catch (QSequenceException ex) {
throw new IOException(ex.getMessage());
}
try {
final QSequenceLineCache baseLines = localResult.getLeftCache();
final QSequenceLineCache localLines = localResult.getRightCache();
final QSequenceLineCache latestLines = latestResult.getRightCache();
final FSMergerBySequenceList local = new FSMergerBySequenceList(localResult.getBlocks());
final FSMergerBySequenceList latest = new FSMergerBySequenceList(latestResult.getBlocks());
final List transformedLocalLines = transformLocalLines(localResult.getBlocks(), localLines);
int baseLineIndex = -1;