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 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.");
}
