builder.addPair("rrnaPair", sequenceIndex, 400, 500);
builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);
final File samFile = File.createTempFile("tmp.collectRnaSeqMetrics.", ".sam");
final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(builder.getHeader(), false, samFile);
for (final SAMRecord rec: builder.getRecords()) samWriter.addAlignment(rec);
samWriter.close();
// Create an interval list with one ribosomal interval.
final Interval rRnaInterval = new Interval(sequence, 300, 520, true, "rRNA");
final IntervalList rRnaIntervalList = new IntervalList(builder.getHeader());
rRnaIntervalList.add(rRnaInterval);