/**
* this is the function that the inheriting class can expect to have called when the command line
* system has initialized.
*
* @return the return code to exit the program with
*/
protected int execute() throws Exception {
engine.setParser(parser);
argumentSources.add(this);
Walker<?, ?> walker = engine.getWalkerByName(getAnalysisName());
try {
// Make sure a valid GATK user key is present, if required.
authorizeGATKRun();
engine.setArguments(getArgumentCollection());
// File lists can require a bit of additional expansion. Set these explicitly by the engine.
engine.setSAMFileIDs(
ListFileUtils.unpackBAMFileList(getArgumentCollection().samFiles, parser));
engine.setWalker(walker);
walker.setToolkit(engine);
Collection<ReadFilter> filters = engine.createFilters();
engine.setFilters(filters);
// load the arguments into the walker / filters.
// TODO: The fact that this extra load call exists here when all the parsing happens at the
// engine
// TODO: level indicates that we're doing something wrong. Turn this around so that the GATK
// can drive
// TODO: argument processing.
loadArgumentsIntoObject(walker);
argumentSources.add(walker);
Collection<RMDTriplet> rodBindings =
ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
engine.setReferenceMetaDataFiles(rodBindings);
for (ReadFilter filter : filters) {
loadArgumentsIntoObject(filter);
argumentSources.add(filter);
}
engine.execute();
generateGATKRunReport(walker);
} catch (Exception e) {
generateGATKRunReport(walker, e);
throw e;
}
// always return 0
return 0;
}
/**
* GATK provides the walker as an argument source.
*
* @return List of walkers to load dynamically.
*/
@Override
protected Class[] getArgumentSources() {
// No walker info? No plugins.
if (getAnalysisName() == null) return new Class[] {};
Collection<Class> argumentSources = new ArrayList<Class>();
Walker walker = engine.getWalkerByName(getAnalysisName());
engine.setArguments(getArgumentCollection());
engine.setWalker(walker);
walker.setToolkit(engine);
argumentSources.add(walker.getClass());
Collection<ReadFilter> filters = engine.createFilters();
for (ReadFilter filter : filters) argumentSources.add(filter.getClass());
Class[] argumentSourcesAsArray = new Class[argumentSources.size()];
return argumentSources.toArray(argumentSourcesAsArray);
}