RefSequence { @NotNull public IndexedBases alignment() { return indexedBases; } RefSequence(@NotNull final GenomeRegion region, @NotNull final ReferenceSequenceFile refGenome); @VisibleForTesting  RefSequence(final ReferenceSequence sequence); @NotNull IndexedBases alignment();  }
@Test public void testRNA() { RefSequence rnaRefSequence = new RefSequence(REF_SEQ); SAMRecord samRecord = buildSamRecord(990, "20M", "GGGGGAAAAATTTTTCCCCC", "XXXXXXXXXXXXXXXXXXXX"); IndexedBases indexedBases = rnaRefSequence.alignment(); assertEquals(1000, indexedBases.position()); }