public Bed2Bar(String[] args) {
try {
processArgs(args);
// load Window[]
for (int i = 0; i < bedFiles.length; i++) {
bedFile = bedFiles[i];
System.out.println("Parsing " + bedFile.getName());
bedLinesHash = Bed.parseBedFile(bedFile, true, false);
if (bedLinesHash == null || bedLinesHash.size() == 0) {
System.out.println("Problem parsing bed file, skipping!");
continue;
}
barDirectory = IO.makeDirectory(bedFile, "");
File bedOutFile =
new File(Misc.removeExtension(bedFile.toString()) + "_" + threshold + "_Filt.bed");
bedOut = new PrintWriter(new FileWriter(bedOutFile));
makeStairStepBarFiles();
}
bedOut.close();
System.out.println("\nDone!\n");
} catch (IOException e) {
e.printStackTrace();
}
}
/// <summary>
/// FileStreamから読み込みながらコンストラクト
/// </summary>
/// <param name="sr">読み込み対象</param>
public VsqHandle(TextMemoryStream sr, int value, StringBuilder last_line) {
try {
this.index = value;
String[] spl;
String[] spl2;
// default値で梅
m_type = VsqHandleType.Vibrato;
iconID = "";
IDS = "normal";
L0 = new Lyric("");
original = 0;
caption = "";
length = 0;
startDepth = 0;
depthBP = null;
int depth_bp_num = 0;
startRate = 0;
rateBP = null;
int rate_bp_num = 0;
language = 0;
program = 0;
duration = 0;
depth = 64;
String tmpDepthBPX = "";
String tmpDepthBPY = "";
String tmpRateBPX = "";
String tmpRateBPY = "";
// "["にぶち当たるまで読込む
last_line.setLength(0);
last_line.append(sr.readLine());
while (!last_line.toString().startsWith("[")) {
spl = Misc.splitString(last_line.toString(), "=");
if (spl[0].equals("Language")) {
m_type = VsqHandleType.Singer;
language = Integer.parseInt(spl[1]);
} else if (spl[0].equals("Program")) {
program = Integer.parseInt(spl[1]);
} else if (spl[0].equals("IconID")) {
iconID = spl[1];
} else if (spl[0].equals("IDS")) {
IDS = spl[1];
} else if (spl[0].equals("Original")) {
original = Integer.parseInt(spl[1]);
} else if (spl[0].equals("Caption")) {
caption = spl[1];
for (int i = 2; i < spl.length; i++) {
caption += "=" + spl[i];
}
} else if (spl[0].equals("Length")) {
length = Integer.parseInt(spl[1]);
} else if (spl[0].equals("StartDepth")) {
startDepth = Integer.parseInt(spl[1]);
} else if (spl[0].equals("DepthBPNum")) {
depth_bp_num = Integer.parseInt(spl[1]);
} else if (spl[0].equals("DepthBPX")) {
tmpDepthBPX = spl[1];
} else if (spl[0].equals("DepthBPY")) {
tmpDepthBPY = spl[1];
} else if (spl[0].equals("StartRate")) {
m_type = VsqHandleType.Vibrato;
startRate = Integer.parseInt(spl[1]);
} else if (spl[0].equals("RateBPNum")) {
rate_bp_num = Integer.parseInt(spl[1]);
} else if (spl[0].equals("RateBPX")) {
tmpRateBPX = spl[1];
} else if (spl[0].equals("RateBPY")) {
tmpRateBPY = spl[1];
} else if (spl[0].equals("L0")) {
m_type = VsqHandleType.Lyric;
L0 = new Lyric(spl[1]);
} else if (spl[0].equals("Duration")) {
m_type = VsqHandleType.NoteHeadHandle;
duration = Integer.parseInt(spl[1]);
} else if (spl[0].equals("Depth")) {
duration = Integer.parseInt(spl[1]);
}
if (sr.peek() < 0) {
break;
}
last_line.setLength(0);
last_line.append(sr.readLine());
}
/*if ( IDS != "normal" ) {
m_type = VsqHandleType.Singer;
} else if ( IconID != "" ) {
m_type = VsqHandleType.Vibrato;
} else {
m_type = VsqHandleType.Lyric;
}*/
// RateBPX, RateBPYの設定
if (m_type == VsqHandleType.Vibrato) {
if (rate_bp_num > 0) {
float[] rate_bp_x = new float[rate_bp_num];
spl2 = tmpRateBPX.split(",");
for (int i = 0; i < rate_bp_num; i++) {
rate_bp_x[i] = Float.parseFloat(spl2[i]);
}
int[] rate_bp_y = new int[rate_bp_num];
spl2 = tmpRateBPY.split(",");
for (int i = 0; i < rate_bp_num; i++) {
rate_bp_y[i] = Integer.parseInt(spl2[i]);
}
rateBP = new VibratoBPList(rate_bp_x, rate_bp_y);
} else {
// m_rate_bp_x = null;
// m_rate_bp_y = null;
rateBP = new VibratoBPList();
}
