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 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();
}
}
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.");
}