@CLNames(
names = {"-msms"},
required = true)
@CLDescription(
"The msms comand line for contex. Need the number of demes and sampling stratagy and -s to be correct. Of course this includes the stats collectors used. Dont forget that each indivd is 2 samples")
public void msmsCmdLine(String[] msmsArgs) {
msmsparser = new CommandLineMarshal();
try {
CmdLineParser<CommandLineMarshal> marshel = CommandLineMarshal.getCacheParser(); // new
// CmdLineParser<CommandLineMarshal>(msmsparser);
marshel.processArguments(msmsArgs, msmsparser);
sampleConfig = msmsparser.getSampleConfig();
collectors = msmsparser.getStatsCollectors();
if (collectors == null || collectors.size() == 0) {
throw new RuntimeException("Need at least one -stat option");
}
for (StatsCollector sc : collectors) {
sc.init();
}
} catch (Exception e) {
System.err.println(
"Error Parsing MSMS comand line. Note that all non msms options must come before the -msms switch.");
throw new RuntimeException(e);
}
}
public static void main(String[] args) {
MStoStats rse = new MStoStats();
CmdLineParser<MStoStats> parser = null;
try {
parser = new CmdLineParser<MStoStats>(MStoStats.class);
} catch (Exception e1) {
e1.printStackTrace();
return;
}
try {
parser.processArguments(args, rse);
if (rse.help) {
System.err.println(parser.longUsage());
System.exit(0);
}
rse.run();
} catch (Exception e) {
System.err.println(parser.longUsage());
if (!rse.help) e.printStackTrace();
}
}