/** This method will process each argument and assign new variables */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
File forExtraction = 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 'v':
forExtraction = new File(args[++i]);
break;
case 'm':
minimumSSC = Float.parseFloat(args[++i]);
break;
case 'a':
minimumCount = Integer.parseInt(args[++i]);
break;
case 'r':
minimumAbsFractionChange = Double.parseDouble(args[++i]);
break;
case 'n':
maximumNormalAltFraction = Double.parseDouble(args[++i]);
break;
default:
Misc.printErrAndExit("\nProblem, unknown option! " + mat.group());
}
} catch (Exception e) {
Misc.printErrAndExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
System.out.println(
"\n" + IO.fetchUSeqVersion() + " Arguments: " + Misc.stringArrayToString(args, " ") + "\n");
// pull vcf files
if (forExtraction == null || forExtraction.exists() == false)
Misc.printErrAndExit(
"\nError: please enter a path to a vcf file or directory containing such.\n");
File[][] tot = new File[3][];
tot[0] = IO.extractFiles(forExtraction, ".vcf");
tot[1] = IO.extractFiles(forExtraction, ".vcf.gz");
tot[2] = IO.extractFiles(forExtraction, ".vcf.zip");
vcfFiles = IO.collapseFileArray(tot);
if (vcfFiles == null || vcfFiles.length == 0 || vcfFiles[0].canRead() == false)
Misc.printExit("\nError: cannot find your xxx.vcf(.zip/.gz OK) file(s)!\n");
}
/** 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();
}
/** This method will process each argument and assign new variables */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
File forExtraction = null;
File ucscDir = 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 'b':
forExtraction = new File(args[++i]);
break;
case 'd':
ucscDir = new File(args[++i]);
break;
case 'v':
versionedGenome = args[++i];
break;
case 'e':
verbose = false;
break;
case 'f':
forceConversion = true;
break;
case 'h':
printDocs();
System.exit(0);
break;
default:
USeqUtilities.printExit("\nProblem, unknown option! " + mat.group());
}
} catch (Exception e) {
USeqUtilities.printExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
if (verbose)
System.out.println(
"\n"
+ IO.fetchUSeqVersion()
+ " Arguments: "
+ USeqUtilities.stringArrayToString(args, " ")
+ "\n");
// versioned genome?
if (versionedGenome == null)
USeqUtilities.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 (e.g. H_sapiens_Mar_2006, H_sapiens_Feb_2009).\n");
// make files
if (ucscDir == null || ucscDir.isDirectory() == false)
USeqUtilities.printExit(
"\nCannot find your directory containing the UCSC wig2BigWig and bed2BigBed apps -> "
+ ucscDir);
bigWigToWig = new File(ucscDir, "bigWigToWig");
bigBedToBed = new File(ucscDir, "bigBedToBed");
// check files
// if (bigWigToBedGraph.canExecute() == false) USeqUtilities.printExit("\nCannot find or execute
// -> "+bigWigToBedGraph+"\n");
if (bigWigToWig.canExecute() == false)
USeqUtilities.printExit("\nCannot find or execute -> " + bigWigToWig + "\n");
if (bigBedToBed.canExecute() == false)
USeqUtilities.printExit("\nCannot find or execute -> " + bigBedToBed + "\n");
// pull ucsc files
if (forExtraction == null || forExtraction.exists() == false)
Misc.printExit(
"\nError: please enter a bw or bb file or directory containing such to convert!\n");
File[][] tot = new File[2][];
tot[0] = USeqUtilities.fetchFilesRecursively(forExtraction, ".bw");
tot[1] = USeqUtilities.fetchFilesRecursively(forExtraction, ".bb");
ucscArchives = IO.collapseFileArray(tot);
if (ucscArchives == null || ucscArchives.length == 0 || ucscArchives[0].canRead() == false)
Misc.printExit("\nError: cannot find or read any xxx.bb or xxx.bw file(s)!\n");
}
/** This method will process each argument and assign new varibles */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
String useqVersion = IO.fetchUSeqVersion();
System.err.println(
"\n" + useqVersion + " Arguments: " + Misc.stringArrayToString(args, " ") + "\n");
File tabixDataDir = 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 'c':
chrLengthFile = new File(args[++i]);
break;
case 'd':
tabixDataDir = new File(args[++i]);
break;
case 'n':
numberThreads = Integer.parseInt(args[++i]);
break;
case 'q':
numberQueriesInChunk = Integer.parseInt(args[++i]);
break;
default:
Misc.printErrAndExit("\nProblem, unknown option! " + mat.group());
}
} catch (Exception e) {
Misc.printErrAndExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
if (chrLengthFile == null)
Misc.printErrAndExit(
"\nError: please provide a bed file of chromosome and their lengths, e.g. X 0 155270560\n");
if (tabixDataDir == null || tabixDataDir.isDirectory() == false)
Misc.printErrAndExit(
"\nError: please provide a directory containing tabix indexed xxx.vcf.gz and xxx.bed.gz files with their associated xxx.gz.tbi indexes");
// pull data sources
vcfDataFiles = IO.fetchFilesRecursively(tabixDataDir, "vcf.gz");
bedDataFiles = IO.fetchFilesRecursively(tabixDataDir, "bed.gz");
mafDataFiles = IO.fetchFilesRecursively(tabixDataDir, "maf.txt.gz");
if (vcfDataFiles.length == 0 && bedDataFiles.length == 0 && mafDataFiles.length == 0)
Misc.printErrAndExit(
"\nError: failed to find any xxx.bed.gz, xxx.vcf.gz, or xxx.maf.txt.gz tabix files in your tabixDataDir -> "
+ tabixDataDir);
// check for index
lookForTabixIndex(vcfDataFiles);
lookForTabixIndex(bedDataFiles);
lookForTabixIndex(mafDataFiles);
// threads to use
int numAvail = Runtime.getRuntime().availableProcessors();
if (numberThreads < 1) numberThreads = numAvail - 1;
System.err.println(
numAvail + " Available processors, using " + numberThreads + " threaded loaders\n");
}