// DepthBPX, DepthBPYの設定
if (depth_bp_num > 0) {
float[] depth_bp_x = new float[depth_bp_num];
spl2 = tmpDepthBPX.split(",");
for (int i = 0; i < depth_bp_num; i++) {
depth_bp_x[i] = Float.parseFloat(spl2[i]);
}
int[] depth_bp_y = new int[depth_bp_num];
spl2 = tmpDepthBPY.split(",");
for (int i = 0; i < depth_bp_num; i++) {
depth_bp_y[i] = Integer.parseInt(spl2[i]);
}
depthBP = new VibratoBPList(depth_bp_x, depth_bp_y);
} else {
depthBP = new VibratoBPList();
// m_depth_bp_x = null;
// m_depth_bp_y = null;
}
} else {
depthBP = new VibratoBPList();
rateBP = new VibratoBPList();
}
} catch (Exception ex) {
System.out.println("VsqHandle(TextMemoryStream,int,StringBuilder); ex=" + ex);
}
}
public static String toHTML(String s) {
s = Misc.string_replace(">", ">", s);
s = Misc.string_replace("<", "<", s);
s = Misc.string_replace(" ", " ", s);
s = Misc.string_replace(" ", "\t", s);
s = Misc.string_replace("<br>", "\n", s);
return s;
}
/** This method will process each argument and assign new varibles */
public void processArgs(String[] args) {
File file = null;
Pattern pat = Pattern.compile("-[a-z]");
for (int i = 0; i < args.length; i++) {
String lcArg = args[i].toLowerCase();
Matcher mat = pat.matcher(lcArg);
if (mat.matches()) {
char test = args[i].charAt(1);
try {
switch (test) {
case 'f':
file = new File(args[i + 1]);
i++;
break;
case 'v':
genomeVersion = args[i + 1];
i++;
break;
case 's':
sumScores = true;
break;
case 't':
threshold = Float.parseFloat(args[++i]);
break;
case 'h':
printDocs();
System.exit(0);
default:
Misc.printExit("\nError, unknown option! " + mat.group());
}
} catch (Exception e) {
System.out.print("\nSorry, something doesn't look right with this parameter: -" + test);
System.out.println();
System.exit(0);
}
}
}
if (file == null || file.exists() == false)
Misc.printErrAndExit("Problem finding your bed files!\n");
// pull files
File[][] tot = new File[3][];
tot[0] = IO.extractFiles(file, ".bed");
tot[1] = IO.extractFiles(file, ".bed.zip");
tot[2] = IO.extractFiles(file, ".bed.gz");
bedFiles = IO.collapseFileArray(tot);
if (bedFiles == null || bedFiles.length == 0)
Misc.printErrAndExit("Problem finding your xxx.bed(.zip/.gz OK) files!\n");
// genome version
if (genomeVersion == null)
Misc.printErrAndExit(
"Please enter a genome version (e.g. H_sapiens_Mar_2006, see http://genome.ucsc.edu/FAQ/FAQreleases\n");
}
/** This method will process each argument and assign new varibles */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
File dir = null;
for (int i = 0; i < args.length; i++) {
String lcArg = args[i].toLowerCase();
Matcher mat = pat.matcher(lcArg);
if (mat.matches()) {
char test = args[i].charAt(1);
try {
switch (test) {
case 'f':
dir = new File(args[i + 1]);
i++;
break;
case 'v':
genomeVersion = args[i + 1];
i++;
break;
case 's':
strand = args[++i];
break;
case 't':
stairStep = true;
break;
case 'h':
printDocs();
System.exit(0);
default:
Misc.printExit("\nError: unknown option! " + mat.group());
}
} catch (Exception e) {
Misc.printExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
if (dir == null || dir.canRead() == false)
Misc.printExit("\nError: cannot find or read your sgr file/ directory.\n");
File[][] tot = new File[3][];
tot[0] = IO.extractFiles(dir, ".sgr");
tot[1] = IO.extractFiles(dir, ".sgr.zip");
tot[2] = IO.extractFiles(dir, ".sgr.gz");
sgrFiles = IO.collapseFileArray(tot);
if (sgrFiles == null || sgrFiles.length == 0)
Misc.printExit("\nError: cannot find your xxx.sgr.zip file(s)");
if (genomeVersion == null)
Misc.printExit(
"\nError: you must supply a genome version. Goto http://genome.ucsc.edu/cgi-"
+ "bin/hgGateway load your organism to find the associated genome version.\n");
}
public void checkPrintFiles() {
