF2SRDL();
if (ui.loadURDF(urdfValue)) {
ArrayList<PlanningGroup> parsedGroups = null;
if (groupsValue != null) {
parsedGroups = ui.loadPlanningGroups(groupsValue);
}
ui.saveSRDL(srdlValue, uriValue, caps, parsedGroups);
}
System.out.println();
}
