@Override
public final void set(E value) {
checkNotNull(value);
checkArgument(options.contains(value), "Value [%s] not permitted", value);
super.set(value);
}
/* main method */
public DefaultParam importCommandLine() {
/* Assigning Parameter ID to an ascending number */
putParameterID();
/* Assigning parameter descriptions to each parameter ID */
addParameterInfo();
/* need a Object parser of PosixParser class for the function parse of CommandLine class */
PosixParser parser = new PosixParser();
/* print out help information */
HelpParam help = new HelpParam(parameter, parameterMap);
/* check each parameter for assignment */
try {
long input_limit = -1;
int threads = Runtime.getRuntime().availableProcessors();
/* Set Object cl of CommandLine class for Parameter storage */
CommandLine cl = parser.parse(parameter, arguments, true);
if (cl.hasOption(HELP)) {
help.printStatisticerHelp();
System.exit(0);
}
if (cl.hasOption(HELP2)) {
help.printStatisticerHelp();
System.exit(0);
}
if (cl.hasOption(VERSION)) {
System.exit(0);
}
/* Checking all parameters */
String value;
if ((value = cl.getOptionValue(PARTITIONS)) != null) {
param.partitions = Integer.decode(value);
}
if ((value = cl.getOptionValue(COLUMN)) != null) {
param.columns = value;
param.columnStart = Integer.decode(value.split("-")[0]);
param.columnEnd = Integer.decode(value.split("-")[1]);
} else {
param.columnStart = Integer.decode(param.columns.split("-")[0]);
param.columnEnd = Integer.decode(param.columns.split("-")[1]);
}
if (cl.hasOption(CACHE)) {
param.cache = true;
}
if ((value = cl.getOptionValue(INPUT_VCF)) != null) {
param.inputFqPath = value;
} else if ((value = cl.getOptionValue(INPUT_TAB)) != null) {
param.inputFqPath = value;
} else {
help.printStatisticerHelp();
System.exit(0);
// throw new IOException("Input file not specified.\nUse -help for list of
// options");
}
/* not applicable for HDFS and S3 */
/* using TextFileBufferInput for such purpose */
// File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
// if (!inputFastq.exists()){
// err.println("Input query file not found.");
// return;
// i }
if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
param.outputPath = value;
} else {
help.printStatisticerHelp();
info.readMessage("Output file not set with -outfile options");
info.screenDump();
System.exit(0);
}
File outfile = new File(param.outputPath).getAbsoluteFile();
if (outfile.exists()) {
info.readParagraphedMessages(
"Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
info.screenDump();
Runtime.getRuntime().exec("rm -rf " + param.outputPath);
}
} catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
info.readMessage("Parameter settings incorrect.");
info.screenDump();
e.printStackTrace();
System.exit(0);
} catch (RuntimeException e) {
info.readMessage("Parameter settings incorrect.");
info.screenDump();
e.printStackTrace();
System.exit(0);
} catch (ParseException e) {
info.readMessage("Parameter settings incorrect.");
info.screenDump();
e.printStackTrace();
System.exit(0);
}
return param;
}