LinkedHashMap<String, File> nameFile = new LinkedHashMap<String, File>();
nameFile.put("Reference directory", referenceDir);
nameFile.put("Pipeline.jar", pJar);
nameFile.put("Pipeline properties", truncPipePropFile);
nameFile.put("Coverage QC bed", bedForCoverageQC);
nameFile.put("Variant calling bed", bedForVarCalling);
nameFile.put("Fasta genome reference", fastaReference);
nameFile.put("Unfiltered bam", unfilteredBam);
nameFile.put("Final bam", finalBam);
nameFile.put("Final vcf", finalVcf);
if (webRootForLinks != null) nameFile.put("Web links dir", webRootForLinks);
nameFile.put("Final output dir", outputDirectory);
boolean missingFile = false;
System.out.println("\nResources (name exists path):");
for (String name : nameFile.keySet()) {
File f = nameFile.get(name);
boolean fExists = true;
if (f == null) {
fExists = false;
missingFile = true;
} else {
fExists = f.exists();
if (fExists == false) missingFile = true;
}
System.out.println(name + "\t" + fExists + "\t" + f);
}
if (missingFile) Misc.printErrAndExit("\nMissing resources! See above.");
}
public String fetchCleanupReviewDirLinkGenXml() {
String s = null;
try {
s = // Organize and Clean Up Section
"<ReviewDirGenerator class='operator.ReviewDirGenerator' destination.dir='"
+ outputDirectory.getCanonicalPath()
+ "' sample='"
+ outputDirectory.getName()
+ "' submitter='"
+ submitter
+ "' analysis.type='"
+ analysisType
+ "'> \n"
+ " <finalVariants /> \n"
+ " <ViewerCSV /> \n"
+ " <InstanceLog class='buffer.InstanceLogFile' /> \n"
+ " <finalBAM /> \n"
+ " <QCOutputFile /> \n"
+ " <bedForVars /> \n"
+ "</ReviewDirGenerator> \n\n";
} catch (IOException e) {
e.printStackTrace();
Misc.printErrAndExit("\nError fetching clean up and review dir links.\n");
}
return s;
}
public void sendXHeader() throws IOException
{
StringBuffer header1 = new StringBuffer();
StringBuffer header2 = new StringBuffer();
int lengthOfXA = param.getRandomLengthOfXA();
int lengthOfXB = param.getRandomLengthOfXB();
for (int i=0 ; i<lengthOfXA ; i++)
{
header1.append(Misc.getRandomByte());
}
for (int i=0 ; i<lengthOfXB ; i++)
{
header2.append(Misc.getRandomByte());
}
socket.getOutputStream().write(("X-" + header1.toString() + ": " + header2.toString() + "\r\n").getBytes());
socket.getOutputStream().flush();
}
// constructor
public Sgr2Bar(String[] args) {
try {
// check for args
processArgs(args);
System.out.println("Genome version -> " + genomeVersion);
System.out.println("Strand -> " + strand);
System.out.println("Stair Step? -> " + stairStep);
System.out.println();
// load tagValues
if (stairStep) tagValues.put(BarParser.GRAPH_TYPE_TAG, BarParser.GRAPH_TYPE_STAIRSTEP);
else tagValues.put(BarParser.GRAPH_TYPE_TAG, BarParser.GRAPH_TYPE_BAR);
for (int x = 0; x < sgrFiles.length; x++) {
System.out.println("\tLoading -> " + sgrFiles[x]);
GrGraph[] grs = GrGraph.loadSgrFile(sgrFiles[x]);
// make save directory
String dirName;
dirName = Misc.removeExtension(sgrFiles[x].getCanonicalPath());
File dir = new File(dirName);
dir.mkdir();
// print bar files
System.out.println("\tSaving...");
for (int i = 0; i < grs.length; i++) {
File barFile = new File(dir, grs[i].getChromosome() + ".bar");
barParser.writeBarFile(
barFile,
grs[i].getChromosome(),
genomeVersion,
strand.charAt(0),
grs[i].getBasePositions(),
grs[i].getValues(),
tagValues);
}
}
System.out.println("\nDone!\n");
} catch (IOException e) {
e.printStackTrace();
Misc.printErrAndExit("\nFailed to parse file!");
}
}
private void buildXmlPropertiesFile() {
System.out.println(
"\nBuilding and checking your pipeline properties file -> " + truncPipePropFile);
StringBuilder toPrint = new StringBuilder();
// walk through the prop file
String[] prop = IO.loadFileIntoStringArray(truncPipePropFile);
