ac8788898448a1442aaa142060191071cb251c02,src/org/broad/igv/ui/Main.java,IGVArgs,parseArgs,#String[]#,408
Before Change
genomeId = (String) parser.getOptionValue(genomeOption);
dataServerURL = (String) parser.getOptionValue(dataServerOption);
genomeServerURL = (String) parser.getOptionValue(genomeServerOption);
indexFile = (String) parser.getOptionValue(indexFileOption);
coverageFile = (String) parser.getOptionValue(coverageFileOption);
name = (String) parser.getOptionValue(nameOption);
igvDirectory = (String) parser.getOptionValue(igvDirectoryOption);
String[] nonOptionArgs = parser.getRemainingArgs();
if (nonOptionArgs != null && nonOptionArgs.length > 0) {
After Change
* firstArg locusString -b batchFile -p preferences
*/
private void parseArgs(String[] args) {
CmdLineParser parser = new CmdLineParser();
CmdLineParser.Option propertyFileOption = parser.addStringOption('o', "preferences");
CmdLineParser.Option batchFileOption = parser.addStringOption('b', "batch");
CmdLineParser.Option portOption = parser.addStringOption('p', "port");
CmdLineParser.Option genomeOption = parser.addStringOption('g', "genome");
CmdLineParser.Option dataServerOption = parser.addStringOption('d', "dataServerURL");
CmdLineParser.Option genomeServerOption = parser.addStringOption('u', "genomeServerURL");
CmdLineParser.Option indexFileOption = parser.addStringOption('i', "indexFile");
CmdLineParser.Option coverageFileOption = parser.addStringOption('c', "coverageFile");
CmdLineParser.Option nameOption = parser.addStringOption('n', "name");
CmdLineParser.Option igvDirectoryOption = parser.addStringOption("igvDirectory");
try {
parser.parse(args);
} catch (CmdLineParser.IllegalOptionValueException e) {
e.printStackTrace(); // This is not logged because the logger is not initialized yet.
} catch (CmdLineParser.UnknownOptionException e) {
e.printStackTrace();
}
propertyOverrides = getDecodedValue(parser, propertyFileOption);
batchFile = getDecodedValue(parser, batchFileOption);
port = (String) parser.getOptionValue(portOption);
genomeId = (String) parser.getOptionValue(genomeOption);
dataServerURL = getDecodedValue(parser, dataServerOption);
genomeServerURL = getDecodedValue(parser, genomeServerOption);
indexFile = getDecodedValue(parser, indexFileOption);
coverageFile = getDecodedValue(parser, coverageFileOption);
name = (String) parser.getOptionValue(nameOption);
igvDirectory = getDecodedValue(parser, igvDirectoryOption);
String[] nonOptionArgs = parser.getRemainingArgs();
if (nonOptionArgs != null && nonOptionArgs.length > 0) {