if (!reader.isIndexed()) {
final String errorMessage = "Goby alignment files must be sorted in order to be loaded in IGV. See the IGV tutorial at http://goby.campagnelab.org/ for details.";
System.err.println(errorMessage);
throw new UnsupportedOperationException(errorMessage);
}
final IndexedIdentifier identifiers = reader.getTargetIdentifiers();
// add MT as a synonym for M:
identifiers.put(new MutableString("M"), identifiers.getInt(new MutableString("MT")));
targetIdentifiers = new DoubleIndexedIdentifier(identifiers);
isIndexed = reader.isIndexed();
// reader.close();
// reader = null;
targetSequenceNames = new ArrayList();
for (MutableString ms : identifiers.keySet()) {
targetSequenceNames.add(ms.toString());
}
}