Pattern val = Pattern.compile("(<entry key.+>)([D|A|B].*)</entry>");
boolean missingFile = false;
for (String s : prop) {
// does it match a file needing prepending? Data/, Apps/, Bed/
Matcher mat = val.matcher(s);
if (mat.matches()) {
File test = new File(referenceDir, mat.group(2));
if (test.exists()) {
System.out.println("Found\t" + test);
toPrint.append(mat.group(1));
toPrint.append(test.toString());
toPrint.append("</entry>");
} else {
System.out.println("Misssing\t" + test);
missingFile = true;
}
}
// threads?
else if (s.contains("threads"))
toPrint.append("<entry key=\"threads\">" + threads + "</entry>");
// nope just save it and add a line return
else toPrint.append(s);
toPrint.append("\n");
}
// anything missing? if so exit
if (missingFile)
Misc.printErrAndExit(
"\nFailed to find all of the files in your properties file, see above.\n");
// OK, write it out
completePipelinePropFile = new File(outputDirectory, "pipelineProperties.xml");
if (IO.writeString(toPrint.toString(), completePipelinePropFile) == false)
Misc.printErrAndExit("Problem writing -> " + truncPipePropFile);
}
public static void main(String[] args) {
File column = new File(args[0]);
try {
// how many different dbs are present
LinkedHashMap dbs = new LinkedHashMap();
BufferedReader in = new BufferedReader(new FileReader(column));
String line;
int index = 0;
while ((line = in.readLine()) != null) {
if (line.trim().length() == 0) continue;
String[] tokens = line.split("\\|");
for (int i = 0; i < tokens.length; i += 2) {
if (dbs.containsKey(tokens[i]) == false) {
dbs.put(tokens[i], new Integer(index++));
}
}
}
in.close();
// print header
Iterator it = dbs.keySet().iterator();
while (it.hasNext()) {
String c = (String) it.next();
System.out.print("Reporter BioSequence DatabaseEntry [" + c + "]\t");
}
System.out.println();
// print lines
in = new BufferedReader(new FileReader(column));
int numColumns = dbs.size();
while ((line = in.readLine()) != null) {
if (line.trim().length() == 0) {
System.out.println();
} else {
String[] columns = new String[numColumns];
String[] tokens = line.split("\\|");
for (int i = 0; i < tokens.length; i += 2) {
// System.out.println(line+"Tok"+tokens[i]);
int columnIndex = ((Integer) dbs.get(tokens[i])).intValue();
if (columns[columnIndex] == null) columns[columnIndex] = tokens[i + 1];
else columns[columnIndex] = columns[columnIndex] + ";" + tokens[i + 1];
}
// print it
for (int i = 0; i < numColumns; i++) {
if (columns[i] == null) columns[i] = "";
}
System.out.println(Misc.stringArrayToString(columns, "\t"));
}
}
in.close();
} catch (Exception e) {
e.printStackTrace();
}
}
private void checkForGzippedVcf() {
String vcfName = finalVcf.getName();
if (vcfName.endsWith(".gz")) {
File uncomp = new File(finalVcf.getParentFile(), vcfName.substring(0, vcfName.length() - 3));
if (uncomp.exists() == false) {
deleteTempVcf = true;
if (IO.uncompress(finalVcf, uncomp) == null)
Misc.printErrAndExit("ERROR: failed to uncompress -> " + finalVcf);
}
finalVcf = uncomp;
}
}
/** This method will process each argument and assign new varibles */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
for (int i = 0; i < args.length; i++) {
String lcArg = args[i].toLowerCase();
Matcher mat = pat.matcher(lcArg);
if (mat.matches()) {
char test = args[i].charAt(1);
try {
switch (test) {
case 'f':
fastas = IO.extractFiles(args[i + 1], "fasta");
i++;
break;
case 'n':
numberOfBases = Integer.parseInt(args[i + 1]);
i++;
break;
case 'i':
indexDirectory = new File(args[i + 1]);
i++;
break;
case 'h':
printDocs();
System.exit(0);
default:
Misc.printExit("\nError: unknown option! " + mat.group());
}
} catch (Exception e) {
Misc.printExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
// make index directory?
