// remove temp files, the pipeline.jar operator isn't working.
public void deleteTempFiles() {
System.out.println("\nRemoving these temp files:");
File workingDir = new File(System.getProperty("user.dir"));
File[] toExamine = workingDir.listFiles();
for (File f : toExamine) {
boolean d = false;
String n = f.getName();
if (n.startsWith("pipeinstancelog")) d = true;
else if (n.contains(".DOC.sample")) d = true;
else if (n.contains("allDepths.")) d = true;
else if (n.startsWith("nocalls.")) d = true;
else if (n.startsWith("snpeff.")) d = true;
else if (n.contains("plice")) d = true;
if (d) {
System.out.println("\t" + n);
f.deleteOnExit();
}
}
// delete the temp uncompressed vcf (required by Pipeline.jar)
if (deleteTempVcf) System.out.println("\t" + finalVcf.getName());
}
