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; }
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); }
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; } }
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, " ")); } }
/** 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(); } }
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."); }
/** 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(); }