if (indexDirectory == null) {
indexDirectory = new File(fastas[0].getParentFile(), "IndexedSequences");
indexDirectory.mkdir();
}
}
private void executePipelineJob() {
String[] cmd = null;
try {
// write out tempTemplate
File template = new File(outputDirectory, "pipelineTemplate.xml");
if (IO.writeString(xmlTemplate, template) == false)
Misc.printErrAndExit("Problem writing -> " + template);
// build and execute cmd
cmd =
new String[] {
"java",
"-jar",
"-Xmx2G",
pJar.getCanonicalPath(),
"-props",
completePipelinePropFile.getCanonicalPath(),
template.getCanonicalPath()
};
String stringCmd = Misc.stringArrayToString(cmd, " ");
System.out.println("\nExecuting:\n" + stringCmd);
System.out.println("\nPipelineOutput:");
String[] out = IO.executeViaProcessBuilder(cmd, true);
// check output for possible errors
for (String line : out) {
String lcLine = line.toLowerCase();
// watch out for cases where error is mentioned in a warning output line.
if (lcLine.contains("error") && lcLine.startsWith("warning") == false)
Misc.printErrAndExit(
"\n\nERROR found in Pipeline.jar output, see above. Aborting!\n" + line);
}
} catch (Exception e) {
e.printStackTrace();
Misc.printErrAndExit("ERROR: executing " + Misc.stringArrayToString(cmd, " "));
}
}
public void checkPrintFields() {
LinkedHashMap<String, String> nameField = new LinkedHashMap<String, String>();
nameField.put("Job ID", jobId);
nameField.put("Sample ID", sampleId);
nameField.put("Submitter", submitter);
nameField.put("Analysis Type", analysisType);
nameField.put("Minimum Align Depth", minimumReadDepth);
nameField.put("Threads", threads);
nameField.put("SnpEff Genome", snpEffGenome);
// set output of booleans
nameField.put("Upload Vars to NGSWeb", uploadVarsToNGSWeb + "");
boolean missingField = false;
System.out.println("Fields:");
for (String name : nameField.keySet()) {
String f = nameField.get(name);
if (f == null || f.length() == 0) missingField = true;
System.out.println(name + "\t" + f);
}
if (missingField) Misc.printErrAndExit("\nMissing Fields! See above.");
}
public static void saveTextFile(File file, String content)
throws UnsupportedEncodingException, FileNotFoundException, IOException {
Misc.saveTextFile(file, content, "UTF-8");
}
@Override
public void run() {
try {
Thread.currentThread().setName("ServerEngine");
System.setOut(new Misc.TimestampLogger(System.out));
System.setErr(new Misc.TimestampLogger(System.err, "./data/err.log"));
address = new InetSocketAddress(host, port);
System.out.println("Starting " + Constants.SERVER_NAME + " on " + address + "...");
// load shutdown hook
Thread shutdownhook = new ShutDownHook();
Runtime.getRuntime().addShutdownHook(shutdownhook);
PacketManager.loadPackets();
Cache.load();
// load scripts
Misc.loadScripts(new File("./data/ruby/"));
GlobalVariables.patchNotes = Misc.loadPatchNotes();
GlobalVariables.info = Misc.loadInfo();
GlobalVariables.npcDump = Misc.getNpcDump();
GlobalVariables.itemDump = Misc.getItemDump();
// load all xstream related files.
