final LiftOver liftOver = new LiftOver(CHAIN);
liftOver.setLiftOverMinMatch(MIN_LIFTOVER_PCT);
final IntervalList fromIntervals = IntervalList.fromFile(INPUT);
final SAMFileHeader toHeader = new SAMFileReader(SEQUENCE_DICTIONARY).getFileHeader();
liftOver.validateToSequences(toHeader.getSequenceDictionary());
final IntervalList toIntervals = new IntervalList(toHeader);
boolean anyFailed = false;
for (final Interval fromInterval : fromIntervals) {
final Interval toInterval = liftOver.liftOver(fromInterval);
if (toInterval != null) {