argCollection.samFiles = Collections.singletonList(inputFile.getAbsolutePath());
engine.setArguments(argCollection);
// Bugs in the engine mean that this has to be set twice.
engine.setSAMFileIDs(Collections.singletonList(new SAMReaderID(inputFile,new Tags())));
engine.setFilters(Collections.<ReadFilter>singletonList(new UnmappedReadFilter()));
engine.setReferenceMetaDataFiles(Collections.<RMDTriplet>emptyList());
// Create the walker
engine.setWalker(walkerType.create());