XStreamUtil.loadAllFiles();
// item weights
ItemDefinition.loadWeight();
// interfaces
RSInterface.load();
// Load plugins
PluginManager.loadPlugins();
// Load regions
ObjectDef.loadConfig();
Region.load();
Rangable.load();
// Load objects
ObjectLoader objectLoader = new ObjectLoader();
objectLoader.load();
GameObjectData.init();
// load combat manager
CombatManager.init();
// Load minute timer
startMinutesCounter();
// global drops
GlobalGroundItem.initialize();
// load npc ls
Npc.loadNpcDrops();
// mage arena timers
AlchemistPlayground.loadAlchemistPlayGround();
EnchantingChamber.loadEnchantingChamber();
CreatureGraveyard.loadCreatureGraveyard();
// spawning world fishing spots
FishingSpots.spawnFishingSpots();
QuestHandler.init();
NpcLoader.loadAutoSpawn("./data/npcs/spawn-config.cfg");
HighscoresManager.load();
// Start up and get a'rollin!
startup();
System.out.println("Online!");
while (!Thread.interrupted()) {
try {
cycle();
sleep();
} catch (Exception ex) {
PlayerSave.saveAllPlayers();
ex.printStackTrace();
}
}
scheduler.schedule(
new Task() {
@Override
protected void execute() {
if (Thread.interrupted()) {
PlayerSave.saveAllPlayers();
stop();
return;
}
try {
cycle();
} catch (Exception ex) {
PlayerSave.saveAllPlayers();
ex.printStackTrace();
stop();
}
}
});
} catch (Exception ex) {
ex.printStackTrace();
}
PluginManager.close();
}
public void sendPOSTBodyRandomByte() throws IOException
{
socket.getOutputStream().write(Misc.getRandomByte());
socket.getOutputStream().flush();
}
/** This method will process each argument and assign new variables */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
System.out.println(
"\n" + IO.fetchUSeqVersion() + " Arguments: " + Misc.stringArrayToString(args, " ") + "\n");
for (int i = 0; i < args.length; i++) {
String lcArg = args[i].toLowerCase();
Matcher mat = pat.matcher(lcArg);
if (mat.matches()) {
char test = args[i].charAt(1);
try {
switch (test) {
case 'o':
jobId = args[++i];
break;
case 's':
sampleId = args[++i];
break;
case 'm':
submitter = args[++i];
break;
case 'y':
analysisType = args[++i];
break;
case 'w':
webRootForLinks = new File(args[++i]);
break;
case 'e':
snpEffGenome = args[++i];
break;
case 'i':
minimumReadDepth = args[++i];
break;
case 't':
threads = args[++i];
break;
case 'l':
uploadVarsToNGSWeb = true;
break;
case 'j':
pJar = new File(args[++i]);
break;
case 'p':
truncPipePropFile = new File(args[++i]);
break;
case 'q':
bedForCoverageQC = new File(args[++i]);
break;
case 'b':
bedForVarCalling = new File(args[++i]);
break;
case 'r':
fastaReference = new File(args[++i]);
break;
case 'u':
unfilteredBam = new File(args[++i]);
break;
case 'f':
finalBam = new File(args[++i]);
break;
case 'v':
finalVcf = new File(args[++i]);
break;
case 'd':
outputDirectory = new File(args[++i]);
break;
case 'c':
referenceDir = new File(args[++i]);
break;
case 'h':
printDocs();
System.exit(0);
default:
Misc.printErrAndExit("\nProblem, unknown option! " + mat.group());
}
} catch (Exception e) {
Misc.printErrAndExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
// check output dir and if needed set sampleId
if (outputDirectory != null) {
outputDirectory.mkdirs();
if (sampleId.length() == 0) sampleId = outputDirectory.getName();
}
// check root directory if needed
if (webRootForLinks != null) {
if (webRootForLinks.exists() == false) webRootForLinks.mkdirs();
// links dir?
File links = new File(webRootForLinks, "links");
if (links.exists() == false) links.mkdirs();
}
// look for required fields and files
checkPrintFields();
checkPrintFiles();
checkForGzippedVcf();
}